Build log for genometools (1.5.8+ds-2) on armhf

genometools → 1.5.8+ds-2 → armhf → 2016-03-19 11:33:47

sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on testwandboard

+==============================================================================+
| genometools 1.5.8+ds-2 (armhf)                             17 Mar 2016 05:06 |
+==============================================================================+

Package: genometools
Version: 1.5.8+ds-2
Source Version: 1.5.8+ds-2
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'build/genometools-GvNxxi/genometools-1.5.8+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/genometools-GvNxxi' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-6ff14986-1a2f-4c72-98c0-a22509cf3ab8' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [8812 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [10.9 MB]
Fetched 19.7 MB in 26s (740 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'genometools' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/genometools.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/genometools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 7782 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main genometools 1.5.8+ds-2 (dsc) [3461 B]
Get:2 http://172.17.0.1/private stretch-staging/main genometools 1.5.8+ds-2 (tar) [7754 kB]
Get:3 http://172.17.0.1/private stretch-staging/main genometools 1.5.8+ds-2 (diff) [23.9 kB]
Fetched 7782 kB in 3s (2460 kB/s)
Download complete and in download only mode

Check architectures
-------------------


Check dependencies
------------------

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-LwYF0B/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-LwYF0B/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-LwYF0B/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-LwYF0B/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-LwYF0B/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-LwYF0B/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-LwYF0B/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-LwYF0B/apt_archive ./ Sources [194 B]
Get:5 file:/<<BUILDDIR>>/resolver-LwYF0B/apt_archive ./ Packages [508 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

+------------------------------------------------------------------------------+
| Install core build dependencies (apt-based resolver)                         |
+------------------------------------------------------------------------------+

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 72 not upgraded.
Need to get 0 B/768 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-LwYF0B/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12685 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
Merged Build-Depends: debhelper (>= 9), dh-python, liblua5.1-0-dev, lua-md5-dev, lua-filesystem-dev, lua-lpeg-dev, libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, libsqlite3-dev, libbam-dev, libpango1.0-dev, libtre-dev, texlive-latex-base, texlive-latex-extra, texlive-fonts-extra, latex-xcolor, texlive-fonts-recommended, python, asciidoc, libxml2-utils, xsltproc, ruby, docbook-xsl, faketime, imagemagick
Filtered Build-Depends: debhelper (>= 9), dh-python, liblua5.1-0-dev, lua-md5-dev, lua-filesystem-dev, lua-lpeg-dev, libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, libsqlite3-dev, libbam-dev, libpango1.0-dev, libtre-dev, texlive-latex-base, texlive-latex-extra, texlive-fonts-extra, latex-xcolor, texlive-fonts-recommended, python, asciidoc, libxml2-utils, xsltproc, ruby, docbook-xsl, faketime, imagemagick
dpkg-deb: building package 'sbuild-build-depends-genometools-dummy' in '/<<BUILDDIR>>/resolver-6xjwOX/apt_archive/sbuild-build-depends-genometools-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-6xjwOX/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-6xjwOX/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-6xjwOX/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-6xjwOX/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-6xjwOX/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-6xjwOX/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-6xjwOX/apt_archive ./ Sources [365 B]
Get:5 file:/<<BUILDDIR>>/resolver-6xjwOX/apt_archive ./ Packages [692 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

+------------------------------------------------------------------------------+
| Install genometools build dependencies (apt-based resolver)                  |
+------------------------------------------------------------------------------+

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  asciidoc autotools-dev bsdmainutils ca-certificates debhelper dh-python
  dh-strip-nondeterminism docbook-xsl faketime file fontconfig
  fontconfig-config fonts-cabin fonts-comfortaa fonts-crosextra-caladea
  fonts-crosextra-carlito fonts-dejavu-core fonts-dejavu-extra
  fonts-ebgaramond fonts-ebgaramond-extra fonts-font-awesome
  fonts-freefont-otf fonts-freefont-ttf fonts-gfs-artemisia
  fonts-gfs-complutum fonts-gfs-didot fonts-gfs-neohellenic fonts-gfs-olga
  fonts-gfs-solomos fonts-junicode fonts-lato fonts-linuxlibertine
  fonts-lobster fonts-lobstertwo fonts-oflb-asana-math fonts-roboto-hinted
  fonts-sil-gentium fonts-sil-gentium-basic fonts-sil-gentiumplus fonts-stix
  gettext gettext-base gir1.2-freedesktop gir1.2-glib-2.0 gir1.2-pango-1.0
  groff-base hicolor-icon-theme imagemagick imagemagick-6.q16
  imagemagick-common intltool-debian libarchive-zip-perl libavahi-client3
  libavahi-common-data libavahi-common3 libbam-dev libbz2-dev
  libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev
  libcroco3 libcups2 libcupsfilters1 libcupsimage2 libdatrie1 libelf1
  libexpat1 libexpat1-dev libfaketime libffi6 libfftw3-double3
  libfile-stripnondeterminism-perl libfontconfig1 libfontconfig1-dev
  libfreetype6 libfreetype6-dev libgirepository-1.0-1 libglib2.0-0
  libglib2.0-bin libglib2.0-data libglib2.0-dev libgnutls30 libgraphite2-3
  libgs9 libgs9-common libgssapi-krb5-2 libharfbuzz-dev libharfbuzz-gobject0
  libharfbuzz-icu0 libharfbuzz0b libhogweed4 libice-dev libice6 libicu55
  libidn11 libijs-0.35 libjbig0 libjbig2dec0 libjpeg62-turbo libk5crypto3
  libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblcms2-2 libldap-2.4-2
  liblqr-1-0 libltdl7 liblua5.1-0 liblua5.1-0-dev liblzo2-2 libmagic1
  libmagickcore-6.q16-2 libmagickwand-6.q16-2 libmpdec2 libncurses5
  libncursesw5 libnettle6 libopenjp2-7 libopenjpeg5 libp11-kit0 libpango-1.0-0
  libpango1.0-dev libpangocairo-1.0-0 libpangoft2-1.0-0 libpangoxft-1.0-0
  libpaper-utils libpaper1 libpcre16-3 libpcre3 libpcre3-dev libpcre32-3
  libpcrecpp0v5 libpipeline1 libpixman-1-0 libpixman-1-dev libpng12-0
  libpng12-dev libpoppler57 libpotrace0 libptexenc1 libpthread-stubs0-dev
  libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib
  libpython3.5-minimal libpython3.5-stdlib libreadline-dev libreadline6-dev
  libruby2.3 libsasl2-2 libsasl2-modules-db libsm-dev libsm6 libsqlite3-0
  libsqlite3-dev libssl1.0.2 libsynctex1 libtasn1-6 libtexlua52 libtexluajit2
  libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev libtinfo5
  libtre-dev libtre5 libunistring0 libx11-6 libx11-data libx11-dev libxau-dev
  libxau6 libxaw7 libxcb-render0 libxcb-render0-dev libxcb-shm0
  libxcb-shm0-dev libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev
  libxext6 libxft-dev libxft2 libxi6 libxml2 libxml2-utils libxmu6 libxpm4
  libxrender-dev libxrender1 libxslt1.1 libxt6 libyaml-0-2 libzzip-0-13
  lua-filesystem lua-filesystem-dev lua-lpeg lua-lpeg-dev lua-md5 lua-md5-dev
  man-db mime-support openssl pkg-config po-debconf poppler-data
  preview-latex-style python python-minimal python2.7 python2.7-minimal
  python3 python3-minimal python3.5 python3.5-minimal rake ruby
  ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert
  ruby-test-unit ruby2.3 rubygems-integration sgml-base t1utils tex-common
  texlive-base texlive-binaries texlive-fonts-extra texlive-fonts-recommended
  texlive-latex-base texlive-latex-extra texlive-latex-recommended
  texlive-pictures ttf-adf-accanthis ttf-adf-gillius ttf-adf-universalis ucf
  x11-common x11proto-core-dev x11proto-input-dev x11proto-kb-dev
  x11proto-render-dev x11proto-xext-dev xdg-utils xml-core xorg-sgml-doctools
  xsltproc xtrans-dev zlib1g-dev
Suggested packages:
  source-highlight vim-addon-manager wamerican | wordlist whois vacation
  dh-make dbtoepub docbook-xsl-doc-html | docbook-xsl-doc-pdf
  | docbook-xsl-doc-text | docbook-xsl-doc docbook-xsl-saxon fop libsaxon-java
  libxalan2-java libxslthl-java xalan fontforge gettext-doc autopoint
  libasprintf-dev libgettextpo-dev groff imagemagick-doc autotrace cups-bsd
  | lpr | lprng curl enscript ffmpeg gimp gnuplot grads graphviz hp2xx html2ps
  libwmf-bin mplayer povray radiance sane-utils transfig ufraw-batch
  libcairo2-doc cups-common libfftw3-bin libfftw3-dev libglib2.0-doc
  gnutls-bin krb5-doc krb5-user libice-doc liblcms2-utils
  libmagickcore-6.q16-2-extra libpango1.0-doc readline-doc libsm-doc
  sqlite3-doc tre-agrep libxcb-doc libxext-doc less www-browser
  libmail-box-perl poppler-utils ghostscript fonts-japanese-mincho
  | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic
  fonts-arphic-ukai fonts-arphic-uming fonts-nanum python-doc python-tk
  python2.7-doc binfmt-support python3-doc python3-tk python3-venv
  python3.5-venv python3.5-doc ri ruby-dev bundler sgml-base-doc perl-tk
  xpdf-reader | pdf-viewer gv | postscript-viewer cm-super libfile-which-perl
  python-pygments libspreadsheet-parseexcel-perl texlive-pstricks dot2tex
  libtcltk-ruby prerex gvfs-bin
Recommended packages:
  dblatex docbook-utils xmlto docbook-xml curl | wget | lynx-cur
  libmagickcore-6.q16-2-extra ghostscript netpbm bzip2-doc shared-mime-info
  xdg-user-dirs fonts-droid-fallback krb5-locales libtool libtool-bin gsfonts
  libgpm2 libsasl2-modules libx11-doc libmail-sendmail-perl zip libjs-jquery
  lmodern wish texlive-fonts-extra-doc texlive-fonts-recommended-doc tex-gyre
  tipa texlive-latex-base-doc texlive-latex-extra-doc prosper
  texlive-latex-recommended-doc tk texlive-pictures-doc libfile-mimeinfo-perl
  libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
  asciidoc autotools-dev bsdmainutils ca-certificates debhelper dh-python
  dh-strip-nondeterminism docbook-xsl faketime file fontconfig
  fontconfig-config fonts-cabin fonts-comfortaa fonts-crosextra-caladea
  fonts-crosextra-carlito fonts-dejavu-core fonts-dejavu-extra
  fonts-ebgaramond fonts-ebgaramond-extra fonts-font-awesome
  fonts-freefont-otf fonts-freefont-ttf fonts-gfs-artemisia
  fonts-gfs-complutum fonts-gfs-didot fonts-gfs-neohellenic fonts-gfs-olga
  fonts-gfs-solomos fonts-junicode fonts-lato fonts-linuxlibertine
  fonts-lobster fonts-lobstertwo fonts-oflb-asana-math fonts-roboto-hinted
  fonts-sil-gentium fonts-sil-gentium-basic fonts-sil-gentiumplus fonts-stix
  gettext gettext-base gir1.2-freedesktop gir1.2-glib-2.0 gir1.2-pango-1.0
  groff-base hicolor-icon-theme imagemagick imagemagick-6.q16
  imagemagick-common intltool-debian libarchive-zip-perl libavahi-client3
  libavahi-common-data libavahi-common3 libbam-dev libbz2-dev
  libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev
  libcroco3 libcups2 libcupsfilters1 libcupsimage2 libdatrie1 libelf1
  libexpat1 libexpat1-dev libfaketime libffi6 libfftw3-double3
  libfile-stripnondeterminism-perl libfontconfig1 libfontconfig1-dev
  libfreetype6 libfreetype6-dev libgirepository-1.0-1 libglib2.0-0
  libglib2.0-bin libglib2.0-data libglib2.0-dev libgnutls30 libgraphite2-3
  libgs9 libgs9-common libgssapi-krb5-2 libharfbuzz-dev libharfbuzz-gobject0
  libharfbuzz-icu0 libharfbuzz0b libhogweed4 libice-dev libice6 libicu55
  libidn11 libijs-0.35 libjbig0 libjbig2dec0 libjpeg62-turbo libk5crypto3
  libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblcms2-2 libldap-2.4-2
  liblqr-1-0 libltdl7 liblua5.1-0 liblua5.1-0-dev liblzo2-2 libmagic1
  libmagickcore-6.q16-2 libmagickwand-6.q16-2 libmpdec2 libnettle6
  libopenjp2-7 libopenjpeg5 libp11-kit0 libpango-1.0-0 libpango1.0-dev
  libpangocairo-1.0-0 libpangoft2-1.0-0 libpangoxft-1.0-0 libpaper-utils
  libpaper1 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1
  libpixman-1-0 libpixman-1-dev libpng12-dev libpoppler57 libpotrace0
  libptexenc1 libpthread-stubs0-dev libpython-stdlib libpython2.7-minimal
  libpython2.7-stdlib libpython3-stdlib libpython3.5-minimal
  libpython3.5-stdlib libreadline-dev libreadline6-dev libruby2.3 libsasl2-2
  libsasl2-modules-db libsm-dev libsm6 libsqlite3-0 libsqlite3-dev libssl1.0.2
  libsynctex1 libtasn1-6 libtexlua52 libtexluajit2 libthai-data libthai0
  libtiff5 libtimedate-perl libtinfo-dev libtre-dev libtre5 libunistring0
  libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxaw7 libxcb-render0
  libxcb-render0-dev libxcb-shm0 libxcb-shm0-dev libxcb1 libxcb1-dev
  libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxft-dev libxft2 libxi6
  libxml2 libxml2-utils libxmu6 libxpm4 libxrender-dev libxrender1 libxslt1.1
  libxt6 libyaml-0-2 libzzip-0-13 lua-filesystem lua-filesystem-dev lua-lpeg
  lua-lpeg-dev lua-md5 lua-md5-dev man-db mime-support openssl pkg-config
  po-debconf poppler-data preview-latex-style python python-minimal python2.7
  python2.7-minimal python3 python3-minimal python3.5 python3.5-minimal rake
  ruby ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert
  ruby-test-unit ruby2.3 rubygems-integration
  sbuild-build-depends-genometools-dummy sgml-base t1utils tex-common
  texlive-base texlive-binaries texlive-fonts-extra texlive-fonts-recommended
  texlive-latex-base texlive-latex-extra texlive-latex-recommended
  texlive-pictures ttf-adf-accanthis ttf-adf-gillius ttf-adf-universalis ucf
  x11-common x11proto-core-dev x11proto-input-dev x11proto-kb-dev
  x11proto-render-dev x11proto-xext-dev xdg-utils xml-core xorg-sgml-doctools
  xsltproc xtrans-dev zlib1g-dev
The following packages will be upgraded:
  libncurses5 libncursesw5 libpcre3 libpng12-0 libtinfo5
5 upgraded, 254 newly installed, 0 to remove and 67 not upgraded.
Need to get 390 MB/390 MB of archives.
After this operation, 1222 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-6xjwOX/apt_archive ./ sbuild-build-depends-genometools-dummy 0.invalid.0 [948 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf libpcre3 armhf 2:8.38-3 [308 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf libtinfo5 armhf 6.0+20160213-1 [281 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libncurses5 armhf 6.0+20160213-1 [74.8 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf libncursesw5 armhf 6.0+20160213-1 [93.3 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.6 [177 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.11-4 [381 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.11-4 [1092 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-1 [40.0 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.59 [36.4 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.1.0-7 [59.8 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-0 armhf 3.11.1-1 [457 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libssl1.0.2 armhf 1.0.2g-1 [886 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.11-4 [1818 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.11-4 [267 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-1 [19.5 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.11-1 [150 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libpng12-0 armhf 1.2.54-4 [160 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libfreetype6 armhf 2.6.3-3 [384 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf ucf all 3.0035 [68.5 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf fonts-dejavu-core all 2.35-1 [1064 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf fontconfig-config all 2.11.0-6.3 [273 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libfontconfig1 armhf 2.11.0-6.3 [311 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf fontconfig armhf 2.11.0-6.3 [402 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf fonts-lato all 2.0-1 [2684 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf imagemagick-common all 8:6.8.9.9-7 [149 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libfftw3-double3 armhf 3.3.4-2+rpi1+b1 [436 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf liblcms2-2 armhf 2.6-3 [113 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.46.2-3 [2482 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf liblqr-1-0 armhf 0.4.2-2 [20.9 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf liblzo2-2 armhf 2.08-1.2 [47.6 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.4.2-2 [104 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libltdl7 armhf 2.4.6-0.1 [42.8 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libtiff5 armhf 4.0.6-1 [201 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libxdmcp6 armhf 1:1.1.2-1.1 [24.9 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libxcb1 armhf 1.11.1-1 [40.9 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libx11-data all 2:1.6.3-1 [128 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libicu55 armhf 55.1-7 [7380 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.3+dfsg1-1 [800 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libmagickcore-6.q16-2 armhf 8:6.8.9.9-7+b1 [1517 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libmagickwand-6.q16-2 armhf 8:6.8.9.9-7+b1 [378 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libmpdec2 armhf 2.4.1-1 [65.8 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libpaper1 armhf 1.1.24+nmu4 [21.4 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libpcrecpp0v5 armhf 2:8.38-3 [148 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libtre5 armhf 0.8.0-4 [51.3 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libxrender1 armhf 1:0.9.9-2 [28.9 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libxft2 armhf 2.3.2-1 [48.3 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libyaml-0-2 armhf 0.1.6-3 [41.5 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libzzip-0-13 armhf 0.13.62-3 [51.3 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf lua-md5 armhf 1.2+git+1+8d87fee-1 [14.6 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf lua-md5-dev armhf 1.2+git+1+8d87fee-1 [22.3 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf poppler-data all 0.4.7-7 [1466 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libpython3.5-minimal armhf 3.5.1-5 [553 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf python3.5-minimal armhf 3.5.1-5 [1333 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf python3-minimal armhf 3.5.1-2 [35.2 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libpython3.5-stdlib armhf 3.5.1-5 [2063 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf python3.5 armhf 3.5.1-5 [194 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libpython3-stdlib armhf 3.5.1-2 [18.5 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf dh-python all 2.20151103 [76.9 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf python3 armhf 3.5.1-2 [21.5 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf sgml-base all 1.26+nmu4 [14.6 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libfaketime armhf 0.9.6-4 [24.9 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf faketime armhf 0.9.6-4 [13.1 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf libnettle6 armhf 3.2-1 [202 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libhogweed4 armhf 3.2-1 [126 kB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf libidn11 armhf 1.32-3 [110 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf libp11-kit0 armhf 0.23.2-3 [93.3 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf libtasn1-6 armhf 4.7-3 [44.4 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf libgnutls30 armhf 3.4.9-2 [711 kB]
Get:82 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-8 [11.5 kB]
Get:83 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.13.2+dfsg-5 [56.6 kB]
Get:84 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.13.2+dfsg-5 [110 kB]
Get:85 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.13.2+dfsg-5 [259 kB]
Get:86 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.13.2+dfsg-5 [130 kB]
Get:87 http://172.17.0.1/private stretch-staging/main armhf libsasl2-modules-db armhf 2.1.26.dfsg1-14+b1 [65.8 kB]
Get:88 http://172.17.0.1/private stretch-staging/main armhf libsasl2-2 armhf 2.1.26.dfsg1-14+b1 [97.1 kB]
Get:89 http://172.17.0.1/private stretch-staging/main armhf libldap-2.4-2 armhf 2.4.42+dfsg-2+rpi1+b2 [198 kB]
Get:90 http://172.17.0.1/private stretch-staging/main armhf asciidoc all 8.6.9-3 [830 kB]
Get:91 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20150820.1 [71.7 kB]
Get:92 http://172.17.0.1/private stretch-staging/main armhf openssl armhf 1.0.2g-1 [666 kB]
Get:93 http://172.17.0.1/private stretch-staging/main armhf ca-certificates all 20160104 [200 kB]
Get:94 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:95 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:96 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:97 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:98 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.56-2 [94.9 kB]
Get:99 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
Get:100 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:101 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.016-1 [6998 B]
Get:102 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160306 [815 kB]
Get:103 http://172.17.0.1/private stretch-staging/main armhf xml-core all 0.13+nmu2 [24.2 kB]
Get:104 http://172.17.0.1/private stretch-staging/main armhf docbook-xsl all 1.79.1+dfsg-1 [1249 kB]
Get:105 http://172.17.0.1/private stretch-staging/main armhf fonts-cabin all 1.5-2 [139 kB]
Get:106 http://172.17.0.1/private stretch-staging/main armhf fonts-comfortaa all 2.003-1 [133 kB]
Get:107 http://172.17.0.1/private stretch-staging/main armhf fonts-crosextra-caladea all 20130214-1 [82.1 kB]
Get:108 http://172.17.0.1/private stretch-staging/main armhf fonts-crosextra-carlito all 20130920-1 [745 kB]
Get:109 http://172.17.0.1/private stretch-staging/main armhf fonts-dejavu-extra all 2.35-1 [1787 kB]
Get:110 http://172.17.0.1/private stretch-staging/main armhf fonts-ebgaramond all 0.015+git20130628-3 [415 kB]
Get:111 http://172.17.0.1/private stretch-staging/main armhf fonts-ebgaramond-extra all 0.015+git20130628-3 [680 kB]
Get:112 http://172.17.0.1/private stretch-staging/main armhf fonts-font-awesome all 4.5.0~dfsg-1 [508 kB]
Get:113 http://172.17.0.1/private stretch-staging/main armhf fonts-freefont-otf all 20120503-4 [3186 kB]
Get:114 http://172.17.0.1/private stretch-staging/main armhf fonts-freefont-ttf all 20120503-4 [4262 kB]
Get:115 http://172.17.0.1/private stretch-staging/main armhf fonts-gfs-artemisia all 1.1-5 [259 kB]
Get:116 http://172.17.0.1/private stretch-staging/main armhf fonts-gfs-complutum all 1.1-6 [41.6 kB]
Get:117 http://172.17.0.1/private stretch-staging/main armhf fonts-gfs-didot all 1.1-6 [278 kB]
Get:118 http://172.17.0.1/private stretch-staging/main armhf fonts-gfs-neohellenic all 1.1-6 [215 kB]
Get:119 http://172.17.0.1/private stretch-staging/main armhf fonts-gfs-olga all 1.1-5 [33.2 kB]
Get:120 http://172.17.0.1/private stretch-staging/main armhf fonts-gfs-solomos all 1.1-5 [40.6 kB]
Get:121 http://172.17.0.1/private stretch-staging/main armhf fonts-junicode all 0.7.8-2 [643 kB]
Get:122 http://172.17.0.1/private stretch-staging/main armhf fonts-linuxlibertine all 5.3.0-2 [1713 kB]
Get:123 http://172.17.0.1/private stretch-staging/main armhf fonts-lobster all 2.0-2 [39.5 kB]
Get:124 http://172.17.0.1/private stretch-staging/main armhf fonts-lobstertwo all 2.0-2 [94.0 kB]
Get:125 http://172.17.0.1/private stretch-staging/main armhf fonts-oflb-asana-math all 000.907-6 [245 kB]
Get:126 http://172.17.0.1/private stretch-staging/main armhf fonts-roboto-hinted all 2:0~20160106-1 [2931 kB]
Get:127 http://172.17.0.1/private stretch-staging/main armhf fonts-sil-gentium all 20081126:1.03-1 [251 kB]
Get:128 http://172.17.0.1/private stretch-staging/main armhf fonts-sil-gentium-basic all 1.1-7 [382 kB]
Get:129 http://172.17.0.1/private stretch-staging/main armhf fonts-sil-gentiumplus all 5.000-1 [2811 kB]
Get:130 http://172.17.0.1/private stretch-staging/main armhf libgirepository-1.0-1 armhf 1.46.0-4 [83.7 kB]
Get:131 http://172.17.0.1/private stretch-staging/main armhf gir1.2-glib-2.0 armhf 1.46.0-4 [143 kB]
Get:132 http://172.17.0.1/private stretch-staging/main armhf libpixman-1-0 armhf 0.33.6-1 [454 kB]
Get:133 http://172.17.0.1/private stretch-staging/main armhf libxcb-render0 armhf 1.11.1-1 [17.0 kB]
Get:134 http://172.17.0.1/private stretch-staging/main armhf libxcb-shm0 armhf 1.11.1-1 [11.5 kB]
Get:135 http://172.17.0.1/private stretch-staging/main armhf libcairo2 armhf 1.14.6-1 [688 kB]
Get:136 http://172.17.0.1/private stretch-staging/main armhf libcairo-gobject2 armhf 1.14.6-1 [332 kB]
Get:137 http://172.17.0.1/private stretch-staging/main armhf gir1.2-freedesktop armhf 1.46.0-4 [22.6 kB]
Get:138 http://172.17.0.1/private stretch-staging/main armhf libthai-data all 0.1.24-2 [163 kB]
Get:139 http://172.17.0.1/private stretch-staging/main armhf libdatrie1 armhf 0.2.10-2 [32.5 kB]
Get:140 http://172.17.0.1/private stretch-staging/main armhf libthai0 armhf 0.1.24-2 [46.6 kB]
Get:141 http://172.17.0.1/private stretch-staging/main armhf libpango-1.0-0 armhf 1.38.1-1 [292 kB]
Get:142 http://172.17.0.1/private stretch-staging/main armhf libgraphite2-3 armhf 1.3.6-1 [61.9 kB]
Get:143 http://172.17.0.1/private stretch-staging/main armhf libharfbuzz0b armhf 1.0.1-1+b1 [501 kB]
Get:144 http://172.17.0.1/private stretch-staging/main armhf libpangoft2-1.0-0 armhf 1.38.1-1 [229 kB]
Get:145 http://172.17.0.1/private stretch-staging/main armhf libpangocairo-1.0-0 armhf 1.38.1-1 [218 kB]
Get:146 http://172.17.0.1/private stretch-staging/main armhf libpangoxft-1.0-0 armhf 1.38.1-1 [214 kB]
Get:147 http://172.17.0.1/private stretch-staging/main armhf gir1.2-pango-1.0 armhf 1.38.1-1 [222 kB]
Get:148 http://172.17.0.1/private stretch-staging/main armhf hicolor-icon-theme all 0.13-1 [8600 B]
Get:149 http://172.17.0.1/private stretch-staging/main armhf imagemagick-6.q16 armhf 8:6.8.9.9-7+b1 [512 kB]
Get:150 http://172.17.0.1/private stretch-staging/main armhf imagemagick armhf 8:6.8.9.9-7+b1 [156 kB]
Get:151 http://172.17.0.1/private stretch-staging/main armhf libavahi-common-data armhf 0.6.32~rc+dfsg-1 [99.5 kB]
Get:152 http://172.17.0.1/private stretch-staging/main armhf libavahi-common3 armhf 0.6.32~rc+dfsg-1 [48.1 kB]
Get:153 http://172.17.0.1/private stretch-staging/main armhf libavahi-client3 armhf 0.6.32~rc+dfsg-1 [50.7 kB]
Get:154 http://172.17.0.1/private stretch-staging/main armhf libbam-dev armhf 0.1.19-2 [109 kB]
Get:155 http://172.17.0.1/private stretch-staging/main armhf libbz2-dev armhf 1.0.6-8 [27.8 kB]
Get:156 http://172.17.0.1/private stretch-staging/main armhf libcairo-script-interpreter2 armhf 1.14.6-1 [360 kB]
Get:157 http://172.17.0.1/private stretch-staging/main armhf libexpat1-dev armhf 2.1.0-7 [114 kB]
Get:158 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:159 http://172.17.0.1/private stretch-staging/main armhf libpng12-dev armhf 1.2.54-4 [233 kB]
Get:160 http://172.17.0.1/private stretch-staging/main armhf libfreetype6-dev armhf 2.6.3-3 [5758 kB]
Get:161 http://172.17.0.1/private stretch-staging/main armhf pkg-config armhf 0.29-3 [59.0 kB]
Get:162 http://172.17.0.1/private stretch-staging/main armhf libfontconfig1-dev armhf 2.11.0-6.3 [875 kB]
Get:163 http://172.17.0.1/private stretch-staging/main armhf xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:164 http://172.17.0.1/private stretch-staging/main armhf x11proto-core-dev all 7.0.28-2 [726 kB]
Get:165 http://172.17.0.1/private stretch-staging/main armhf libxau-dev armhf 1:1.0.8-1 [23.0 kB]
Get:166 http://172.17.0.1/private stretch-staging/main armhf libxdmcp-dev armhf 1:1.1.2-1.1 [40.8 kB]
Get:167 http://172.17.0.1/private stretch-staging/main armhf x11proto-input-dev all 2.3.1-1 [157 kB]
Get:168 http://172.17.0.1/private stretch-staging/main armhf x11proto-kb-dev all 1.0.7-1 [233 kB]
Get:169 http://172.17.0.1/private stretch-staging/main armhf xtrans-dev all 1.3.5-1 [100 kB]
Get:170 http://172.17.0.1/private stretch-staging/main armhf libpthread-stubs0-dev armhf 0.3-4 [4042 B]
Get:171 http://172.17.0.1/private stretch-staging/main armhf libxcb1-dev armhf 1.11.1-1 [75.9 kB]
Get:172 http://172.17.0.1/private stretch-staging/main armhf libx11-dev armhf 2:1.6.3-1 [749 kB]
Get:173 http://172.17.0.1/private stretch-staging/main armhf x11proto-render-dev all 2:0.11.1-2 [20.8 kB]
Get:174 http://172.17.0.1/private stretch-staging/main armhf libxrender-dev armhf 1:0.9.9-2 [36.5 kB]
Get:175 http://172.17.0.1/private stretch-staging/main armhf x11proto-xext-dev all 7.3.0-1 [212 kB]
Get:176 http://172.17.0.1/private stretch-staging/main armhf libxext-dev armhf 2:1.3.3-1 [102 kB]
Get:177 http://172.17.0.1/private stretch-staging/main armhf x11-common all 1:7.7+14 [251 kB]
Get:178 http://172.17.0.1/private stretch-staging/main armhf libice6 armhf 2:1.0.9-1+b1 [51.9 kB]
Get:179 http://172.17.0.1/private stretch-staging/main armhf libsm6 armhf 2:1.2.2-1+b1 [31.2 kB]
Get:180 http://172.17.0.1/private stretch-staging/main armhf libice-dev armhf 2:1.0.9-1+b1 [59.0 kB]
Get:181 http://172.17.0.1/private stretch-staging/main armhf libsm-dev armhf 2:1.2.2-1+b1 [33.5 kB]
Get:182 http://172.17.0.1/private stretch-staging/main armhf libpixman-1-dev armhf 0.33.6-1 [476 kB]
Get:183 http://172.17.0.1/private stretch-staging/main armhf libxcb-render0-dev armhf 1.11.1-1 [20.8 kB]
Get:184 http://172.17.0.1/private stretch-staging/main armhf libxcb-shm0-dev armhf 1.11.1-1 [12.6 kB]
Get:185 http://172.17.0.1/private stretch-staging/main armhf libelf1 armhf 0.163-5.1 [162 kB]
Get:186 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-data all 2.46.2-3 [2418 kB]
Get:187 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-bin armhf 2.46.2-3 [1566 kB]
Get:188 http://172.17.0.1/private stretch-staging/main armhf libpcre16-3 armhf 2:8.38-3 [229 kB]
Get:189 http://172.17.0.1/private stretch-staging/main armhf libpcre32-3 armhf 2:8.38-3 [223 kB]
Get:190 http://172.17.0.1/private stretch-staging/main armhf libpcre3-dev armhf 2:8.38-3 [556 kB]
Get:191 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-dev armhf 2.46.2-3 [2715 kB]
Get:192 http://172.17.0.1/private stretch-staging/main armhf libcairo2-dev armhf 1.14.6-1 [812 kB]
Get:193 http://172.17.0.1/private stretch-staging/main armhf libcups2 armhf 2.1.3-3 [266 kB]
Get:194 http://172.17.0.1/private stretch-staging/main armhf libcupsimage2 armhf 2.1.3-3 [117 kB]
Get:195 http://172.17.0.1/private stretch-staging/main armhf libcupsfilters1 armhf 1.8.2-3 [112 kB]
Get:196 http://172.17.0.1/private stretch-staging/main armhf libijs-0.35 armhf 0.35-12 [16.0 kB]
Get:197 http://172.17.0.1/private stretch-staging/main armhf libjbig2dec0 armhf 0.12+20150918-1 [50.7 kB]
Get:198 http://172.17.0.1/private stretch-staging/main armhf libopenjp2-7 armhf 2.1.0-2.1 [103 kB]
Get:199 http://172.17.0.1/private stretch-staging/main armhf libgs9-common all 9.18~dfsg-4 [3027 kB]
Get:200 http://172.17.0.1/private stretch-staging/main armhf libgs9 armhf 9.18~dfsg-4 [1697 kB]
Get:201 http://172.17.0.1/private stretch-staging/main armhf libharfbuzz-icu0 armhf 1.0.1-1+b1 [390 kB]
Get:202 http://172.17.0.1/private stretch-staging/main armhf libharfbuzz-gobject0 armhf 1.0.1-1+b1 [395 kB]
Get:203 http://172.17.0.1/private stretch-staging/main armhf libharfbuzz-dev armhf 1.0.1-1+b1 [548 kB]
Get:204 http://172.17.0.1/private stretch-staging/main armhf libkpathsea6 armhf 2015.20160222.37495-1 [148 kB]
Get:205 http://172.17.0.1/private stretch-staging/main armhf liblua5.1-0 armhf 5.1.5-8 [83.3 kB]
Get:206 http://172.17.0.1/private stretch-staging/main armhf libtinfo-dev armhf 6.0+20160213-1 [66.0 kB]
Get:207 http://172.17.0.1/private stretch-staging/main armhf libreadline6-dev armhf 6.3-8+b3 [105 kB]
Get:208 http://172.17.0.1/private stretch-staging/main armhf libreadline-dev armhf 6.3-8+b3 [958 B]
Get:209 http://172.17.0.1/private stretch-staging/main armhf liblua5.1-0-dev armhf 5.1.5-8 [115 kB]
Get:210 http://172.17.0.1/private stretch-staging/main armhf libxft-dev armhf 2.3.2-1 [59.1 kB]
Get:211 http://172.17.0.1/private stretch-staging/main armhf libpango1.0-dev armhf 1.38.1-1 [450 kB]
Get:212 http://172.17.0.1/private stretch-staging/main armhf libpaper-utils armhf 1.1.24+nmu4 [17.2 kB]
Get:213 http://172.17.0.1/private stretch-staging/main armhf libopenjpeg5 armhf 1:1.5.2-3.1+b4 [93.0 kB]
Get:214 http://172.17.0.1/private stretch-staging/main armhf libpoppler57 armhf 0.38.0-2 [1117 kB]
Get:215 http://172.17.0.1/private stretch-staging/main armhf libpotrace0 armhf 1.13-2 [22.8 kB]
Get:216 http://172.17.0.1/private stretch-staging/main armhf libptexenc1 armhf 2015.20160222.37495-1 [53.7 kB]
Get:217 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-dev armhf 3.11.1-1 [587 kB]
Get:218 http://172.17.0.1/private stretch-staging/main armhf libsynctex1 armhf 2015.20160222.37495-1 [56.3 kB]
Get:219 http://172.17.0.1/private stretch-staging/main armhf libtexlua52 armhf 2015.20160222.37495-1 [84.6 kB]
Get:220 http://172.17.0.1/private stretch-staging/main armhf libtexluajit2 armhf 2015.20160222.37495-1 [186 kB]
Get:221 http://172.17.0.1/private stretch-staging/main armhf libtre-dev armhf 0.8.0-4 [27.1 kB]
Get:222 http://172.17.0.1/private stretch-staging/main armhf libxt6 armhf 1:1.1.5-1 [155 kB]
Get:223 http://172.17.0.1/private stretch-staging/main armhf libxmu6 armhf 2:1.1.2-2 [52.0 kB]
Get:224 http://172.17.0.1/private stretch-staging/main armhf libxpm4 armhf 1:3.5.11-1+b1 [42.4 kB]
Get:225 http://172.17.0.1/private stretch-staging/main armhf libxaw7 armhf 2:1.0.13-1 [164 kB]
Get:226 http://172.17.0.1/private stretch-staging/main armhf libxi6 armhf 2:1.7.6-1 [75.9 kB]
Get:227 http://172.17.0.1/private stretch-staging/main armhf libxml2-utils armhf 2.9.3+dfsg1-1 [101 kB]
Get:228 http://172.17.0.1/private stretch-staging/main armhf libxslt1.1 armhf 1.1.28-2.1 [211 kB]
Get:229 http://172.17.0.1/private stretch-staging/main armhf lua-filesystem armhf 1.6.3-1 [9984 B]
Get:230 http://172.17.0.1/private stretch-staging/main armhf lua-filesystem-dev armhf 1.6.3-1 [24.4 kB]
Get:231 http://172.17.0.1/private stretch-staging/main armhf lua-lpeg armhf 0.12.2-1 [25.4 kB]
Get:232 http://172.17.0.1/private stretch-staging/main armhf lua-lpeg-dev armhf 0.12.2-1 [44.3 kB]
Get:233 http://172.17.0.1/private stretch-staging/main armhf tex-common all 6.04 [564 kB]
Get:234 http://172.17.0.1/private stretch-staging/main armhf preview-latex-style all 11.87-3+deb8u1 [318 kB]
Get:235 http://172.17.0.1/private stretch-staging/main armhf rubygems-integration all 1.10 [4882 B]
Get:236 http://172.17.0.1/private stretch-staging/main armhf ruby-did-you-mean all 1.0.0-2 [11.2 kB]
Get:237 http://172.17.0.1/private stretch-staging/main armhf ruby-minitest all 5.8.4-2 [50.3 kB]
Get:238 http://172.17.0.1/private stretch-staging/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB]
Get:239 http://172.17.0.1/private stretch-staging/main armhf ruby-power-assert all 0.2.7-1 [7578 B]
Get:240 http://172.17.0.1/private stretch-staging/main armhf ruby-test-unit all 3.1.7-2 [69.6 kB]
Get:241 http://172.17.0.1/private stretch-staging/main armhf libruby2.3 armhf 2.3.0-4 [2833 kB]
Get:242 http://172.17.0.1/private stretch-staging/main armhf ruby2.3 armhf 2.3.0-4 [167 kB]
Get:243 http://172.17.0.1/private stretch-staging/main armhf ruby all 1:2.3.0+1 [10.2 kB]
Get:244 http://172.17.0.1/private stretch-staging/main armhf rake all 10.5.0-2 [49.4 kB]
Get:245 http://172.17.0.1/private stretch-staging/main armhf t1utils armhf 1.39-2 [52.7 kB]
Get:246 http://172.17.0.1/private stretch-staging/main armhf texlive-binaries armhf 2015.20160222.37495-1 [5341 kB]
Get:247 http://172.17.0.1/private stretch-staging/main armhf xdg-utils all 1.1.1-1 [71.1 kB]
Get:248 http://172.17.0.1/private stretch-staging/main armhf texlive-base all 2015.20160223-1 [18.1 MB]
Get:249 http://172.17.0.1/private stretch-staging/main armhf ttf-adf-accanthis all 0.20090423-2 [401 kB]
Get:250 http://172.17.0.1/private stretch-staging/main armhf fonts-stix all 1.1.1-4 [590 kB]
Get:251 http://172.17.0.1/private stretch-staging/main armhf ttf-adf-universalis all 0.20090423-2 [221 kB]
Get:252 http://172.17.0.1/private stretch-staging/main armhf ttf-adf-gillius all 0.20090423-2 [400 kB]
Get:253 http://172.17.0.1/private stretch-staging/main armhf texlive-fonts-extra all 2015.20160223-2 [232 MB]
Get:254 http://172.17.0.1/private stretch-staging/main armhf texlive-fonts-recommended all 2015.20160223-1 [5686 kB]
Get:255 http://172.17.0.1/private stretch-staging/main armhf texlive-latex-base all 2015.20160223-1 [868 kB]
Get:256 http://172.17.0.1/private stretch-staging/main armhf texlive-latex-recommended all 2015.20160223-1 [8440 kB]
Get:257 http://172.17.0.1/private stretch-staging/main armhf texlive-pictures all 2015.20160223-1 [3214 kB]
Get:258 http://172.17.0.1/private stretch-staging/main armhf texlive-latex-extra all 2015.20160223-2 [10.3 MB]
Get:259 http://172.17.0.1/private stretch-staging/main armhf xsltproc armhf 1.1.28-2.1 [118 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 390 MB in 2min 37s (2472 kB/s)
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12685 files and directories currently installed.)
Preparing to unpack .../libpcre3_2%3a8.38-3_armhf.deb ...
Unpacking libpcre3:armhf (2:8.38-3) over (2:8.38-1) ...
Processing triggers for libc-bin (2.21-7) ...
Setting up libpcre3:armhf (2:8.38-3) ...
Processing triggers for libc-bin (2.21-7) ...
Selecting previously unselected package groff-base.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12685 files and directories currently installed.)
Preparing to unpack .../groff-base_1.22.3-7_armhf.deb ...
Unpacking groff-base (1.22.3-7) ...
Preparing to unpack .../libtinfo5_6.0+20160213-1_armhf.deb ...
Unpacking libtinfo5:armhf (6.0+20160213-1) over (6.0+20151024-2) ...
Processing triggers for libc-bin (2.21-7) ...
Setting up libtinfo5:armhf (6.0+20160213-1) ...
Processing triggers for libc-bin (2.21-7) ...
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12870 files and directories currently installed.)
Preparing to unpack .../libncurses5_6.0+20160213-1_armhf.deb ...
Unpacking libncurses5:armhf (6.0+20160213-1) over (6.0+20151024-2) ...
Processing triggers for libc-bin (2.21-7) ...
Setting up libncurses5:armhf (6.0+20160213-1) ...
Processing triggers for libc-bin (2.21-7) ...
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12870 files and directories currently installed.)
Preparing to unpack .../libncursesw5_6.0+20160213-1_armhf.deb ...
Unpacking libncursesw5:armhf (6.0+20160213-1) over (6.0+20151024-2) ...
Processing triggers for libc-bin (2.21-7) ...
Setting up libncursesw5:armhf (6.0+20160213-1) ...
Processing triggers for libc-bin (2.21-7) ...
Selecting previously unselected package bsdmainutils.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12870 files and directories currently installed.)
Preparing to unpack .../bsdmainutils_9.0.6_armhf.deb ...
Unpacking bsdmainutils (9.0.6) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../libpipeline1_1.4.1-2_armhf.deb ...
Unpacking libpipeline1:armhf (1.4.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../man-db_2.7.5-1_armhf.deb ...
Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package libpython2.7-minimal:armhf.
Preparing to unpack .../libpython2.7-minimal_2.7.11-4_armhf.deb ...
Unpacking libpython2.7-minimal:armhf (2.7.11-4) ...
Selecting previously unselected package python2.7-minimal.
Preparing to unpack .../python2.7-minimal_2.7.11-4_armhf.deb ...
Unpacking python2.7-minimal (2.7.11-4) ...
Selecting previously unselected package python-minimal.
Preparing to unpack .../python-minimal_2.7.11-1_armhf.deb ...
Unpacking python-minimal (2.7.11-1) ...
Selecting previously unselected package mime-support.
Preparing to unpack .../mime-support_3.59_all.deb ...
Unpacking mime-support (3.59) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../libexpat1_2.1.0-7_armhf.deb ...
Unpacking libexpat1:armhf (2.1.0-7) ...
Selecting previously unselected package libffi6:armhf.
Preparing to unpack .../libffi6_3.2.1-4_armhf.deb ...
Unpacking libffi6:armhf (3.2.1-4) ...
Selecting previously unselected package libsqlite3-0:armhf.
Preparing to unpack .../libsqlite3-0_3.11.1-1_armhf.deb ...
Unpacking libsqlite3-0:armhf (3.11.1-1) ...
Selecting previously unselected package libssl1.0.2:armhf.
Preparing to unpack .../libssl1.0.2_1.0.2g-1_armhf.deb ...
Unpacking libssl1.0.2:armhf (1.0.2g-1) ...
Selecting previously unselected package libpython2.7-stdlib:armhf.
Preparing to unpack .../libpython2.7-stdlib_2.7.11-4_armhf.deb ...
Unpacking libpython2.7-stdlib:armhf (2.7.11-4) ...
Selecting previously unselected package python2.7.
Preparing to unpack .../python2.7_2.7.11-4_armhf.deb ...
Unpacking python2.7 (2.7.11-4) ...
Selecting previously unselected package libpython-stdlib:armhf.
Preparing to unpack .../libpython-stdlib_2.7.11-1_armhf.deb ...
Unpacking libpython-stdlib:armhf (2.7.11-1) ...
Processing triggers for libc-bin (2.21-7) ...
Setting up libpython2.7-minimal:armhf (2.7.11-4) ...
Setting up python2.7-minimal (2.7.11-4) ...
Setting up python-minimal (2.7.11-1) ...
Selecting previously unselected package python.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 14048 files and directories currently installed.)
Preparing to unpack .../python_2.7.11-1_armhf.deb ...
Unpacking python (2.7.11-1) ...
Preparing to unpack .../libpng12-0_1.2.54-4_armhf.deb ...
Unpacking libpng12-0:armhf (1.2.54-4) over (1.2.54-1) ...
Selecting previously unselected package libfreetype6:armhf.
Preparing to unpack .../libfreetype6_2.6.3-3_armhf.deb ...
Unpacking libfreetype6:armhf (2.6.3-3) ...
Selecting previously unselected package ucf.
Preparing to unpack .../archives/ucf_3.0035_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0035) ...
Selecting previously unselected package fonts-dejavu-core.
Preparing to unpack .../fonts-dejavu-core_2.35-1_all.deb ...
Unpacking fonts-dejavu-core (2.35-1) ...
Selecting previously unselected package fontconfig-config.
Preparing to unpack .../fontconfig-config_2.11.0-6.3_all.deb ...
Unpacking fontconfig-config (2.11.0-6.3) ...
Selecting previously unselected package libfontconfig1:armhf.
Preparing to unpack .../libfontconfig1_2.11.0-6.3_armhf.deb ...
Unpacking libfontconfig1:armhf (2.11.0-6.3) ...
Selecting previously unselected package fontconfig.
Preparing to unpack .../fontconfig_2.11.0-6.3_armhf.deb ...
Unpacking fontconfig (2.11.0-6.3) ...
Selecting previously unselected package fonts-lato.
Preparing to unpack .../fonts-lato_2.0-1_all.deb ...
Unpacking fonts-lato (2.0-1) ...
Selecting previously unselected package imagemagick-common.
Preparing to unpack .../imagemagick-common_8%3a6.8.9.9-7_all.deb ...
Unpacking imagemagick-common (8:6.8.9.9-7) ...
Selecting previously unselected package libfftw3-double3:armhf.
Preparing to unpack .../libfftw3-double3_3.3.4-2+rpi1+b1_armhf.deb ...
Unpacking libfftw3-double3:armhf (3.3.4-2+rpi1+b1) ...
Selecting previously unselected package libjbig0:armhf.
Preparing to unpack .../libjbig0_2.1-3.1_armhf.deb ...
Unpacking libjbig0:armhf (2.1-3.1) ...
Selecting previously unselected package liblcms2-2:armhf.
Preparing to unpack .../liblcms2-2_2.6-3_armhf.deb ...
Unpacking liblcms2-2:armhf (2.6-3) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../libglib2.0-0_2.46.2-3_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.46.2-3) ...
Selecting previously unselected package liblqr-1-0:armhf.
Preparing to unpack .../liblqr-1-0_0.4.2-2_armhf.deb ...
Unpacking liblqr-1-0:armhf (0.4.2-2) ...
Selecting previously unselected package liblzo2-2:armhf.
Preparing to unpack .../liblzo2-2_2.08-1.2_armhf.deb ...
Unpacking liblzo2-2:armhf (2.08-1.2) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
Preparing to unpack .../libjpeg62-turbo_1%3a1.4.2-2_armhf.deb ...
Unpacking libjpeg62-turbo:armhf (1:1.4.2-2) ...
Selecting previously unselected package libltdl7:armhf.
Preparing to unpack .../libltdl7_2.4.6-0.1_armhf.deb ...
Unpacking libltdl7:armhf (2.4.6-0.1) ...
Selecting previously unselected package libtiff5:armhf.
Preparing to unpack .../libtiff5_4.0.6-1_armhf.deb ...
Unpacking libtiff5:armhf (4.0.6-1) ...
Selecting previously unselected package libxau6:armhf.
Preparing to unpack .../libxau6_1%3a1.0.8-1_armhf.deb ...
Unpacking libxau6:armhf (1:1.0.8-1) ...
Selecting previously unselected package libxdmcp6:armhf.
Preparing to unpack .../libxdmcp6_1%3a1.1.2-1.1_armhf.deb ...
Unpacking libxdmcp6:armhf (1:1.1.2-1.1) ...
Selecting previously unselected package libxcb1:armhf.
Preparing to unpack .../libxcb1_1.11.1-1_armhf.deb ...
Unpacking libxcb1:armhf (1.11.1-1) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../libx11-data_2%3a1.6.3-1_all.deb ...
Unpacking libx11-data (2:1.6.3-1) ...
Selecting previously unselected package libx11-6:armhf.
Preparing to unpack .../libx11-6_2%3a1.6.3-1_armhf.deb ...
Unpacking libx11-6:armhf (2:1.6.3-1) ...
Selecting previously unselected package libxext6:armhf.
Preparing to unpack .../libxext6_2%3a1.3.3-1_armhf.deb ...
Unpacking libxext6:armhf (2:1.3.3-1) ...
Selecting previously unselected package libicu55:armhf.
Preparing to unpack .../libicu55_55.1-7_armhf.deb ...
Unpacking libicu55:armhf (55.1-7) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../libxml2_2.9.3+dfsg1-1_armhf.deb ...
Unpacking libxml2:armhf (2.9.3+dfsg1-1) ...
Selecting previously unselected package libmagickcore-6.q16-2:armhf.
Preparing to unpack .../libmagickcore-6.q16-2_8%3a6.8.9.9-7+b1_armhf.deb ...
Unpacking libmagickcore-6.q16-2:armhf (8:6.8.9.9-7+b1) ...
Selecting previously unselected package libmagickwand-6.q16-2:armhf.
Preparing to unpack .../libmagickwand-6.q16-2_8%3a6.8.9.9-7+b1_armhf.deb ...
Unpacking libmagickwand-6.q16-2:armhf (8:6.8.9.9-7+b1) ...
Selecting previously unselected package libmpdec2:armhf.
Preparing to unpack .../libmpdec2_2.4.1-1_armhf.deb ...
Unpacking libmpdec2:armhf (2.4.1-1) ...
Selecting previously unselected package libpaper1:armhf.
Preparing to unpack .../libpaper1_1.1.24+nmu4_armhf.deb ...
Unpacking libpaper1:armhf (1.1.24+nmu4) ...
Selecting previously unselected package libpcrecpp0v5:armhf.
Preparing to unpack .../libpcrecpp0v5_2%3a8.38-3_armhf.deb ...
Unpacking libpcrecpp0v5:armhf (2:8.38-3) ...
Selecting previously unselected package libtre5:armhf.
Preparing to unpack .../libtre5_0.8.0-4_armhf.deb ...
Unpacking libtre5:armhf (0.8.0-4) ...
Selecting previously unselected package libunistring0:armhf.
Preparing to unpack .../libunistring0_0.9.3-5.2_armhf.deb ...
Unpacking libunistring0:armhf (0.9.3-5.2) ...
Selecting previously unselected package libxrender1:armhf.
Preparing to unpack .../libxrender1_1%3a0.9.9-2_armhf.deb ...
Unpacking libxrender1:armhf (1:0.9.9-2) ...
Selecting previously unselected package libxft2:armhf.
Preparing to unpack .../libxft2_2.3.2-1_armhf.deb ...
Unpacking libxft2:armhf (2.3.2-1) ...
Selecting previously unselected package libyaml-0-2:armhf.
Preparing to unpack .../libyaml-0-2_0.1.6-3_armhf.deb ...
Unpacking libyaml-0-2:armhf (0.1.6-3) ...
Selecting previously unselected package libzzip-0-13:armhf.
Preparing to unpack .../libzzip-0-13_0.13.62-3_armhf.deb ...
Unpacking libzzip-0-13:armhf (0.13.62-3) ...
Selecting previously unselected package lua-md5:armhf.
Preparing to unpack .../lua-md5_1.2+git+1+8d87fee-1_armhf.deb ...
Unpacking lua-md5:armhf (1.2+git+1+8d87fee-1) ...
Selecting previously unselected package lua-md5-dev:armhf.
Preparing to unpack .../lua-md5-dev_1.2+git+1+8d87fee-1_armhf.deb ...
Unpacking lua-md5-dev:armhf (1.2+git+1+8d87fee-1) ...
Selecting previously unselected package poppler-data.
Preparing to unpack .../poppler-data_0.4.7-7_all.deb ...
Unpacking poppler-data (0.4.7-7) ...
Selecting previously unselected package libpython3.5-minimal:armhf.
Preparing to unpack .../libpython3.5-minimal_3.5.1-5_armhf.deb ...
Unpacking libpython3.5-minimal:armhf (3.5.1-5) ...
Selecting previously unselected package python3.5-minimal.
Preparing to unpack .../python3.5-minimal_3.5.1-5_armhf.deb ...
Unpacking python3.5-minimal (3.5.1-5) ...
Selecting previously unselected package python3-minimal.
Preparing to unpack .../python3-minimal_3.5.1-2_armhf.deb ...
Unpacking python3-minimal (3.5.1-2) ...
Selecting previously unselected package libpython3.5-stdlib:armhf.
Preparing to unpack .../libpython3.5-stdlib_3.5.1-5_armhf.deb ...
Unpacking libpython3.5-stdlib:armhf (3.5.1-5) ...
Selecting previously unselected package python3.5.
Preparing to unpack .../python3.5_3.5.1-5_armhf.deb ...
Unpacking python3.5 (3.5.1-5) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../libpython3-stdlib_3.5.1-2_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.5.1-2) ...
Selecting previously unselected package dh-python.
Preparing to unpack .../dh-python_2.20151103_all.deb ...
Unpacking dh-python (2.20151103) ...
Processing triggers for libc-bin (2.21-7) ...
Setting up libssl1.0.2:armhf (1.0.2g-1) ...
Setting up libpython3.5-minimal:armhf (3.5.1-5) ...
Setting up libexpat1:armhf (2.1.0-7) ...
Setting up python3.5-minimal (3.5.1-5) ...
Setting up python3-minimal (3.5.1-2) ...
Processing triggers for libc-bin (2.21-7) ...
Selecting previously unselected package python3.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 16551 files and directories currently installed.)
Preparing to unpack .../python3_3.5.1-2_armhf.deb ...
Unpacking python3 (3.5.1-2) ...
Selecting previously unselected package sgml-base.
Preparing to unpack .../sgml-base_1.26+nmu4_all.deb ...
Unpacking sgml-base (1.26+nmu4) ...
Selecting previously unselected package libfaketime:armhf.
Preparing to unpack .../libfaketime_0.9.6-4_armhf.deb ...
Unpacking libfaketime:armhf (0.9.6-4) ...
Selecting previously unselected package faketime.
Preparing to unpack .../faketime_0.9.6-4_armhf.deb ...
Unpacking faketime (0.9.6-4) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../libmagic1_1%3a5.25-2_armhf.deb ...
Unpacking libmagic1:armhf (1:5.25-2) ...
Selecting previously unselected package file.
Preparing to unpack .../file_1%3a5.25-2_armhf.deb ...
Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.7-2_armhf.deb ...
Unpacking gettext-base (0.19.7-2) ...
Selecting previously unselected package libnettle6:armhf.
Preparing to unpack .../libnettle6_3.2-1_armhf.deb ...
Unpacking libnettle6:armhf (3.2-1) ...
Selecting previously unselected package libhogweed4:armhf.
Preparing to unpack .../libhogweed4_3.2-1_armhf.deb ...
Unpacking libhogweed4:armhf (3.2-1) ...
Selecting previously unselected package libidn11:armhf.
Preparing to unpack .../libidn11_1.32-3_armhf.deb ...
Unpacking libidn11:armhf (1.32-3) ...
Selecting previously unselected package libp11-kit0:armhf.
Preparing to unpack .../libp11-kit0_0.23.2-3_armhf.deb ...
Unpacking libp11-kit0:armhf (0.23.2-3) ...
Selecting previously unselected package libtasn1-6:armhf.
Preparing to unpack .../libtasn1-6_4.7-3_armhf.deb ...
Unpacking libtasn1-6:armhf (4.7-3) ...
Selecting previously unselected package libgnutls30:armhf.
Preparing to unpack .../libgnutls30_3.4.9-2_armhf.deb ...
Unpacking libgnutls30:armhf (3.4.9-2) ...
Selecting previously unselected package libkeyutils1:armhf.
Preparing to unpack .../libkeyutils1_1.5.9-8_armhf.deb ...
Unpacking libkeyutils1:armhf (1.5.9-8) ...
Selecting previously unselected package libkrb5support0:armhf.
Preparing to unpack .../libkrb5support0_1.13.2+dfsg-5_armhf.deb ...
Unpacking libkrb5support0:armhf (1.13.2+dfsg-5) ...
Selecting previously unselected package libk5crypto3:armhf.
Preparing to unpack .../libk5crypto3_1.13.2+dfsg-5_armhf.deb ...
Unpacking libk5crypto3:armhf (1.13.2+dfsg-5) ...
Selecting previously unselected package libkrb5-3:armhf.
Preparing to unpack .../libkrb5-3_1.13.2+dfsg-5_armhf.deb ...
Unpacking libkrb5-3:armhf (1.13.2+dfsg-5) ...
Selecting previously unselected package libgssapi-krb5-2:armhf.
Preparing to unpack .../libgssapi-krb5-2_1.13.2+dfsg-5_armhf.deb ...
Unpacking libgssapi-krb5-2:armhf (1.13.2+dfsg-5) ...
Selecting previously unselected package libsasl2-modules-db:armhf.
Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-14+b1_armhf.deb ...
Unpacking libsasl2-modules-db:armhf (2.1.26.dfsg1-14+b1) ...
Selecting previously unselected package libsasl2-2:armhf.
Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-14+b1_armhf.deb ...
Unpacking libsasl2-2:armhf (2.1.26.dfsg1-14+b1) ...
Selecting previously unselected package libldap-2.4-2:armhf.
Preparing to unpack .../libldap-2.4-2_2.4.42+dfsg-2+rpi1+b2_armhf.deb ...
Unpacking libldap-2.4-2:armhf (2.4.42+dfsg-2+rpi1+b2) ...
Selecting previously unselected package asciidoc.
Preparing to unpack .../asciidoc_8.6.9-3_all.deb ...
Unpacking asciidoc (8.6.9-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../autotools-dev_20150820.1_all.deb ...
Unpacking autotools-dev (20150820.1) ...
Selecting previously unselected package openssl.
Preparing to unpack .../openssl_1.0.2g-1_armhf.deb ...
Unpacking openssl (1.0.2g-1) ...
Selecting previously unselected package ca-certificates.
Preparing to unpack .../ca-certificates_20160104_all.deb ...
Unpacking ca-certificates (20160104) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../libcroco3_0.6.11-1_armhf.deb ...
Unpacking libcroco3:armhf (0.6.11-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../gettext_0.19.7-2_armhf.deb ...
Unpacking gettext (0.19.7-2) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.4) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../po-debconf_1.0.19_all.deb ...
Unpacking po-debconf (1.0.19) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../libarchive-zip-perl_1.56-2_all.deb ...
Unpacking libarchive-zip-perl (1.56-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../libfile-stripnondeterminism-perl_0.016-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (0.016-1) ...
Selecting previously unselected package libtimedate-perl.
Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ...
Unpacking libtimedate-perl (2.3000-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../dh-strip-nondeterminism_0.016-1_all.deb ...
Unpacking dh-strip-nondeterminism (0.016-1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../debhelper_9.20160306_all.deb ...
Unpacking debhelper (9.20160306) ...
Selecting previously unselected package xml-core.
Preparing to unpack .../xml-core_0.13+nmu2_all.deb ...
Unpacking xml-core (0.13+nmu2) ...
Selecting previously unselected package docbook-xsl.
Preparing to unpack .../docbook-xsl_1.79.1+dfsg-1_all.deb ...
Unpacking docbook-xsl (1.79.1+dfsg-1) ...
Selecting previously unselected package fonts-cabin.
Preparing to unpack .../fonts-cabin_1.5-2_all.deb ...
Unpacking fonts-cabin (1.5-2) ...
Selecting previously unselected package fonts-comfortaa.
Preparing to unpack .../fonts-comfortaa_2.003-1_all.deb ...
Unpacking fonts-comfortaa (2.003-1) ...
Selecting previously unselected package fonts-crosextra-caladea.
Preparing to unpack .../fonts-crosextra-caladea_20130214-1_all.deb ...
Unpacking fonts-crosextra-caladea (20130214-1) ...
Selecting previously unselected package fonts-crosextra-carlito.
Preparing to unpack .../fonts-crosextra-carlito_20130920-1_all.deb ...
Unpacking fonts-crosextra-carlito (20130920-1) ...
Selecting previously unselected package fonts-dejavu-extra.
Preparing to unpack .../fonts-dejavu-extra_2.35-1_all.deb ...
Unpacking fonts-dejavu-extra (2.35-1) ...
Selecting previously unselected package fonts-ebgaramond.
Preparing to unpack .../fonts-ebgaramond_0.015+git20130628-3_all.deb ...
Unpacking fonts-ebgaramond (0.015+git20130628-3) ...
Selecting previously unselected package fonts-ebgaramond-extra.
Preparing to unpack .../fonts-ebgaramond-extra_0.015+git20130628-3_all.deb ...
Unpacking fonts-ebgaramond-extra (0.015+git20130628-3) ...
Selecting previously unselected package fonts-font-awesome.
Preparing to unpack .../fonts-font-awesome_4.5.0~dfsg-1_all.deb ...
Unpacking fonts-font-awesome (4.5.0~dfsg-1) ...
Selecting previously unselected package fonts-freefont-otf.
Preparing to unpack .../fonts-freefont-otf_20120503-4_all.deb ...
Unpacking fonts-freefont-otf (20120503-4) ...
Selecting previously unselected package fonts-freefont-ttf.
Preparing to unpack .../fonts-freefont-ttf_20120503-4_all.deb ...
Unpacking fonts-freefont-ttf (20120503-4) ...
Selecting previously unselected package fonts-gfs-artemisia.
Preparing to unpack .../fonts-gfs-artemisia_1.1-5_all.deb ...
Unpacking fonts-gfs-artemisia (1.1-5) ...
Selecting previously unselected package fonts-gfs-complutum.
Preparing to unpack .../fonts-gfs-complutum_1.1-6_all.deb ...
Unpacking fonts-gfs-complutum (1.1-6) ...
Selecting previously unselected package fonts-gfs-didot.
Preparing to unpack .../fonts-gfs-didot_1.1-6_all.deb ...
Unpacking fonts-gfs-didot (1.1-6) ...
Selecting previously unselected package fonts-gfs-neohellenic.
Preparing to unpack .../fonts-gfs-neohellenic_1.1-6_all.deb ...
Unpacking fonts-gfs-neohellenic (1.1-6) ...
Selecting previously unselected package fonts-gfs-olga.
Preparing to unpack .../fonts-gfs-olga_1.1-5_all.deb ...
Unpacking fonts-gfs-olga (1.1-5) ...
Selecting previously unselected package fonts-gfs-solomos.
Preparing to unpack .../fonts-gfs-solomos_1.1-5_all.deb ...
Unpacking fonts-gfs-solomos (1.1-5) ...
Selecting previously unselected package fonts-junicode.
Preparing to unpack .../fonts-junicode_0.7.8-2_all.deb ...
Unpacking fonts-junicode (0.7.8-2) ...
Selecting previously unselected package fonts-linuxlibertine.
Preparing to unpack .../fonts-linuxlibertine_5.3.0-2_all.deb ...
Unpacking fonts-linuxlibertine (5.3.0-2) ...
Selecting previously unselected package fonts-lobster.
Preparing to unpack .../fonts-lobster_2.0-2_all.deb ...
Unpacking fonts-lobster (2.0-2) ...
Selecting previously unselected package fonts-lobstertwo.
Preparing to unpack .../fonts-lobstertwo_2.0-2_all.deb ...
Unpacking fonts-lobstertwo (2.0-2) ...
Selecting previously unselected package fonts-oflb-asana-math.
Preparing to unpack .../fonts-oflb-asana-math_000.907-6_all.deb ...
Unpacking fonts-oflb-asana-math (000.907-6) ...
Selecting previously unselected package fonts-roboto-hinted.
Preparing to unpack .../fonts-roboto-hinted_2%3a0~20160106-1_all.deb ...
Unpacking fonts-roboto-hinted (2:0~20160106-1) ...
Selecting previously unselected package fonts-sil-gentium.
Preparing to unpack .../fonts-sil-gentium_20081126%3a1.03-1_all.deb ...
Unpacking fonts-sil-gentium (20081126:1.03-1) ...
Selecting previously unselected package fonts-sil-gentium-basic.
Preparing to unpack .../fonts-sil-gentium-basic_1.1-7_all.deb ...
Unpacking fonts-sil-gentium-basic (1.1-7) ...
Selecting previously unselected package fonts-sil-gentiumplus.
Preparing to unpack .../fonts-sil-gentiumplus_5.000-1_all.deb ...
Unpacking fonts-sil-gentiumplus (5.000-1) ...
Selecting previously unselected package libgirepository-1.0-1:armhf.
Preparing to unpack .../libgirepository-1.0-1_1.46.0-4_armhf.deb ...
Unpacking libgirepository-1.0-1:armhf (1.46.0-4) ...
Selecting previously unselected package gir1.2-glib-2.0:armhf.
Preparing to unpack .../gir1.2-glib-2.0_1.46.0-4_armhf.deb ...
Unpacking gir1.2-glib-2.0:armhf (1.46.0-4) ...
Selecting previously unselected package libpixman-1-0:armhf.
Preparing to unpack .../libpixman-1-0_0.33.6-1_armhf.deb ...
Unpacking libpixman-1-0:armhf (0.33.6-1) ...
Selecting previously unselected package libxcb-render0:armhf.
Preparing to unpack .../libxcb-render0_1.11.1-1_armhf.deb ...
Unpacking libxcb-render0:armhf (1.11.1-1) ...
Selecting previously unselected package libxcb-shm0:armhf.
Preparing to unpack .../libxcb-shm0_1.11.1-1_armhf.deb ...
Unpacking libxcb-shm0:armhf (1.11.1-1) ...
Selecting previously unselected package libcairo2:armhf.
Preparing to unpack .../libcairo2_1.14.6-1_armhf.deb ...
Unpacking libcairo2:armhf (1.14.6-1) ...
Selecting previously unselected package libcairo-gobject2:armhf.
Preparing to unpack .../libcairo-gobject2_1.14.6-1_armhf.deb ...
Unpacking libcairo-gobject2:armhf (1.14.6-1) ...
Selecting previously unselected package gir1.2-freedesktop:armhf.
Preparing to unpack .../gir1.2-freedesktop_1.46.0-4_armhf.deb ...
Unpacking gir1.2-freedesktop:armhf (1.46.0-4) ...
Selecting previously unselected package libthai-data.
Preparing to unpack .../libthai-data_0.1.24-2_all.deb ...
Unpacking libthai-data (0.1.24-2) ...
Selecting previously unselected package libdatrie1:armhf.
Preparing to unpack .../libdatrie1_0.2.10-2_armhf.deb ...
Unpacking libdatrie1:armhf (0.2.10-2) ...
Selecting previously unselected package libthai0:armhf.
Preparing to unpack .../libthai0_0.1.24-2_armhf.deb ...
Unpacking libthai0:armhf (0.1.24-2) ...
Selecting previously unselected package libpango-1.0-0:armhf.
Preparing to unpack .../libpango-1.0-0_1.38.1-1_armhf.deb ...
Unpacking libpango-1.0-0:armhf (1.38.1-1) ...
Selecting previously unselected package libgraphite2-3:armhf.
Preparing to unpack .../libgraphite2-3_1.3.6-1_armhf.deb ...
Unpacking libgraphite2-3:armhf (1.3.6-1) ...
Selecting previously unselected package libharfbuzz0b:armhf.
Preparing to unpack .../libharfbuzz0b_1.0.1-1+b1_armhf.deb ...
Unpacking libharfbuzz0b:armhf (1.0.1-1+b1) ...
Selecting previously unselected package libpangoft2-1.0-0:armhf.
Preparing to unpack .../libpangoft2-1.0-0_1.38.1-1_armhf.deb ...
Unpacking libpangoft2-1.0-0:armhf (1.38.1-1) ...
Selecting previously unselected package libpangocairo-1.0-0:armhf.
Preparing to unpack .../libpangocairo-1.0-0_1.38.1-1_armhf.deb ...
Unpacking libpangocairo-1.0-0:armhf (1.38.1-1) ...
Selecting previously unselected package libpangoxft-1.0-0:armhf.
Preparing to unpack .../libpangoxft-1.0-0_1.38.1-1_armhf.deb ...
Unpacking libpangoxft-1.0-0:armhf (1.38.1-1) ...
Selecting previously unselected package gir1.2-pango-1.0:armhf.
Preparing to unpack .../gir1.2-pango-1.0_1.38.1-1_armhf.deb ...
Unpacking gir1.2-pango-1.0:armhf (1.38.1-1) ...
Selecting previously unselected package hicolor-icon-theme.
Preparing to unpack .../hicolor-icon-theme_0.13-1_all.deb ...
Unpacking hicolor-icon-theme (0.13-1) ...
Selecting previously unselected package imagemagick-6.q16.
Preparing to unpack .../imagemagick-6.q16_8%3a6.8.9.9-7+b1_armhf.deb ...
Unpacking imagemagick-6.q16 (8:6.8.9.9-7+b1) ...
Selecting previously unselected package imagemagick.
Preparing to unpack .../imagemagick_8%3a6.8.9.9-7+b1_armhf.deb ...
Unpacking imagemagick (8:6.8.9.9-7+b1) ...
Selecting previously unselected package libavahi-common-data:armhf.
Preparing to unpack .../libavahi-common-data_0.6.32~rc+dfsg-1_armhf.deb ...
Unpacking libavahi-common-data:armhf (0.6.32~rc+dfsg-1) ...
Selecting previously unselected package libavahi-common3:armhf.
Preparing to unpack .../libavahi-common3_0.6.32~rc+dfsg-1_armhf.deb ...
Unpacking libavahi-common3:armhf (0.6.32~rc+dfsg-1) ...
Selecting previously unselected package libavahi-client3:armhf.
Preparing to unpack .../libavahi-client3_0.6.32~rc+dfsg-1_armhf.deb ...
Unpacking libavahi-client3:armhf (0.6.32~rc+dfsg-1) ...
Selecting previously unselected package libbam-dev.
Preparing to unpack .../libbam-dev_0.1.19-2_armhf.deb ...
Unpacking libbam-dev (0.1.19-2) ...
Selecting previously unselected package libbz2-dev:armhf.
Preparing to unpack .../libbz2-dev_1.0.6-8_armhf.deb ...
Unpacking libbz2-dev:armhf (1.0.6-8) ...
Selecting previously unselected package libcairo-script-interpreter2:armhf.
Preparing to unpack .../libcairo-script-interpreter2_1.14.6-1_armhf.deb ...
Unpacking libcairo-script-interpreter2:armhf (1.14.6-1) ...
Selecting previously unselected package libexpat1-dev:armhf.
Preparing to unpack .../libexpat1-dev_2.1.0-7_armhf.deb ...
Unpacking libexpat1-dev:armhf (2.1.0-7) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Selecting previously unselected package libpng12-dev:armhf.
Preparing to unpack .../libpng12-dev_1.2.54-4_armhf.deb ...
Unpacking libpng12-dev:armhf (1.2.54-4) ...
Selecting previously unselected package libfreetype6-dev.
Preparing to unpack .../libfreetype6-dev_2.6.3-3_armhf.deb ...
Unpacking libfreetype6-dev (2.6.3-3) ...
Selecting previously unselected package pkg-config.
Preparing to unpack .../pkg-config_0.29-3_armhf.deb ...
Unpacking pkg-config (0.29-3) ...
Selecting previously unselected package libfontconfig1-dev:armhf.
Preparing to unpack .../libfontconfig1-dev_2.11.0-6.3_armhf.deb ...
Unpacking libfontconfig1-dev:armhf (2.11.0-6.3) ...
Selecting previously unselected package xorg-sgml-doctools.
Preparing to unpack .../xorg-sgml-doctools_1%3a1.11-1_all.deb ...
Unpacking xorg-sgml-doctools (1:1.11-1) ...
Selecting previously unselected package x11proto-core-dev.
Preparing to unpack .../x11proto-core-dev_7.0.28-2_all.deb ...
Unpacking x11proto-core-dev (7.0.28-2) ...
Selecting previously unselected package libxau-dev:armhf.
Preparing to unpack .../libxau-dev_1%3a1.0.8-1_armhf.deb ...
Unpacking libxau-dev:armhf (1:1.0.8-1) ...
Selecting previously unselected package libxdmcp-dev:armhf.
Preparing to unpack .../libxdmcp-dev_1%3a1.1.2-1.1_armhf.deb ...
Unpacking libxdmcp-dev:armhf (1:1.1.2-1.1) ...
Selecting previously unselected package x11proto-input-dev.
Preparing to unpack .../x11proto-input-dev_2.3.1-1_all.deb ...
Unpacking x11proto-input-dev (2.3.1-1) ...
Selecting previously unselected package x11proto-kb-dev.
Preparing to unpack .../x11proto-kb-dev_1.0.7-1_all.deb ...
Unpacking x11proto-kb-dev (1.0.7-1) ...
Selecting previously unselected package xtrans-dev.
Preparing to unpack .../xtrans-dev_1.3.5-1_all.deb ...
Unpacking xtrans-dev (1.3.5-1) ...
Selecting previously unselected package libpthread-stubs0-dev:armhf.
Preparing to unpack .../libpthread-stubs0-dev_0.3-4_armhf.deb ...
Unpacking libpthread-stubs0-dev:armhf (0.3-4) ...
Selecting previously unselected package libxcb1-dev:armhf.
Preparing to unpack .../libxcb1-dev_1.11.1-1_armhf.deb ...
Unpacking libxcb1-dev:armhf (1.11.1-1) ...
Selecting previously unselected package libx11-dev:armhf.
Preparing to unpack .../libx11-dev_2%3a1.6.3-1_armhf.deb ...
Unpacking libx11-dev:armhf (2:1.6.3-1) ...
Selecting previously unselected package x11proto-render-dev.
Preparing to unpack .../x11proto-render-dev_2%3a0.11.1-2_all.deb ...
Unpacking x11proto-render-dev (2:0.11.1-2) ...
Selecting previously unselected package libxrender-dev:armhf.
Preparing to unpack .../libxrender-dev_1%3a0.9.9-2_armhf.deb ...
Unpacking libxrender-dev:armhf (1:0.9.9-2) ...
Selecting previously unselected package x11proto-xext-dev.
Preparing to unpack .../x11proto-xext-dev_7.3.0-1_all.deb ...
Unpacking x11proto-xext-dev (7.3.0-1) ...
Selecting previously unselected package libxext-dev:armhf.
Preparing to unpack .../libxext-dev_2%3a1.3.3-1_armhf.deb ...
Unpacking libxext-dev:armhf (2:1.3.3-1) ...
Selecting previously unselected package x11-common.
Preparing to unpack .../x11-common_1%3a7.7+14_all.deb ...
Unpacking x11-common (1:7.7+14) ...
Selecting previously unselected package libice6:armhf.
Preparing to unpack .../libice6_2%3a1.0.9-1+b1_armhf.deb ...
Unpacking libice6:armhf (2:1.0.9-1+b1) ...
Selecting previously unselected package libsm6:armhf.
Preparing to unpack .../libsm6_2%3a1.2.2-1+b1_armhf.deb ...
Unpacking libsm6:armhf (2:1.2.2-1+b1) ...
Selecting previously unselected package libice-dev:armhf.
Preparing to unpack .../libice-dev_2%3a1.0.9-1+b1_armhf.deb ...
Unpacking libice-dev:armhf (2:1.0.9-1+b1) ...
Selecting previously unselected package libsm-dev:armhf.
Preparing to unpack .../libsm-dev_2%3a1.2.2-1+b1_armhf.deb ...
Unpacking libsm-dev:armhf (2:1.2.2-1+b1) ...
Selecting previously unselected package libpixman-1-dev.
Preparing to unpack .../libpixman-1-dev_0.33.6-1_armhf.deb ...
Unpacking libpixman-1-dev (0.33.6-1) ...
Selecting previously unselected package libxcb-render0-dev:armhf.
Preparing to unpack .../libxcb-render0-dev_1.11.1-1_armhf.deb ...
Unpacking libxcb-render0-dev:armhf (1.11.1-1) ...
Selecting previously unselected package libxcb-shm0-dev:armhf.
Preparing to unpack .../libxcb-shm0-dev_1.11.1-1_armhf.deb ...
Unpacking libxcb-shm0-dev:armhf (1.11.1-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../libelf1_0.163-5.1_armhf.deb ...
Unpacking libelf1:armhf (0.163-5.1) ...
Selecting previously unselected package libglib2.0-data.
Preparing to unpack .../libglib2.0-data_2.46.2-3_all.deb ...
Unpacking libglib2.0-data (2.46.2-3) ...
Selecting previously unselected package libglib2.0-bin.
Preparing to unpack .../libglib2.0-bin_2.46.2-3_armhf.deb ...
Unpacking libglib2.0-bin (2.46.2-3) ...
Selecting previously unselected package libpcre16-3:armhf.
Preparing to unpack .../libpcre16-3_2%3a8.38-3_armhf.deb ...
Unpacking libpcre16-3:armhf (2:8.38-3) ...
Selecting previously unselected package libpcre32-3:armhf.
Preparing to unpack .../libpcre32-3_2%3a8.38-3_armhf.deb ...
Unpacking libpcre32-3:armhf (2:8.38-3) ...
Selecting previously unselected package libpcre3-dev:armhf.
Preparing to unpack .../libpcre3-dev_2%3a8.38-3_armhf.deb ...
Unpacking libpcre3-dev:armhf (2:8.38-3) ...
Selecting previously unselected package libglib2.0-dev.
Preparing to unpack .../libglib2.0-dev_2.46.2-3_armhf.deb ...
Unpacking libglib2.0-dev (2.46.2-3) ...
Selecting previously unselected package libcairo2-dev.
Preparing to unpack .../libcairo2-dev_1.14.6-1_armhf.deb ...
Unpacking libcairo2-dev (1.14.6-1) ...
Selecting previously unselected package libcups2:armhf.
Preparing to unpack .../libcups2_2.1.3-3_armhf.deb ...
Unpacking libcups2:armhf (2.1.3-3) ...
Selecting previously unselected package libcupsimage2:armhf.
Preparing to unpack .../libcupsimage2_2.1.3-3_armhf.deb ...
Unpacking libcupsimage2:armhf (2.1.3-3) ...
Selecting previously unselected package libcupsfilters1:armhf.
Preparing to unpack .../libcupsfilters1_1.8.2-3_armhf.deb ...
Unpacking libcupsfilters1:armhf (1.8.2-3) ...
Selecting previously unselected package libijs-0.35:armhf.
Preparing to unpack .../libijs-0.35_0.35-12_armhf.deb ...
Unpacking libijs-0.35:armhf (0.35-12) ...
Selecting previously unselected package libjbig2dec0.
Preparing to unpack .../libjbig2dec0_0.12+20150918-1_armhf.deb ...
Unpacking libjbig2dec0 (0.12+20150918-1) ...
Selecting previously unselected package libopenjp2-7:armhf.
Preparing to unpack .../libopenjp2-7_2.1.0-2.1_armhf.deb ...
Unpacking libopenjp2-7:armhf (2.1.0-2.1) ...
Selecting previously unselected package libgs9-common.
Preparing to unpack .../libgs9-common_9.18~dfsg-4_all.deb ...
Unpacking libgs9-common (9.18~dfsg-4) ...
Selecting previously unselected package libgs9.
Preparing to unpack .../libgs9_9.18~dfsg-4_armhf.deb ...
Unpacking libgs9 (9.18~dfsg-4) ...
Selecting previously unselected package libharfbuzz-icu0:armhf.
Preparing to unpack .../libharfbuzz-icu0_1.0.1-1+b1_armhf.deb ...
Unpacking libharfbuzz-icu0:armhf (1.0.1-1+b1) ...
Selecting previously unselected package libharfbuzz-gobject0:armhf.
Preparing to unpack .../libharfbuzz-gobject0_1.0.1-1+b1_armhf.deb ...
Unpacking libharfbuzz-gobject0:armhf (1.0.1-1+b1) ...
Selecting previously unselected package libharfbuzz-dev.
Preparing to unpack .../libharfbuzz-dev_1.0.1-1+b1_armhf.deb ...
Unpacking libharfbuzz-dev (1.0.1-1+b1) ...
Selecting previously unselected package libkpathsea6:armhf.
Preparing to unpack .../libkpathsea6_2015.20160222.37495-1_armhf.deb ...
Unpacking libkpathsea6:armhf (2015.20160222.37495-1) ...
Selecting previously unselected package liblua5.1-0:armhf.
Preparing to unpack .../liblua5.1-0_5.1.5-8_armhf.deb ...
Unpacking liblua5.1-0:armhf (5.1.5-8) ...
Selecting previously unselected package libtinfo-dev:armhf.
Preparing to unpack .../libtinfo-dev_6.0+20160213-1_armhf.deb ...
Unpacking libtinfo-dev:armhf (6.0+20160213-1) ...
Selecting previously unselected package libreadline6-dev:armhf.
Preparing to unpack .../libreadline6-dev_6.3-8+b3_armhf.deb ...
Unpacking libreadline6-dev:armhf (6.3-8+b3) ...
Selecting previously unselected package libreadline-dev:armhf.
Preparing to unpack .../libreadline-dev_6.3-8+b3_armhf.deb ...
Unpacking libreadline-dev:armhf (6.3-8+b3) ...
Selecting previously unselected package liblua5.1-0-dev:armhf.
Preparing to unpack .../liblua5.1-0-dev_5.1.5-8_armhf.deb ...
Unpacking liblua5.1-0-dev:armhf (5.1.5-8) ...
Selecting previously unselected package libxft-dev.
Preparing to unpack .../libxft-dev_2.3.2-1_armhf.deb ...
Unpacking libxft-dev (2.3.2-1) ...
Selecting previously unselected package libpango1.0-dev.
Preparing to unpack .../libpango1.0-dev_1.38.1-1_armhf.deb ...
Unpacking libpango1.0-dev (1.38.1-1) ...
Selecting previously unselected package libpaper-utils.
Preparing to unpack .../libpaper-utils_1.1.24+nmu4_armhf.deb ...
Unpacking libpaper-utils (1.1.24+nmu4) ...
Selecting previously unselected package libopenjpeg5:armhf.
Preparing to unpack .../libopenjpeg5_1%3a1.5.2-3.1+b4_armhf.deb ...
Unpacking libopenjpeg5:armhf (1:1.5.2-3.1+b4) ...
Selecting previously unselected package libpoppler57:armhf.
Preparing to unpack .../libpoppler57_0.38.0-2_armhf.deb ...
Unpacking libpoppler57:armhf (0.38.0-2) ...
Selecting previously unselected package libpotrace0.
Preparing to unpack .../libpotrace0_1.13-2_armhf.deb ...
Unpacking libpotrace0 (1.13-2) ...
Selecting previously unselected package libptexenc1:armhf.
Preparing to unpack .../libptexenc1_2015.20160222.37495-1_armhf.deb ...
Unpacking libptexenc1:armhf (2015.20160222.37495-1) ...
Selecting previously unselected package libsqlite3-dev:armhf.
Preparing to unpack .../libsqlite3-dev_3.11.1-1_armhf.deb ...
Unpacking libsqlite3-dev:armhf (3.11.1-1) ...
Selecting previously unselected package libsynctex1:armhf.
Preparing to unpack .../libsynctex1_2015.20160222.37495-1_armhf.deb ...
Unpacking libsynctex1:armhf (2015.20160222.37495-1) ...
Selecting previously unselected package libtexlua52:armhf.
Preparing to unpack .../libtexlua52_2015.20160222.37495-1_armhf.deb ...
Unpacking libtexlua52:armhf (2015.20160222.37495-1) ...
Selecting previously unselected package libtexluajit2:armhf.
Preparing to unpack .../libtexluajit2_2015.20160222.37495-1_armhf.deb ...
Unpacking libtexluajit2:armhf (2015.20160222.37495-1) ...
Selecting previously unselected package libtre-dev.
Preparing to unpack .../libtre-dev_0.8.0-4_armhf.deb ...
Unpacking libtre-dev (0.8.0-4) ...
Selecting previously unselected package libxt6:armhf.
Preparing to unpack .../libxt6_1%3a1.1.5-1_armhf.deb ...
Unpacking libxt6:armhf (1:1.1.5-1) ...
Selecting previously unselected package libxmu6:armhf.
Preparing to unpack .../libxmu6_2%3a1.1.2-2_armhf.deb ...
Unpacking libxmu6:armhf (2:1.1.2-2) ...
Selecting previously unselected package libxpm4:armhf.
Preparing to unpack .../libxpm4_1%3a3.5.11-1+b1_armhf.deb ...
Unpacking libxpm4:armhf (1:3.5.11-1+b1) ...
Selecting previously unselected package libxaw7:armhf.
Preparing to unpack .../libxaw7_2%3a1.0.13-1_armhf.deb ...
Unpacking libxaw7:armhf (2:1.0.13-1) ...
Selecting previously unselected package libxi6:armhf.
Preparing to unpack .../libxi6_2%3a1.7.6-1_armhf.deb ...
Unpacking libxi6:armhf (2:1.7.6-1) ...
Selecting previously unselected package libxml2-utils.
Preparing to unpack .../libxml2-utils_2.9.3+dfsg1-1_armhf.deb ...
Unpacking libxml2-utils (2.9.3+dfsg1-1) ...
Selecting previously unselected package libxslt1.1:armhf.
Preparing to unpack .../libxslt1.1_1.1.28-2.1_armhf.deb ...
Unpacking libxslt1.1:armhf (1.1.28-2.1) ...
Selecting previously unselected package lua-filesystem:armhf.
Preparing to unpack .../lua-filesystem_1.6.3-1_armhf.deb ...
Unpacking lua-filesystem:armhf (1.6.3-1) ...
Selecting previously unselected package lua-filesystem-dev:armhf.
Preparing to unpack .../lua-filesystem-dev_1.6.3-1_armhf.deb ...
Unpacking lua-filesystem-dev:armhf (1.6.3-1) ...
Selecting previously unselected package lua-lpeg:armhf.
Preparing to unpack .../lua-lpeg_0.12.2-1_armhf.deb ...
Unpacking lua-lpeg:armhf (0.12.2-1) ...
Selecting previously unselected package lua-lpeg-dev:armhf.
Preparing to unpack .../lua-lpeg-dev_0.12.2-1_armhf.deb ...
Unpacking lua-lpeg-dev:armhf (0.12.2-1) ...
Selecting previously unselected package tex-common.
Preparing to unpack .../tex-common_6.04_all.deb ...
Unpacking tex-common (6.04) ...
Selecting previously unselected package preview-latex-style.
Preparing to unpack .../preview-latex-style_11.87-3+deb8u1_all.deb ...
Unpacking preview-latex-style (11.87-3+deb8u1) ...
Selecting previously unselected package rubygems-integration.
Preparing to unpack .../rubygems-integration_1.10_all.deb ...
Unpacking rubygems-integration (1.10) ...
Selecting previously unselected package ruby-did-you-mean.
Preparing to unpack .../ruby-did-you-mean_1.0.0-2_all.deb ...
Unpacking ruby-did-you-mean (1.0.0-2) ...
Selecting previously unselected package ruby-minitest.
Preparing to unpack .../ruby-minitest_5.8.4-2_all.deb ...
Unpacking ruby-minitest (5.8.4-2) ...
Selecting previously unselected package ruby-net-telnet.
Preparing to unpack .../ruby-net-telnet_0.1.1-2_all.deb ...
Unpacking ruby-net-telnet (0.1.1-2) ...
Selecting previously unselected package ruby-power-assert.
Preparing to unpack .../ruby-power-assert_0.2.7-1_all.deb ...
Unpacking ruby-power-assert (0.2.7-1) ...
Selecting previously unselected package ruby-test-unit.
Preparing to unpack .../ruby-test-unit_3.1.7-2_all.deb ...
Unpacking ruby-test-unit (3.1.7-2) ...
Selecting previously unselected package libruby2.3:armhf.
Preparing to unpack .../libruby2.3_2.3.0-4_armhf.deb ...
Unpacking libruby2.3:armhf (2.3.0-4) ...
Selecting previously unselected package ruby2.3.
Preparing to unpack .../ruby2.3_2.3.0-4_armhf.deb ...
Unpacking ruby2.3 (2.3.0-4) ...
Selecting previously unselected package ruby.
Preparing to unpack .../ruby_1%3a2.3.0+1_all.deb ...
Unpacking ruby (1:2.3.0+1) ...
Selecting previously unselected package rake.
Preparing to unpack .../archives/rake_10.5.0-2_all.deb ...
Unpacking rake (10.5.0-2) ...
Selecting previously unselected package t1utils.
Preparing to unpack .../t1utils_1.39-2_armhf.deb ...
Unpacking t1utils (1.39-2) ...
Selecting previously unselected package texlive-binaries.
Preparing to unpack .../texlive-binaries_2015.20160222.37495-1_armhf.deb ...
Unpacking texlive-binaries (2015.20160222.37495-1) ...
Selecting previously unselected package xdg-utils.
Preparing to unpack .../xdg-utils_1.1.1-1_all.deb ...
Unpacking xdg-utils (1.1.1-1) ...
Selecting previously unselected package texlive-base.
Preparing to unpack .../texlive-base_2015.20160223-1_all.deb ...
Unpacking texlive-base (2015.20160223-1) ...
Selecting previously unselected package ttf-adf-accanthis.
Preparing to unpack .../ttf-adf-accanthis_0.20090423-2_all.deb ...
Unpacking ttf-adf-accanthis (0.20090423-2) ...
Selecting previously unselected package fonts-stix.
Preparing to unpack .../fonts-stix_1.1.1-4_all.deb ...
Unpacking fonts-stix (1.1.1-4) ...
Selecting previously unselected package ttf-adf-universalis.
Preparing to unpack .../ttf-adf-universalis_0.20090423-2_all.deb ...
Unpacking ttf-adf-universalis (0.20090423-2) ...
Selecting previously unselected package ttf-adf-gillius.
Preparing to unpack .../ttf-adf-gillius_0.20090423-2_all.deb ...
Unpacking ttf-adf-gillius (0.20090423-2) ...
Selecting previously unselected package texlive-fonts-extra.
Preparing to unpack .../texlive-fonts-extra_2015.20160223-2_all.deb ...
Unpacking texlive-fonts-extra (2015.20160223-2) ...
Selecting previously unselected package texlive-fonts-recommended.
Preparing to unpack .../texlive-fonts-recommended_2015.20160223-1_all.deb ...
Unpacking texlive-fonts-recommended (2015.20160223-1) ...
Selecting previously unselected package texlive-latex-base.
Preparing to unpack .../texlive-latex-base_2015.20160223-1_all.deb ...
Unpacking texlive-latex-base (2015.20160223-1) ...
Selecting previously unselected package texlive-latex-recommended.
Preparing to unpack .../texlive-latex-recommended_2015.20160223-1_all.deb ...
Unpacking texlive-latex-recommended (2015.20160223-1) ...
Selecting previously unselected package texlive-pictures.
Preparing to unpack .../texlive-pictures_2015.20160223-1_all.deb ...
Unpacking texlive-pictures (2015.20160223-1) ...
Selecting previously unselected package texlive-latex-extra.
Preparing to unpack .../texlive-latex-extra_2015.20160223-2_all.deb ...
Unpacking texlive-latex-extra (2015.20160223-2) ...
Selecting previously unselected package xsltproc.
Preparing to unpack .../xsltproc_1.1.28-2.1_armhf.deb ...
Unpacking xsltproc (1.1.28-2.1) ...
Selecting previously unselected package sbuild-build-depends-genometools-dummy.
Preparing to unpack .../sbuild-build-depends-genometools-dummy.deb ...
Unpacking sbuild-build-depends-genometools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.21-7) ...
Processing triggers for systemd (228-6) ...
Setting up groff-base (1.22.3-7) ...
Setting up bsdmainutils (9.0.6) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up mime-support (3.59) ...
Setting up libffi6:armhf (3.2.1-4) ...
Setting up libsqlite3-0:armhf (3.11.1-1) ...
Setting up libpython2.7-stdlib:armhf (2.7.11-4) ...
Setting up python2.7 (2.7.11-4) ...
Setting up libpython-stdlib:armhf (2.7.11-1) ...
Setting up python (2.7.11-1) ...
Setting up libpng12-0:armhf (1.2.54-4) ...
Setting up libfreetype6:armhf (2.6.3-3) ...
Setting up ucf (3.0035) ...
Setting up fonts-dejavu-core (2.35-1) ...
Setting up fontconfig-config (2.11.0-6.3) ...
Setting up libfontconfig1:armhf (2.11.0-6.3) ...
Setting up fontconfig (2.11.0-6.3) ...
Regenerating fonts cache... done.
Setting up fonts-lato (2.0-1) ...
Setting up imagemagick-common (8:6.8.9.9-7) ...
Setting up libfftw3-double3:armhf (3.3.4-2+rpi1+b1) ...
Setting up libjbig0:armhf (2.1-3.1) ...
Setting up liblcms2-2:armhf (2.6-3) ...
Setting up libglib2.0-0:armhf (2.46.2-3) ...
No schema files found: doing nothing.
Setting up liblqr-1-0:armhf (0.4.2-2) ...
Setting up liblzo2-2:armhf (2.08-1.2) ...
Setting up libjpeg62-turbo:armhf (1:1.4.2-2) ...
Setting up libltdl7:armhf (2.4.6-0.1) ...
Setting up libtiff5:armhf (4.0.6-1) ...
Setting up libxau6:armhf (1:1.0.8-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-1.1) ...
Setting up libxcb1:armhf (1.11.1-1) ...
Setting up libx11-data (2:1.6.3-1) ...
Setting up libx11-6:armhf (2:1.6.3-1) ...
Setting up libxext6:armhf (2:1.3.3-1) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1) ...
Setting up libmagickcore-6.q16-2:armhf (8:6.8.9.9-7+b1) ...
Setting up libmagickwand-6.q16-2:armhf (8:6.8.9.9-7+b1) ...
Setting up libmpdec2:armhf (2.4.1-1) ...
Setting up libpaper1:armhf (1.1.24+nmu4) ...

Creating config file /etc/papersize with new version
Setting up libpcrecpp0v5:armhf (2:8.38-3) ...
Setting up libtre5:armhf (0.8.0-4) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libxrender1:armhf (1:0.9.9-2) ...
Setting up libxft2:armhf (2.3.2-1) ...
Setting up libyaml-0-2:armhf (0.1.6-3) ...
Setting up libzzip-0-13:armhf (0.13.62-3) ...
Setting up lua-md5:armhf (1.2+git+1+8d87fee-1) ...
Setting up lua-md5-dev:armhf (1.2+git+1+8d87fee-1) ...
Setting up poppler-data (0.4.7-7) ...
Setting up libpython3.5-stdlib:armhf (3.5.1-5) ...
Setting up python3.5 (3.5.1-5) ...
Setting up libpython3-stdlib:armhf (3.5.1-2) ...
Setting up sgml-base (1.26+nmu4) ...
Setting up libfaketime:armhf (0.9.6-4) ...
Setting up faketime (0.9.6-4) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
Setting up libnettle6:armhf (3.2-1) ...
Setting up libhogweed4:armhf (3.2-1) ...
Setting up libidn11:armhf (1.32-3) ...
Setting up libp11-kit0:armhf (0.23.2-3) ...
Setting up libtasn1-6:armhf (4.7-3) ...
Setting up libgnutls30:armhf (3.4.9-2) ...
Setting up libkeyutils1:armhf (1.5.9-8) ...
Setting up libkrb5support0:armhf (1.13.2+dfsg-5) ...
Setting up libk5crypto3:armhf (1.13.2+dfsg-5) ...
Setting up libkrb5-3:armhf (1.13.2+dfsg-5) ...
Setting up libgssapi-krb5-2:armhf (1.13.2+dfsg-5) ...
Setting up libsasl2-modules-db:armhf (2.1.26.dfsg1-14+b1) ...
Setting up libsasl2-2:armhf (2.1.26.dfsg1-14+b1) ...
Setting up libldap-2.4-2:armhf (2.4.42+dfsg-2+rpi1+b2) ...
Setting up asciidoc (8.6.9-3) ...
Setting up autotools-dev (20150820.1) ...
Setting up openssl (1.0.2g-1) ...
Setting up ca-certificates (20160104) ...
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.19) ...
Setting up libarchive-zip-perl (1.56-2) ...
Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up xml-core (0.13+nmu2) ...
Setting up fonts-cabin (1.5-2) ...
Setting up fonts-comfortaa (2.003-1) ...
Setting up fonts-crosextra-caladea (20130214-1) ...
Setting up fonts-crosextra-carlito (20130920-1) ...
Setting up fonts-dejavu-extra (2.35-1) ...
Setting up fonts-ebgaramond (0.015+git20130628-3) ...
Setting up fonts-ebgaramond-extra (0.015+git20130628-3) ...
Setting up fonts-font-awesome (4.5.0~dfsg-1) ...
Setting up fonts-freefont-otf (20120503-4) ...
Setting up fonts-freefont-ttf (20120503-4) ...
Setting up fonts-gfs-artemisia (1.1-5) ...
Setting up fonts-gfs-complutum (1.1-6) ...
Setting up fonts-gfs-didot (1.1-6) ...
Setting up fonts-gfs-neohellenic (1.1-6) ...
Setting up fonts-gfs-olga (1.1-5) ...
Setting up fonts-gfs-solomos (1.1-5) ...
Setting up fonts-junicode (0.7.8-2) ...
Setting up fonts-linuxlibertine (5.3.0-2) ...
Setting up fonts-lobster (2.0-2) ...
Setting up fonts-lobstertwo (2.0-2) ...
Setting up fonts-oflb-asana-math (000.907-6) ...
Setting up fonts-roboto-hinted (2:0~20160106-1) ...
Setting up fonts-sil-gentium (20081126:1.03-1) ...
Setting up fonts-sil-gentium-basic (1.1-7) ...
Setting up fonts-sil-gentiumplus (5.000-1) ...
Setting up libgirepository-1.0-1:armhf (1.46.0-4) ...
Setting up gir1.2-glib-2.0:armhf (1.46.0-4) ...
Setting up libpixman-1-0:armhf (0.33.6-1) ...
Setting up libxcb-render0:armhf (1.11.1-1) ...
Setting up libxcb-shm0:armhf (1.11.1-1) ...
Setting up libcairo2:armhf (1.14.6-1) ...
Setting up libcairo-gobject2:armhf (1.14.6-1) ...
Setting up gir1.2-freedesktop:armhf (1.46.0-4) ...
Setting up libthai-data (0.1.24-2) ...
Setting up libdatrie1:armhf (0.2.10-2) ...
Setting up libthai0:armhf (0.1.24-2) ...
Setting up libpango-1.0-0:armhf (1.38.1-1) ...
Setting up libgraphite2-3:armhf (1.3.6-1) ...
Setting up libharfbuzz0b:armhf (1.0.1-1+b1) ...
Setting up libpangoft2-1.0-0:armhf (1.38.1-1) ...
Setting up libpangocairo-1.0-0:armhf (1.38.1-1) ...
Setting up libpangoxft-1.0-0:armhf (1.38.1-1) ...
Setting up gir1.2-pango-1.0:armhf (1.38.1-1) ...
Setting up hicolor-icon-theme (0.13-1) ...
Setting up imagemagick-6.q16 (8:6.8.9.9-7+b1) ...
Setting up imagemagick (8:6.8.9.9-7+b1) ...
update-alternatives: using /usr/bin/compare-im6 to provide /usr/bin/compare (compare) in auto mode
update-alternatives: using /usr/bin/animate-im6 to provide /usr/bin/animate (animate) in auto mode
update-alternatives: using /usr/bin/convert-im6 to provide /usr/bin/convert (convert) in auto mode
update-alternatives: using /usr/bin/composite-im6 to provide /usr/bin/composite (composite) in auto mode
update-alternatives: using /usr/bin/conjure-im6 to provide /usr/bin/conjure (conjure) in auto mode
update-alternatives: using /usr/bin/import-im6 to provide /usr/bin/import (import) in auto mode
update-alternatives: using /usr/bin/identify-im6 to provide /usr/bin/identify (identify) in auto mode
update-alternatives: using /usr/bin/stream-im6 to provide /usr/bin/stream (stream) in auto mode
update-alternatives: using /usr/bin/display-im6 to provide /usr/bin/display (display) in auto mode
update-alternatives: using /usr/bin/montage-im6 to provide /usr/bin/montage (montage) in auto mode
update-alternatives: using /usr/bin/mogrify-im6 to provide /usr/bin/mogrify (mogrify) in auto mode
Setting up libavahi-common-data:armhf (0.6.32~rc+dfsg-1) ...
Setting up libavahi-common3:armhf (0.6.32~rc+dfsg-1) ...
Setting up libavahi-client3:armhf (0.6.32~rc+dfsg-1) ...
Setting up libbam-dev (0.1.19-2) ...
Setting up libbz2-dev:armhf (1.0.6-8) ...
Setting up libcairo-script-interpreter2:armhf (1.14.6-1) ...
Setting up libexpat1-dev:armhf (2.1.0-7) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up libpng12-dev:armhf (1.2.54-4) ...
Setting up libfreetype6-dev (2.6.3-3) ...
Setting up pkg-config (0.29-3) ...
Setting up libfontconfig1-dev:armhf (2.11.0-6.3) ...
Setting up xorg-sgml-doctools (1:1.11-1) ...
Setting up x11proto-core-dev (7.0.28-2) ...
Setting up libxau-dev:armhf (1:1.0.8-1) ...
Setting up libxdmcp-dev:armhf (1:1.1.2-1.1) ...
Setting up x11proto-input-dev (2.3.1-1) ...
Setting up x11proto-kb-dev (1.0.7-1) ...
Setting up xtrans-dev (1.3.5-1) ...
Setting up libpthread-stubs0-dev:armhf (0.3-4) ...
Setting up libxcb1-dev:armhf (1.11.1-1) ...
Setting up libx11-dev:armhf (2:1.6.3-1) ...
Setting up x11proto-render-dev (2:0.11.1-2) ...
Setting up libxrender-dev:armhf (1:0.9.9-2) ...
Setting up x11proto-xext-dev (7.3.0-1) ...
Setting up libxext-dev:armhf (2:1.3.3-1) ...
Setting up x11-common (1:7.7+14) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
Running in chroot, ignoring request.
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libice6:armhf (2:1.0.9-1+b1) ...
Setting up libsm6:armhf (2:1.2.2-1+b1) ...
Setting up libice-dev:armhf (2:1.0.9-1+b1) ...
Setting up libsm-dev:armhf (2:1.2.2-1+b1) ...
Setting up libpixman-1-dev (0.33.6-1) ...
Setting up libxcb-render0-dev:armhf (1.11.1-1) ...
Setting up libxcb-shm0-dev:armhf (1.11.1-1) ...
Setting up libelf1:armhf (0.163-5.1) ...
Setting up libglib2.0-data (2.46.2-3) ...
Setting up libglib2.0-bin (2.46.2-3) ...
Setting up libpcre16-3:armhf (2:8.38-3) ...
Setting up libpcre32-3:armhf (2:8.38-3) ...
Setting up libpcre3-dev:armhf (2:8.38-3) ...
Setting up libglib2.0-dev (2.46.2-3) ...
Setting up libcairo2-dev (1.14.6-1) ...
Setting up libcups2:armhf (2.1.3-3) ...
Setting up libijs-0.35:armhf (0.35-12) ...
Setting up libjbig2dec0 (0.12+20150918-1) ...
Setting up libopenjp2-7:armhf (2.1.0-2.1) ...
Setting up libgs9-common (9.18~dfsg-4) ...
Setting up libharfbuzz-icu0:armhf (1.0.1-1+b1) ...
Setting up libharfbuzz-gobject0:armhf (1.0.1-1+b1) ...
Setting up libharfbuzz-dev (1.0.1-1+b1) ...
Setting up libkpathsea6:armhf (2015.20160222.37495-1) ...
Setting up liblua5.1-0:armhf (5.1.5-8) ...
Setting up libtinfo-dev:armhf (6.0+20160213-1) ...
Setting up libreadline6-dev:armhf (6.3-8+b3) ...
Setting up libreadline-dev:armhf (6.3-8+b3) ...
Setting up liblua5.1-0-dev:armhf (5.1.5-8) ...
Setting up libxft-dev (2.3.2-1) ...
Setting up libpango1.0-dev (1.38.1-1) ...
Setting up libpaper-utils (1.1.24+nmu4) ...
Setting up libopenjpeg5:armhf (1:1.5.2-3.1+b4) ...
Setting up libpoppler57:armhf (0.38.0-2) ...
Setting up libpotrace0 (1.13-2) ...
Setting up libptexenc1:armhf (2015.20160222.37495-1) ...
Setting up libsqlite3-dev:armhf (3.11.1-1) ...
Setting up libsynctex1:armhf (2015.20160222.37495-1) ...
Setting up libtexlua52:armhf (2015.20160222.37495-1) ...
Setting up libtexluajit2:armhf (2015.20160222.37495-1) ...
Setting up libtre-dev (0.8.0-4) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up libxmu6:armhf (2:1.1.2-2) ...
Setting up libxpm4:armhf (1:3.5.11-1+b1) ...
Setting up libxaw7:armhf (2:1.0.13-1) ...
Setting up libxi6:armhf (2:1.7.6-1) ...
Setting up libxml2-utils (2.9.3+dfsg1-1) ...
Setting up libxslt1.1:armhf (1.1.28-2.1) ...
Setting up lua-filesystem:armhf (1.6.3-1) ...
Setting up lua-filesystem-dev:armhf (1.6.3-1) ...
Setting up lua-lpeg:armhf (0.12.2-1) ...
Setting up lua-lpeg-dev:armhf (0.12.2-1) ...
Setting up tex-common (6.04) ...
update-language: texlive-base not installed and configured, doing nothing!
Setting up preview-latex-style (11.87-3+deb8u1) ...
update-language: texlive-base not installed and configured, doing nothing!
Regenerating '/var/lib/texmf/fmtutil.cnf-DEBIAN'... done.
Regenerating '/var/lib/texmf/fmtutil.cnf-TEXLIVEDIST'... done.
update-fmtutil has updated the following file(s):
	/var/lib/texmf/fmtutil.cnf-DEBIAN
	/var/lib/texmf/fmtutil.cnf-TEXLIVEDIST
If you want to activate the changes in the above file(s),
you should run fmtutil-sys or fmtutil.
Setting up rubygems-integration (1.10) ...
Setting up ruby-did-you-mean (1.0.0-2) ...
Setting up ruby-minitest (5.8.4-2) ...
Setting up ruby-net-telnet (0.1.1-2) ...
Setting up ruby-power-assert (0.2.7-1) ...
Setting up ruby-test-unit (3.1.7-2) ...
Setting up t1utils (1.39-2) ...
Setting up xdg-utils (1.1.1-1) ...
Setting up ttf-adf-accanthis (0.20090423-2) ...
Setting up fonts-stix (1.1.1-4) ...
Setting up ttf-adf-universalis (0.20090423-2) ...
Setting up ttf-adf-gillius (0.20090423-2) ...
Setting up xsltproc (1.1.28-2.1) ...
Processing triggers for sgml-base (1.26+nmu4) ...
Setting up docbook-xsl (1.79.1+dfsg-1) ...
Setting up rake (10.5.0-2) ...
Setting up libruby2.3:armhf (2.3.0-4) ...
Setting up ruby2.3 (2.3.0-4) ...
Setting up dh-python (2.20151103) ...
Setting up python3 (3.5.1-2) ...
Setting up dh-strip-nondeterminism (0.016-1) ...
Setting up debhelper (9.20160306) ...
Setting up libcupsimage2:armhf (2.1.3-3) ...
Setting up libcupsfilters1:armhf (1.8.2-3) ...
Setting up libgs9 (9.18~dfsg-4) ...
Setting up ruby (1:2.3.0+1) ...
Setting up texlive-binaries (2015.20160222.37495-1) ...
update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
Processing triggers for tex-common (6.04) ...
update-language: texlive-base not installed and configured, doing nothing!
texlive-base is not ready, skipping fmtutil-sys --all call
Setting up texlive-base (2015.20160223-1) ...
/usr/bin/tl-paper: setting paper size for dvips to a4.
/usr/bin/tl-paper: setting paper size for dvipdfmx to a4.
/usr/bin/tl-paper: setting paper size for xdvi to a4.
/usr/bin/tl-paper: setting paper size for pdftex to a4.
Processing triggers for tex-common (6.04) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Building format(s) --all.
	This may take some time... done.
Setting up texlive-fonts-recommended (2015.20160223-1) ...
Setting up texlive-latex-base (2015.20160223-1) ...
Setting up texlive-fonts-extra (2015.20160223-2) ...
Processing triggers for tex-common (6.04) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Building format(s) --all.
	This may take some time... done.
Setting up texlive-latex-recommended (2015.20160223-1) ...
Setting up texlive-pictures (2015.20160223-1) ...
Processing triggers for tex-common (6.04) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Setting up texlive-latex-extra (2015.20160223-2) ...
Processing triggers for tex-common (6.04) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Setting up sbuild-build-depends-genometools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.21-7) ...
Processing triggers for ca-certificates (20160104) ...
Updating certificates in /etc/ssl/certs...
173 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for systemd (228-6) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.3.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-3 dpkg-dev_1.18.4 g++-5_5.3.1-8+rpi1 gcc-5_5.3.1-8+rpi1 libc6-dev_2.21-7 libstdc++-5-dev_5.3.1-8+rpi1 libstdc++6_5.3.1-8+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.113+nmu3 apt_1.2.3 asciidoc_8.6.9-3 autotools-dev_20150820.1 base-files_9.5+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.26-3 bsdmainutils_9.0.6 bsdutils_1:2.27.1-3 build-essential_11.7 bzip2_1.0.6-8 ca-certificates_20160104 coreutils_8.24-1 cpio_2.11+dfsg-4.1 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-8+rpi1 dash_0.5.8-2.1 debconf_1.5.58 debfoster_2.7-2 debhelper_9.20160306 debianutils_4.7 dh-python_2.20151103 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.115-2 docbook-xsl_1.79.1+dfsg-1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 faketime_0.9.6-4 file_1:5.25-2 findutils_4.6.0+git+20160126-2 fontconfig_2.11.0-6.3 fontconfig-config_2.11.0-6.3 fonts-cabin_1.5-2 fonts-comfortaa_2.003-1 fonts-crosextra-caladea_20130214-1 fonts-crosextra-carlito_20130920-1 fonts-dejavu-core_2.35-1 fonts-dejavu-extra_2.35-1 fonts-ebgaramond_0.015+git20130628-3 fonts-ebgaramond-extra_0.015+git20130628-3 fonts-font-awesome_4.5.0~dfsg-1 fonts-freefont-otf_20120503-4 fonts-freefont-ttf_20120503-4 fonts-gfs-artemisia_1.1-5 fonts-gfs-complutum_1.1-6 fonts-gfs-didot_1.1-6 fonts-gfs-neohellenic_1.1-6 fonts-gfs-olga_1.1-5 fonts-gfs-solomos_1.1-5 fonts-junicode_0.7.8-2 fonts-lato_2.0-1 fonts-linuxlibertine_5.3.0-2 fonts-lobster_2.0-2 fonts-lobstertwo_2.0-2 fonts-oflb-asana-math_000.907-6 fonts-roboto-hinted_2:0~20160106-1 fonts-sil-gentium_20081126:1.03-1 fonts-sil-gentium-basic_1.1-7 fonts-sil-gentiumplus_5.000-1 fonts-stix_1.1.1-4 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-8+rpi1 gcc_4:5.3.1-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-10 gcc-5_5.3.1-8+rpi1 gcc-5-base_5.3.1-8+rpi1 gettext_0.19.7-2 gettext-base_0.19.7-2 gir1.2-freedesktop_1.46.0-4 gir1.2-glib-2.0_1.46.0-4 gir1.2-pango-1.0_1.38.1-1 gnupg_1.4.20-1 gpgv_1.4.20-1 grep_2.22-1 groff-base_1.22.3-7 gzip_1.6-4 hicolor-icon-theme_0.13-1 hostname_3.16 imagemagick_8:6.8.9.9-7+b1 imagemagick-6.q16_8:6.8.9.9-7+b1 imagemagick-common_8:6.8.9.9-7 init_1.24 init-system-helpers_1.24 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5.2 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-7+rpi1 kmod_22-1 libacl1_2.2.52-3 libapparmor1_2.10-3 libapt-pkg5.0_1.2.3 libarchive-zip-perl_1.56-2 libasan2_5.3.1-8+rpi1 libatomic1_5.3.1-8+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libavahi-client3_0.6.32~rc+dfsg-1 libavahi-common-data_0.6.32~rc+dfsg-1 libavahi-common3_0.6.32~rc+dfsg-1 libbam-dev_0.1.19-2 libblkid1_2.27.1-3 libbz2-1.0_1.0.6-8 libbz2-dev_1.0.6-8 libc-bin_2.21-7 libc-dev-bin_2.21-7 libc6_2.21-7 libc6-dev_2.21-7 libcairo-gobject2_1.14.6-1 libcairo-script-interpreter2_1.14.6-1 libcairo2_1.14.6-1 libcairo2-dev_1.14.6-1 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-8+rpi1 libcomerr2_1.42.13-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libcups2_2.1.3-3 libcupsfilters1_1.8.2-3 libcupsimage2_2.1.3-3 libdatrie1_0.2.10-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1 libdebconfclient0_0.204 libdevmapper1.02.1_2:1.02.115-2 libdpkg-perl_1.18.4 libdrm2_2.4.66-2 libelf1_0.163-5.1 libexpat1_2.1.0-7 libexpat1-dev_2.1.0-7 libfakeroot_1.20.2-1 libfaketime_0.9.6-4 libfdisk1_2.27.1-3 libffi6_3.2.1-4 libfftw3-double3_3.3.4-2+rpi1+b1 libfile-stripnondeterminism-perl_0.016-1 libfontconfig1_2.11.0-6.3 libfontconfig1-dev_2.11.0-6.3 libfreetype6_2.6.3-3 libfreetype6-dev_2.6.3-3 libgc1c2_1:7.4.2-7.3 libgcc-5-dev_5.3.1-8+rpi1 libgcc1_1:5.3.1-8+rpi1 libgcrypt20_1.6.4-5 libgdbm3_1.8.3-13.1 libgirepository-1.0-1_1.46.0-4 libglib2.0-0_2.46.2-3 libglib2.0-bin_2.46.2-3 libglib2.0-data_2.46.2-3 libglib2.0-dev_2.46.2-3 libgmp10_2:6.1.0+dfsg-2 libgnutls30_3.4.9-2 libgomp1_5.3.1-8+rpi1 libgpg-error0_1.21-1 libgraphite2-3_1.3.6-1 libgs9_9.18~dfsg-4 libgs9-common_9.18~dfsg-4 libgssapi-krb5-2_1.13.2+dfsg-5 libharfbuzz-dev_1.0.1-1+b1 libharfbuzz-gobject0_1.0.1-1+b1 libharfbuzz-icu0_1.0.1-1+b1 libharfbuzz0b_1.0.1-1+b1 libhogweed4_3.2-1 libice-dev_2:1.0.9-1+b1 libice6_2:1.0.9-1+b1 libicu55_55.1-7 libidn11_1.32-3 libijs-0.35_0.35-12 libisl15_0.16.1-1 libjbig0_2.1-3.1 libjbig2dec0_0.12+20150918-1 libjpeg62-turbo_1:1.4.2-2 libk5crypto3_1.13.2+dfsg-5 libkeyutils1_1.5.9-8 libklibc_2.0.4-7+rpi1 libkmod2_22-1 libkpathsea6_2015.20160222.37495-1 libkrb5-3_1.13.2+dfsg-5 libkrb5support0_1.13.2+dfsg-5 liblcms2-2_2.6-3 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b2 liblqr-1-0_0.4.2-2 libltdl7_2.4.6-0.1 liblua5.1-0_5.1.5-8 liblua5.1-0-dev_5.1.5-8 liblz4-1_0.0~r131-1 liblzma5_5.1.1alpha+20120614-2.1 liblzo2-2_2.08-1.2 libmagic1_1:5.25-2 libmagickcore-6.q16-2_8:6.8.9.9-7+b1 libmagickwand-6.q16-2_8:6.8.9.9-7+b1 libmount1_2.27.1-3 libmpc3_1.0.3-1 libmpdec2_2.4.1-1 libmpfr4_3.1.3-2 libncurses5_6.0+20160213-1 libncursesw5_6.0+20160213-1 libnettle6_3.2-1 libopenjp2-7_2.1.0-2.1 libopenjpeg5_1:1.5.2-3.1+b4 libp11-kit0_0.23.2-3 libpam-modules_1.1.8-3.2 libpam-modules-bin_1.1.8-3.2 libpam-runtime_1.1.8-3.2 libpam0g_1.1.8-3.2 libpango-1.0-0_1.38.1-1 libpango1.0-dev_1.38.1-1 libpangocairo-1.0-0_1.38.1-1 libpangoft2-1.0-0_1.38.1-1 libpangoxft-1.0-0_1.38.1-1 libpaper-utils_1.1.24+nmu4 libpaper1_1.1.24+nmu4 libpcre16-3_2:8.38-3 libpcre3_2:8.38-3 libpcre3-dev_2:8.38-3 libpcre32-3_2:8.38-3 libpcrecpp0v5_2:8.38-3 libperl5.22_5.22.1-5 libpipeline1_1.4.1-2 libpixman-1-0_0.33.6-1 libpixman-1-dev_0.33.6-1 libplymouth4_0.9.2-3 libpng12-0_1.2.54-4 libpng12-dev_1.2.54-4 libpoppler57_0.38.0-2 libpotrace0_1.13-2 libprocps5_2:3.3.11-3 libptexenc1_2015.20160222.37495-1 libpthread-stubs0-dev_0.3-4 libpython-stdlib_2.7.11-1 libpython2.7-minimal_2.7.11-4 libpython2.7-stdlib_2.7.11-4 libpython3-stdlib_3.5.1-2 libpython3.5-minimal_3.5.1-5 libpython3.5-stdlib_3.5.1-5 libreadline-dev_6.3-8+b3 libreadline6_6.3-8+b3 libreadline6-dev_6.3-8+b3 libruby2.3_2.3.0-4 libsasl2-2_2.1.26.dfsg1-14+b1 libsasl2-modules-db_2.1.26.dfsg1-14+b1 libseccomp2_2.2.3-2 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsm-dev_2:1.2.2-1+b1 libsm6_2:1.2.2-1+b1 libsmartcols1_2.27.1-3 libsqlite3-0_3.11.1-1 libsqlite3-dev_3.11.1-1 libss2_1.42.13-1 libssl1.0.2_1.0.2g-1 libstdc++-5-dev_5.3.1-8+rpi1 libstdc++6_5.3.1-8+rpi1 libsynctex1_2015.20160222.37495-1 libsystemd0_228-6 libtasn1-6_4.7-3 libtexlua52_2015.20160222.37495-1 libtexluajit2_2015.20160222.37495-1 libtext-charwidth-perl_0.04-7+b6 libtext-iconv-perl_1.7-5+b7 libtext-wrapi18n-perl_0.06-7.1 libthai-data_0.1.24-2 libthai0_0.1.24-2 libtiff5_4.0.6-1 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20160213-1 libtinfo5_6.0+20160213-1 libtre-dev_0.8.0-4 libtre5_0.8.0-4 libubsan0_5.3.1-8+rpi1 libudev1_228-6 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-3 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libx11-dev_2:1.6.3-1 libxau-dev_1:1.0.8-1 libxau6_1:1.0.8-1 libxaw7_2:1.0.13-1 libxcb-render0_1.11.1-1 libxcb-render0-dev_1.11.1-1 libxcb-shm0_1.11.1-1 libxcb-shm0-dev_1.11.1-1 libxcb1_1.11.1-1 libxcb1-dev_1.11.1-1 libxdmcp-dev_1:1.1.2-1.1 libxdmcp6_1:1.1.2-1.1 libxext-dev_2:1.3.3-1 libxext6_2:1.3.3-1 libxft-dev_2.3.2-1 libxft2_2.3.2-1 libxi6_2:1.7.6-1 libxml2_2.9.3+dfsg1-1 libxml2-utils_2.9.3+dfsg1-1 libxmu6_2:1.1.2-2 libxpm4_1:3.5.11-1+b1 libxrender-dev_1:0.9.9-2 libxrender1_1:0.9.9-2 libxslt1.1_1.1.28-2.1 libxt6_1:1.1.5-1 libyaml-0-2_0.1.6-3 libzzip-0-13_0.13.62-3 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160110+rpi1 lua-filesystem_1.6.3-1 lua-filesystem-dev_1.6.3-1 lua-lpeg_0.12.2-1 lua-lpeg-dev_0.12.2-1 lua-md5_1.2+git+1+8d87fee-1 lua-md5-dev_1.2+git+1+8d87fee-1 make_4.1-5 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.04-1 mawk_1.3.3-17 mime-support_3.59 mount_2.27.1-3 multiarch-support_2.21-7 ncurses-base_6.0+20151024-2 ncurses-bin_6.0+20151024-2 openssl_1.0.2g-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-5 perl-base_5.22.1-5 perl-modules-5.22_5.22.1-7 pkg-config_0.29-3 plymouth_0.9.2-3 po-debconf_1.0.19 poppler-data_0.4.7-7 preview-latex-style_11.87-3+deb8u1 procps_2:3.3.11-3 python_2.7.11-1 python-minimal_2.7.11-1 python2.7_2.7.11-4 python2.7-minimal_2.7.11-4 python3_3.5.1-2 python3-minimal_3.5.1-2 python3.5_3.5.1-5 python3.5-minimal_3.5.1-5 rake_10.5.0-2 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 ruby_1:2.3.0+1 ruby-did-you-mean_1.0.0-2 ruby-minitest_5.8.4-2 ruby-net-telnet_0.1.1-2 ruby-power-assert_0.2.7-1 ruby-test-unit_3.1.7-2 ruby2.3_2.3.0-4 rubygems-integration_1.10 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-genometools-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 sgml-base_1.26+nmu4 startpar_0.59-3 systemd_228-6 systemd-sysv_228-6 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 t1utils_1.39-2 tar_1.28-2.1 tex-common_6.04 texlive-base_2015.20160223-1 texlive-binaries_2015.20160222.37495-1 texlive-fonts-extra_2015.20160223-2 texlive-fonts-recommended_2015.20160223-1 texlive-latex-base_2015.20160223-1 texlive-latex-extra_2015.20160223-2 texlive-latex-recommended_2015.20160223-1 texlive-pictures_2015.20160223-1 ttf-adf-accanthis_0.20090423-2 ttf-adf-gillius_0.20090423-2 ttf-adf-universalis_0.20090423-2 tzdata_2016a-1 ucf_3.0035 udev_228-6 util-linux_2.27.1-3 x11-common_1:7.7+14 x11proto-core-dev_7.0.28-2 x11proto-input-dev_2.3.1-1 x11proto-kb-dev_1.0.7-1 x11proto-render-dev_2:0.11.1-2 x11proto-xext-dev_7.3.0-1 xdg-utils_1.1.1-1 xml-core_0.13+nmu2 xorg-sgml-doctools_1:1.11-1 xsltproc_1.1.28-2.1 xtrans-dev_1.3.5-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Fri Mar 11 18:42:30 2016 UTC using RSA key ID F09F4872
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./genometools_1.5.8+ds-2.dsc
dpkg-source: info: extracting genometools in genometools-1.5.8+ds
dpkg-source: info: unpacking genometools_1.5.8+ds.orig.tar.xz
dpkg-source: info: unpacking genometools_1.5.8+ds-2.debian.tar.xz
dpkg-source: info: applying spelling
dpkg-source: info: applying remove_png_timestamps
dpkg-source: info: applying use-pkgconfig
dpkg-source: info: applying adding_soname
dpkg-source: info: applying libbam-fix
dpkg-source: info: applying remove-gitignores
dpkg-source: info: applying fix-exports
dpkg-source: info: applying split-manuals
dpkg-source: info: applying use-mx32
dpkg-source: info: applying gtdoc-traverse-sorted

Check disc space
----------------

Sufficient free space for build

User Environment
----------------

DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-6ff14986-1a2f-4c72-98c0-a22509cf3ab8
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: source package genometools
dpkg-buildpackage: source version 1.5.8+ds-2
dpkg-buildpackage: source distribution unstable
 dpkg-source --before-build genometools-1.5.8+ds
dpkg-buildpackage: host architecture armhf
 fakeroot debian/rules clean
dh clean --with python2
   dh_testdir
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/genometools-1.5.8+ds'
mkdir obj
/usr/bin/make cleanup
make[2]: Entering directory '/<<BUILDDIR>>/genometools-1.5.8+ds'
rm -rf lib
find obj -name '*.o' -delete
rm -f obj/amalgamation.c
rm -rf testsuite/stest_testsuite testsuite/stest_stest_tests
/usr/bin/make -s -C /<<BUILDDIR>>/genometools-1.5.8+ds/doc/devguide clean
make[3]: Entering directory '/<<BUILDDIR>>/genometools-1.5.8+ds/doc/devguide'
make[3]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.8+ds/doc/devguide'
/usr/bin/make -s -C /<<BUILDDIR>>/genometools-1.5.8+ds/doc/manuals clean
make[3]: Entering directory '/<<BUILDDIR>>/genometools-1.5.8+ds/doc/manuals'
make[3]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.8+ds/doc/manuals'
rm -f doc/manuals/api_reference.tex \
          doc/manuals/gtscript_reference.tex
find doc . -name "*.toc" -delete
rm -f www/genometools.org/htdocs/images/callbacks.png \
          www/genometools.org/htdocs/images/parsed.png    \
          www/genometools.org/htdocs/images/constructed.png \
          doc/manuals/annotationsketch.pdf
rm -f www/genometools.org/htdocs/examples.html
rm -rf doc/manpages
find testdata \( -name '*.esq' -o -name '*.sds' -o -name '*.ssp' \
	 -o -name '*.ois' -o -name '*.al1' \)  \
   -a ! \( -name 'foo.[36][24].*' \) -delete
find obj -name '*.splint' -delete
find obj -name '*.check' -delete
find obj -name '*.sb' -delete
rm -rf bin obj
rm -rf gtpython/build
/usr/bin/make -s -C /<<BUILDDIR>>/genometools-1.5.8+ds/doc/manuals cleanup
make[3]: Entering directory '/<<BUILDDIR>>/genometools-1.5.8+ds/doc/manuals'
make[3]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.8+ds/doc/manuals'
make[2]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.8+ds'
cd doc/manuals; /usr/bin/make cleanup
make[2]: Entering directory '/<<BUILDDIR>>/genometools-1.5.8+ds/doc/manuals'
rm -f *.aux  *.log *.bbl  *.blg *.dvi *.mer *.mct *.mbd comment.cut
rm -f *.out *.toc
rm -f U89959.fna read[12].fna 
rm -f reads.al1 reads.esq reads.lcp reads.llv reads.prj reads.suf
rm -f tallymer-tmp.tex
rm -f tagerator-tmp.tex Q1.gz pck-human.*
rm -f readjoiner.pdf hop.pdf ltrharvest.pdf ltrdigest.pdf uniquesub.pdf matstat.pdf mgth.pdf packedindex.pdf repfind.pdf tallymer.pdf tagerator.pdf genomediff.pdf
make[2]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.8+ds/doc/manuals'
# should be deleted inside doc/manuals/Makefile
rm -f doc/manuals/annotationsketch.out \
      doc/manuals/api_reference.tex    \
      doc/manuals/gtscript_reference.tex
find doc . -name "*.toc" -delete
find testdata \( -name '*.ois' -or -name '*.sds' -or -name '*.esq' -or \
      -name '*.ssp' -or -name '*.des' -or -name "*.md5"  \) -and \( -not \
      -name '*foo.32.*' -not -name '*foo.64.*' \) -delete
rm -f www/genometools.org/htdocs/images/callbacks.png \
      www/genometools.org/htdocs/images/parsed.png    \
      www/genometools.org/htdocs/images/constructed.png \
      doc/manuals/annotationsketch.pdf
rm -f www/genometools.org/htdocs/examples.html \
      www/genometools.org/htdocs/libgenometools.html
rm -rf gtpython/build
rm -rf obj
make[1]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.8+ds'
   dh_clean
 debian/rules build-arch
dh build-arch --with python2
   dh_testdir -a
   dh_update_autotools_config -a
   dh_auto_configure -a
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/genometools-1.5.8+ds'
faketime -f "`TZ=UTC date -d @1457712642 +'%Y-%m-%d %H:%M:%S'`" dh_auto_build -- useshared=yes x32=no 64bit=no errorcheck=no all docs manuals
	make -j1 useshared=yes x32=no 64bit=no errorcheck=no all docs manuals
make[2]: Entering directory '/<<BUILDDIR>>/genometools-1.5.8+ds'
[create obj/gt_config.h]
[compile alphabet.o]
[compile array.o]
[compile array2dim.o]
[compile array2dim_sparse.o]
[compile array3dim.o]
[compile basename.o]
[compile bioseq.o]
[compile bioseq_col.o]
[compile bioseq_iterator.o]
[compile bitbuffer.o]
[compile bitpackstringop.o]
[compile bitpackstringop16.o]
[compile bitpackstringop32.o]
[compile bitpackstringop64.o]
[compile bitpackstringop8.o]
[compile bittab.o]
[compile bool_matrix.o]
[compile bsearch.o]
[compile byte_popcount.o]
[compile byte_select.o]
[compile checkbitpackarray.o]
[compile checkbitpackstring-int.o]
[compile checkbitpackstring.o]
[compile checkbitpackstring16.o]
[compile checkbitpackstring32.o]
[compile checkbitpackstring64.o]
[compile checkbitpackstring8.o]
[compile class_alloc.o]
[compile class_alloc_lock.o]
[compile codon_iterator.o]
[compile codon_iterator_encseq.o]
[compile codon_iterator_simple.o]
[compile colorspace.o]
[compile combinatorics.o]
[compile compact_ulong_store.o]
[compile compat.o]
[compile complement.o]
[compile countingsort.o]
[compile cstr.o]
[compile cstr_array.o]
[compile cstr_table.o]
[compile desc_buffer.o]
[compile disc_distri.o]
[compile dlist.o]
[compile dual-pivot-qsort.o]
[compile dyn_bittab.o]
[compile dynalloc.o]
[compile eansi.o]
[compile ebzlib.o]
[compile encseq.o]
[compile encseq_access_type.o]
[compile encseq_col.o]
[compile encseq_metadata.o]
[compile encseq_options.o]
[compile encseq_ptr.o]
[compile endianess.o]
[compile error.o]
[compile example.o]
[compile example_a.o]
[compile example_b.o]
[compile ezlib.o]
[compile fa.o]
[compile fasta.o]
[compile fasta_reader.o]
[compile fasta_reader_fsm.o]
[compile fasta_reader_rec.o]
[compile fasta_reader_seqit.o]
[compile fastq.o]
[compile file.o]
[compile fileutils.o]
[compile gc_content.o]
[compile grep.o]
[compile gtdatapath.o]
[compile hashmap.o]
[compile hashtable.o]
[compile init.o]
[compile interval_tree.o]
[compile io.o]
[compile log.o]
[compile logger.o]
[compile ma.o]
[compile mapspec.o]
[compile mathsupport.o]
[compile md5_encoder.o]
[compile md5_fingerprint.o]
[compile md5_seqid.o]
[compile md5_tab.o]
[compile msort.o]
[compile multithread.o]
[compile option.o]
[compile orf.o]
[compile output_file.o]
[compile parseutils.o]
[compile password_entry.o]
[compile phase.o]
[compile process.o]
[compile progressbar.o]
[compile qsort-ulong.o]
[compile qsort_r.o]
[compile quality.o]
[compile queue.o]
[compile radix_sort.o]
[compile range.o]
[compile readmode.o]
[compile safearith.o]
[compile score_function.o]
[compile score_matrix.o]
[compile seq.o]
[compile seq_col.o]
[compile seq_info_cache.o]
[compile seq_iterator.o]
[compile seq_iterator_fastq.o]
[compile seq_iterator_sequence_buffer.o]
[compile sequence_buffer.o]
[compile sequence_buffer_embl.o]
[compile sequence_buffer_fasta.o]
[compile sequence_buffer_fastq.o]
[compile sequence_buffer_gb.o]
[compile sequence_buffer_plain.o]
[compile showtime.o]
[compile sig.o]
[compile spacepeak.o]
[compile splitter.o]
[compile str.o]
[compile str_array.o]
[compile str_cache.o]
[compile strand.o]
[compile strcmp.o]
[compile string_distri.o]
[compile symbol.o]
[compile thread.o]
[compile timer.o]
[compile tokenizer.o]
[compile tool.o]
[compile tool_iterator.o]
[compile toolbox.o]
[compile tooldriver.o]
[compile trans_table.o]
[compile translator.o]
[compile unit_testing.o]
[compile version.o]
[compile versionfunc.o]
[compile warning.o]
[compile xansi.o]
[compile xbsd.o]
[compile xbzlib.o]
[compile xposix.o]
[compile xzlib.o]
[compile yarandom.o]
[compile add_ids_stream.o]
[compile add_ids_visitor.o]
[compile add_introns_stream.o]
[compile affinealign.o]
[compile aligned_segment.o]
[compile aligned_segments_pile.o]
[compile alignment.o]
[compile anno_db_gfflike.o]
[compile anno_db_schema.o]
[compile array_in_stream.o]
[compile array_out_stream.o]
[compile assembly_stats_calculator.o]
[compile bed_in_stream.o]
[compile bed_parser.o]
[compile bitinstream.o]
[compile bitoutstream.o]
[compile blast_process_call.o]
[compile buffer_stream.o]
[compile cds_check_stream.o]
[compile cds_check_visitor.o]
[compile cds_stream.o]
[compile cds_visitor.o]
[compile chain.o]
[compile check_boundaries_visitor.o]
[compile chseqids_stream.o]
[compile clustered_set.o]
[compile clustered_set_uf.o]
[compile coin_hmm.o]
[compile collect_ids_visitor.o]
[compile comment_node.o]
[compile compressed_bitsequence.o]
[compile condenseq.o]
[compile condenseq_creator.o]
[compile condenseq_search_arguments.o]
[compile consensus_sa.o]
[compile csa_gene.o]
[compile csa_splice_form.o]
[compile csa_stream.o]
[compile csa_variable_strands.o]
[compile csa_visitor.o]
[compile cstr_iterator.o]
[compile diagonalbandalign.o]
[compile diagonalbandalign_affinegapcost.o]
[compile dice_hmm.o]
[compile dot_out_stream.o]
[compile dot_visitor.o]
[compile dup_feature_stream.o]
[compile dup_feature_visitor.o]
[compile editscript.o]
[compile elias_gamma.o]
[compile encdesc.o]
[compile encdesc_header_io.o]
[compile eof_node.o]
[compile evaluator.o]
[compile extract_feature_sequence.o]
[compile extract_feature_stream.o]
[compile extract_feature_visitor.o]
[compile fasta_header_iterator.o]
[compile feature_in_stream.o]
[compile feature_index.o]
[compile feature_index_memory.o]
[compile feature_info.o]
[compile feature_node.o]
[compile feature_node_iterator.o]
[compile feature_node_observer.o]
[compile feature_out_stream.o]
[compile feature_stream.o]
[compile feature_visitor.o]
[compile gap_str.o]
[compile genome_node.o]
[compile gff3_escaping.o]
[compile gff3_in_stream.o]
[compile gff3_in_stream_plain.o]
[compile gff3_linesorted_out_stream.o]
[compile gff3_numsorted_out_stream.o]
[compile gff3_out_stream.o]
[compile gff3_output.o]
[compile gff3_parser.o]
[compile gff3_visitor.o]
[compile globalchaining.o]
[compile golomb.o]
[compile gtdatahelp.o]
[compile gtf_in_stream.o]
[compile gtf_out_stream.o]
[compile gtf_parser.o]
[compile gtf_visitor.o]
[compile hcr.o]
[compile hmm.o]
[compile hpol_processor.o]
[compile huffcode.o]
[compile id_to_md5_stream.o]
[compile id_to_md5_visitor.o]
[compile inter_feature_stream.o]
[compile inter_feature_visitor.o]
[compile intset.o]
[compile intset_16.o]
[compile intset_32.o]
[compile intset_8.o]
[compile intset_combined.o]
[compile io_function_pointers.o]
[compile kmer_database.o]
[compile linearalign.o]
[compile linearalign_affinegapcost.o]
[compile linspace_management.o]
[compile load_stream.o]
[compile luahelper.o]
[compile luaserialize.o]
[compile mapping.o]
[compile match.o]
[compile match_blast.o]
[compile match_iterator.o]
[compile match_iterator_blast.o]
[compile match_iterator_last.o]
[compile match_iterator_open.o]
[compile match_iterator_sw.o]
[compile match_last.o]
[compile match_open.o]
[compile match_sw.o]
[compile match_visitor.o]
[compile maxcoordvalue.o]
[compile md5_to_id_stream.o]
[compile md5_to_id_visitor.o]
[compile md5set.o]
[compile merge_feature_stream.o]
[compile merge_feature_visitor.o]
[compile merge_stream.o]
[compile meta_node.o]
[compile multi_sanitizer_visitor.o]
[compile multieoplist.o]
[compile mutate.o]
[compile node_stream.o]
[compile node_visitor.o]
[compile obo_parse_tree.o]
[compile obo_stanza.o]
[compile orf_finder_stream.o]
[compile orf_finder_visitor.o]
[compile orf_iterator.o]
[compile orphanage.o]
[compile permute_words.o]
[compile popcount_tab.o]
[compile priority_queue.o]
[compile ranked_list.o]
[compile rbtree.o]
[compile rcr.o]
[compile rdb.o]
[compile rdb_sqlite.o]
[compile rdb_visitor.o]
[compile reconstructalignment.o]
[compile region_mapping.o]
[compile region_node.o]
[compile region_node_builder.o]
[compile regioncov_visitor.o]
[compile regular_seqid.o]
[compile reverse.o]
[compile rmq.o]
[compile safe_popen.o]
[compile sam_alignment.o]
[compile sam_query_name_iterator.o]
[compile samfile_encseq_mapping.o]
[compile samfile_iterator.o]
[compile sampling.o]
[compile scorehandler.o]
[compile script_filter.o]
[compile script_wrapper_stream.o]
[compile script_wrapper_visitor.o]
[compile select_stream.o]
[compile select_visitor.o]
[compile seqid2file.o]
[compile seqid2seqnum_mapping.o]
[compile seqpos_classifier.o]
[compile sequence_node.o]
[compile sequence_node_add_stream.o]
[compile sequence_node_out_stream.o]
[compile sequence_node_out_visitor.o]
[compile set_source_visitor.o]
[compile shredder.o]
[compile snp_annotator_stream.o]
[compile snp_annotator_visitor.o]
[compile sort_stream.o]
[compile spec_results.o]
[compile spec_visitor.o]
[compile splice_site_info_stream.o]
[compile splice_site_info_visitor.o]
[compile splicedseq.o]
[compile squarealign.o]
[compile sspliced_alignment.o]
[compile sspliced_alignment_parsing.o]
[compile stat_stream.o]
[compile stat_visitor.o]
[compile stream_evaluator.o]
[compile string_matching.o]
[compile swalign.o]
[compile tag_value_map.o]
[compile targetbest_select_stream.o]
[compile tidy_region_node_stream.o]
[compile tidy_region_node_visitor.o]
[compile tir_stream.o]
[compile transcript_bittabs.o]
[compile transcript_counts.o]
[compile transcript_evaluators.o]
[compile transcript_exons.o]
[compile transcript_used_exons.o]
[compile type_checker.o]
[compile type_checker_builtin.o]
[compile type_checker_obo.o]
[compile type_graph.o]
[compile type_node.o]
[compile typecheck_info.o]
[compile uint64hashtable.o]
[compile union_find.o]
[compile uniq_stream.o]
[compile visitor_stream.o]
[compile wtree.o]
[compile wtree_encseq.o]
[compile xrf_abbr_entry.o]
[compile xrf_abbr_parse_tree.o]
[compile xrf_checker.o]
[compile xrfcheck_info.o]
[compile alphabet_lua.o]
[compile annotationsketch_lua.o]
[compile bittab_lua.o]
[compile canvas_lua.o]
[compile cds_stream_lua.o]
[compile csa_stream_lua.o]
[compile diagram_lua.o]
[compile encseq_lua.o]
[compile feature_index_lua.o]
[compile feature_node_iterator_lua.o]
[compile feature_stream_lua.o]
[compile feature_visitor_lua.o]
[compile genome_node_lua.o]
[compile genome_stream_lua.o]
[compile genome_visitor_lua.o]
[compile gt_lua.o]
[compile gtcore_lua.o]
[compile gtext_lua.o]
[compile image_info_lua.o]
[compile layout_lua.o]
[compile mathsupport_lua.o]
[compile range_lua.o]
[compile region_mapping_lua.o]
[compile score_matrix_lua.o]
[compile stream_evaluator_lua.o]
[compile translate_lua.o]
[compile apmeoveridx.o]
[compile asqg_writer.o]
[compile bare-encseq.o]
[compile bcktab.o]
[compile cgr_spacedseed.o]
[compile chain2dim.o]
[compile chainofin.o]
[compile cutendpfx.o]
[compile diagbandseed.o]
[compile dist-short.o]
[compile echoseq.o]
[compile eis-blockcomp-param.o]
[compile eis-blockcomp.o]
[compile eis-bwtseq-construct.o]
[compile eis-bwtseq-context-param.o]
[compile eis-bwtseq-context.o]
[compile eis-bwtseq-extinfo.o]
[compile eis-bwtseq-param.o]
[compile eis-bwtseq-sass.o]
[compile eis-bwtseq.o]
[compile eis-encidxseq-construct.o]
[compile eis-encidxseq-param.o]
[compile eis-encidxseq.o]
[compile eis-mrangealphabet.o]
[compile eis-sa-common.o]
[compile eis-seqblocktranslate.o]
[compile eis-seqranges.o]
[compile eis-sequencemultiread.o]
[compile eis-specialsrank.o]
[compile eis-suffixarray-interface.o]
[compile eis-suffixerator-interface.o]
[compile eis-voiditf.o]
[compile encseq2offset.o]
[compile enum-patt.o]
[compile esa-bottomup.o]
[compile esa-dfs.o]
[compile esa-lcpintervals.o]
[compile esa-map.o]
[compile esa-maxpairs.o]
[compile esa-merge.o]
[compile esa-minunique.o]
[compile esa-mmsearch.o]
[compile esa-scanprj.o]
[compile esa-seqread.o]
[compile esa-shulen.o]
[compile esa-splititv-simple.o]
[compile esa-splititv.o]
[compile esa-spmitvs.o]
[compile esa-spmsk.o]
[compile esa_lcpintervals_visitor.o]
[compile esa_spmitvs_visitor.o]
[compile esa_visitor.o]
[compile firstcodes-accum.o]
[compile firstcodes-cache.o]
[compile firstcodes-insert.o]
[compile firstcodes-psbuf.o]
[compile firstcodes-scan.o]
[compile firstcodes-spacelog.o]
[compile firstcodes-tab.o]
[compile firstcodes.o]
[compile fmi-fwduni.o]
[compile fmi-keyval.o]
[compile fmi-locate.o]
[compile fmi-map.o]
[compile fmi-mapspec.o]
[compile fmi-mkindex.o]
[compile fmi-save.o]
[compile fmi-sufbwtstream.o]
[compile ft-front-generation.o]
[compile ft-front-prune.o]
[compile ft-polish.o]
[compile ft-trimstat.o]
[compile giextract.o]
[compile greedyedist.o]
[compile greedyfwdmat.o]
[compile hashfirstcodes.o]
[compile hlk-version.o]
[compile hplstore.o]
[compile idx-limdfs.o]
[compile idxlocali.o]
[compile idxlocalidp.o]
[compile idxlocalisw.o]
[compile index_options.o]
[compile initbasepower.o]
[compile initeqsvec.o]
[compile iter-window.o]
[compile kmer2string.o]
[compile lua_tools.o]
[compile marksubstring.o]
[compile merger-trie.o]
[compile mssufpat.o]
[compile myersapm.o]
[compile nullcols.o]
[compile optionargmode.o]
[compile pck-count-nodes.o]
[compile pckbucket.o]
[compile pckdfs.o]
[compile prsqualint.o]
[compile pssm.o]
[compile querymatch-align.o]
[compile querymatch.o]
[compile radixsort_str.o]
[compile randomcodes-correct.o]
[compile randomcodes-find-seldom.o]
[compile randomcodes-hpcorrect.o]
[compile randomcodes-insert.o]
[compile randomcodes-sfx-partssuf.o]
[compile randomcodes-tab.o]
[compile randomcodes.o]
[compile rdj-cntlist.o]
[compile rdj-contfind-bottomup.o]
[compile rdj-contfinder.o]
[compile rdj-contigpaths.o]
[compile rdj-contigs-graph.o]
[compile rdj-contigs-writer.o]
[compile rdj-errfind.o]
[compile rdj-ovlfind-bf.o]
[compile rdj-ovlfind-dp.o]
[compile rdj-ovlfind-gusfield.o]
[compile rdj-ovlfind-kmp.o]
[compile rdj-pairwise.o]
[compile rdj-spmfind.o]
[compile rdj-spmlist.o]
[compile rdj-spmproc.o]
[compile rdj-strgraph.o]
[compile rdj-twobitenc-editor.o]
[compile rdj-version.o]
[compile reads2twobit.o]
[compile reads_libraries_table.o]
[compile revcompl.o]
[compile seed-extend-iter.o]
[compile seed-extend.o]
[compile seqabstract.o]
[compile seqnumrelpos.o]
[compile sfx-apfxlen.o]
[compile sfx-bentsedg.o]
[compile sfx-bltrie.o]
[compile sfx-copysort.o]
[compile sfx-diffcov.o]
[compile sfx-enumcodes.o]
[compile sfx-lcpvalues.o]
[compile sfx-linlcp.o]
[compile sfx-lwcheck.o]
[compile sfx-mappedstr.o]
[compile sfx-maprange.o]
[compile sfx-opt.o]
[compile sfx-outprj.o]
[compile sfx-partssuf.o]
[compile sfx-radixsort.o]
[compile sfx-run.o]
[compile sfx-sain.o]
[compile sfx-shortreadsort.o]
[compile sfx-suffixer.o]
[compile sfx-suffixgetset.o]
[compile sfx-suftaborder.o]
[compile shu-dfs.o]
[compile shu-divergence.o]
[compile shu-encseq-gc.o]
[compile shu-genomediff.o]
[compile shu_unitfile.o]
[compile spaced-seeds.o]
[compile specialrank.o]
[compile spmsuftab.o]
[compile squarededist.o]
[compile substriter.o]
[compile tagerator.o]
[compile test-mappedstr.o]
[compile test-maxpairs.o]
[compile test-mergeesa.o]
[compile test-mtrieins.o]
[compile test-pairwise.o]
[compile turnwheels.o]
[compile twobits2kmers.o]
[compile tyr-map.o]
[compile tyr-mersplit.o]
[compile tyr-mkindex.o]
[compile tyr-occratio.o]
[compile tyr-search.o]
[compile xdrop.o]
[compile ags.o]
[compile ags_build.o]
[compile align_dna.o]
[compile align_protein.o]
[compile backtrace_path.o]
[compile bssm_helper.o]
[compile bssm_param.o]
[compile bssm_param_rmsd.o]
[compile bssm_seq_processor.o]
[compile bssm_train_stream.o]
[compile bssm_train_visitor.o]
[compile call_info.o]
[compile chain_collection.o]
[compile chaining.o]
[compile compute_scores.o]
[compile desc_cache.o]
[compile dp_options_core.o]
[compile dp_options_est.o]
[compile dp_options_postpro.o]
[compile dp_param.o]
[compile dp_scores_protein.o]
[compile editoperation.o]
[compile gff3_pgl_visitor.o]
[compile gff3_sa_visitor.o]
[compile gt_gth.o]
[compile gt_gthbssmbuild.o]
[compile gt_gthbssmfileinfo.o]
[compile gt_gthbssmprint.o]
[compile gt_gthbssmrmsd.o]
[compile gt_gthbssmtrain.o]
[compile gt_gthconsensus.o]
[compile gt_gthfilestat.o]
[compile gt_gthmkbssmfiles.o]
[compile gt_gthsplit.o]
[compile gthalignment.o]
[compile gthchain.o]
[compile gthcluster.o]
[compile gthcutoffsminimal.o]
[compile gthcutoffsrelaxed.o]
[compile gthcutoffsstrict.o]
[compile gthmatch.o]
[compile gthorf.o]
[compile gthoutput.o]
[compile gthsadistri.o]
[compile gthsortags.o]
[compile gthsplicesitescr.o]
[compile gthtrans.o]
[compile gthtravalign.o]
[compile gthverbosefunc.o]
[compile gthverbosefuncvm.o]
[compile gthxml.o]
[compile indent.o]
[compile input.o]
[compile intermediate.o]
[compile md5_cache.o]
[compile parse_options.o]
[compile path_matrix.o]
[compile path_walker.o]
[compile pgl.o]
[compile pgl_collection.o]
[compile pgl_visitor.o]
[compile proc_sa_collection.o]
[compile region_factory.o]
[compile run_header.o]
[compile sa.o]
[compile sa_cmp.o]
[compile sa_collection.o]
[compile sa_filter.o]
[compile sa_visitor.o]
[compile seq_con.o]
[compile similarity_filter.o]
[compile splice_site_model.o]
[compile spliced_seq.o]
[compile stat.o]
[compile time.o]
[compile txt_pgl_visitor.o]
[compile txt_sa_visitor.o]
[compile xml_final_sa_visitor.o]
[compile xml_inter_sa_visitor.o]
[compile xml_pgl_visitor.o]
[compile gt_ltrclustering.o]
[compile gt_ltrdigest.o]
[compile gt_ltrharvest.o]
[compile ltr_classify_stream.o]
[compile ltr_cluster_prepare_seq_visitor.o]
[compile ltr_cluster_stream.o]
[compile ltr_four_char_motif.o]
[compile ltr_input_check_visitor.o]
[compile ltr_orf_annotator_stream.o]
[compile ltr_refseq_match_stream.o]
[compile ltrdigest_file_out_stream.o]
[compile ltrdigest_pbs_visitor.o]
[compile ltrdigest_pdom_visitor.o]
[compile ltrdigest_ppt_visitor.o]
[compile ltrdigest_strand_assign_visitor.o]
[compile ltrharvest_fasta_out_stream.o]
[compile ltrharvest_fasta_out_visitor.o]
[compile ltrharvest_stream.o]
[compile ltrharvest_tabout_stream.o]
[compile ltrharvest_tabout_visitor.o]
[compile pdom_model_set.o]
[compile metagenomethreader.o]
[compile mg_codon.o]
[compile mg_combinedscore.o]
[compile mg_compute_gene_prediction.o]
[compile mg_computepath.o]
[compile mg_outputwriter.o]
[compile mg_reverse.o]
[compile mg_xmlparser.o]
[compile block.o]
[compile canvas.o]
[compile canvas_cairo.o]
[compile canvas_cairo_context.o]
[compile canvas_cairo_file.o]
[compile color.o]
[compile coords.o]
[compile custom_track.o]
[compile custom_track_example.o]
[compile custom_track_gc_content.o]
[compile custom_track_script_wrapper.o]
[compile diagram.o]
[compile drawing_range.o]
[compile element.o]
[compile graphics.o]
[compile graphics_cairo.o]
[compile gt_sketch.o]
[compile gt_sketch_page.o]
[compile image_info.o]
[compile layout.o]
[compile line.o]
[compile line_breaker.o]
[compile line_breaker_bases.o]
[compile line_breaker_captions.o]
[compile luastyle.o]
[compile rec_map.o]
[compile style.o]
[compile text_width_calculator.o]
[compile text_width_calculator_cairo.o]
[compile track.o]
[link libgenometools.a]
ar: creating lib/libgenometools.a
[gathering public API symbols to obj/public_symbols.lst]
[link libgenometools.so]
[compile gt.o]
[compile gtr.o]
[compile gtt.o]
[compile interactive.o]
[compile gt_bed_to_gff3.o]
[compile gt_cds.o]
[compile gt_chain2dim.o]
[compile gt_chseqids.o]
[compile gt_clean.o]
[compile gt_compreads.o]
[compile gt_compreads_compress.o]
[compile gt_compreads_decompress.o]
[compile gt_compreads_refcompress.o]
[compile gt_compreads_refdecompress.o]
[compile gt_compressedbits.o]
[compile gt_condenseq.o]
[compile gt_condenseq_blast.o]
[compile gt_condenseq_compress.o]
[compile gt_condenseq_extract.o]
[compile gt_condenseq_hmmsearch.o]
[compile gt_condenseq_info.o]
[compile gt_condenseq_search.o]
[compile gt_congruence.o]
[compile gt_consensus_sa.o]
[compile gt_convertseq.o]
[compile gt_csa.o]
[compile gt_dev.o]
[compile gt_dot.o]
[compile gt_dupfeat.o]
[compile gt_encseq.o]
[compile gt_encseq2spm.o]
[compile gt_encseq_bench.o]
[compile gt_encseq_bitextract.o]
[compile gt_encseq_check.o]
[compile gt_encseq_decode.o]
[compile gt_encseq_encode.o]
[compile gt_encseq_info.o]
[compile gt_encseq_md5.o]
[compile gt_encseq_sample.o]
[compile gt_eval.o]
[compile gt_extractfeat.o]
[compile gt_extractseq.o]
[compile gt_extracttarget.o]
[compile gt_fastq_sample.o]
[compile gt_featureindex.o]
[compile gt_fingerprint.o]
[compile gt_gdiffcalc.o]
[compile gt_genomediff.o]
[compile gt_gff3.o]
[compile gt_gff3_to_gtf.o]
[compile gt_gff3validator.o]
[compile gt_gtf_to_gff3.o]
[compile gt_guessprot.o]
[compile gt_hop.o]
[compile gt_id_to_md5.o]
[compile gt_idxlocali.o]
[compile gt_inlineseq_add.o]
[compile gt_inlineseq_split.o]
[compile gt_interfeat.o]
[compile gt_kmer_database.o]
[compile gt_linspace_align.o]
[compile gt_loccheck.o]
[compile gt_magicmatch.o]
[compile gt_matchtool.o]
[compile gt_matstat.o]
[compile gt_md5_to_id.o]
[compile gt_merge.o]
[compile gt_mergeesa.o]
[compile gt_mergefeat.o]
[compile gt_mgth.o]
[compile gt_mkfeatureindex.o]
[compile gt_mkfmindex.o]
[compile gt_mmapandread.o]
[compile gt_orffinder.o]
[compile gt_packedindex.o]
[compile gt_packedindex_chk_integrity.o]
[compile gt_packedindex_chk_search.o]
[compile gt_packedindex_mkctxmap.o]
[compile gt_packedindex_trsuftab.o]
[compile gt_paircmp.o]
[compile gt_parsexrf.o]
[compile gt_patternmatch.o]
[compile gt_prebwt.o]
[compile gt_readjoiner.o]
[compile gt_readjoiner_asqg.o]
[compile gt_readjoiner_assembly.o]
[compile gt_readjoiner_cgraph.o]
[compile gt_readjoiner_cnttest.o]
[compile gt_readjoiner_correct.o]
[compile gt_readjoiner_graph.o]
[compile gt_readjoiner_overlap.o]
[compile gt_readjoiner_prefilter.o]
[compile gt_readjoiner_spmtest.o]
[compile gt_readreads.o]
[compile gt_regioncov.o]
[compile gt_repfind.o]
[compile gt_sain.o]
[compile gt_sam_interface.o]
[compile gt_script_filter.o]
[compile gt_seed_extend.o]
[compile gt_select.o]
[compile gt_seq.o]
[compile gt_seqcorrect.o]
[compile gt_seqfilter.o]
[compile gt_seqids.o]
[compile gt_seqlensort.o]
[compile gt_seqmutate.o]
[compile gt_seqorder.o]
[compile gt_seqstat.o]
[compile gt_seqtransform.o]
[compile gt_seqtranslate.o]
[compile gt_sequniq.o]
[compile gt_sfxmap.o]
[compile gt_show_seedext.o]
[compile gt_shredder.o]
[compile gt_shulen.o]
[compile gt_simreads.o]
[compile gt_skproto.o]
[compile gt_snpper.o]
[compile gt_sortbench.o]
[compile gt_speck.o]
[compile gt_splicesiteinfo.o]
[compile gt_splitfasta.o]
[compile gt_stat.o]
[compile gt_suffixerator.o]
[compile gt_tagerator.o]
[compile gt_tallymer.o]
[compile gt_template.o]
[compile gt_tir.o]
[compile gt_trieins.o]
[compile gt_uniq.o]
[compile gt_wtree.o]
[compile gt_wtree_bench.o]
[link gt]
[compile custom_stream.o]
[link custom_stream]
[compile gff3sort.o]
[link gff3sort]
[compile gff3validator.o]
[link gff3validator]
[compile noop.o]
[link noop]
[compile sketch_constructed.o]
[link sketch_constructed]
[compile sketch_parsed_with_ctrack.o]
[link sketch_parsed_with_ctrack]
[compile sketch_parsed_with_ordering.o]
[link sketch_parsed_with_ordering]
[compile sketch_parsed.o]
[link sketch_parsed]
bin/gt gtscripts/gtdoc.lua -html /<<BUILDDIR>>/genometools-1.5.8+ds \
        > www/genometools.org/htdocs/libgenometools.html
bin/gt gtscripts/gtdoc.lua -lua -html /<<BUILDDIR>>/genometools-1.5.8+ds \
        > www/genometools.org/htdocs/docs.html
bin/examples/sketch_parsed gtdata/sketch/default.style \
          www/genometools.org/htdocs/images/parsed.png \
          testdata/eden.gff3
bin/examples/sketch_parsed \
  www/genometools.org/htdocs/annotationsketch/callbacks.style \
  www/genometools.org/htdocs/images/callbacks.png \
          www/genometools.org/htdocs/annotationsketch/callback_examples_with_score.gff3
bin/examples/sketch_constructed gtdata/sketch/default.style \
  www/genometools.org/htdocs/images/constructed.png
mogrify -format jpg +set date:create +set date:modify \
  -define png:exclude-chunk=time \
  www/genometools.org/htdocs/images/*.png && \
  rm -rf www/genometools.org/htdocs/images/*.png
sed -nf scripts/incl.sed \
  www/genometools.org/htdocs/examples_tmpl.html | \
          sed 'N;N;s/\n//' > /tmp/tmp.sed.$$ && \
sed -f /tmp/tmp.sed.$$ \
  www/genometools.org/htdocs/examples_tmpl.html > \
  www/genometools.org/htdocs/examples.html; rm -f /tmp/tmp.sed.$$
bin/gt gtscripts/gtdoc.lua -tex /<<BUILDDIR>>/genometools-1.5.8+ds \
> doc/manuals/api_reference.tex
bin/gt gtscripts/gtdoc.lua -lua -tex /<<BUILDDIR>>/genometools-1.5.8+ds \
> doc/manuals/gtscript_reference.tex
make -C /<<BUILDDIR>>/genometools-1.5.8+ds/doc/devguide
make[3]: Entering directory '/<<BUILDDIR>>/genometools-1.5.8+ds/doc/devguide'
while (pdflatex --shell-escape devguide ; \
grep -q "Rerun to get cross" devguide.log ) do true ; \
done
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
(./devguide.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo))
(/usr/share/texlive/texmf-dist/tex/latex/a4wide/a4wide.sty
(/usr/share/texlive/texmf-dist/tex/latex/ntgclass/a4.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))))
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty)
(/usr/share/texlive/texmf-dist/tex/latex/caption/caption.sty
(/usr/share/texlive/texmf-dist/tex/latex/caption/caption3.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/mathptmx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
No file devguide.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omlztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omxztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [2] [3]
Overfull \hbox (5.07777pt too wide) in paragraph at lines 292--301
[]\OT1/ptm/m/n/10.95 The [][][] stores a func-tion pointer to the spe-cific fun
c-tion im-ple-ment-ing the [][][][]
[4]
Overfull \hbox (10.48648pt too wide) in paragraph at lines 307--311
[]\OT1/ptm/m/n/10.95 returns an ob-ject of the in-ter-face type, al-lo-cat-ing 
mem-ory to hold both a pointer to a [][][]

LaTeX Warning: Reference `simpleclasses' on page 5 undefined on input line 349.


[5]
Overfull \hbox (4.09738pt too wide) in paragraph at lines 386--390
[]\OT1/ptm/m/n/10.95 a pointer to a [][][] in-ter-face im-ple-men-ta-tion, so i
t can be used safely with the [][][][]

LaTeX Warning: Reference `fig:interfacememlayout' on page 6 undefined on input 
line 394.

<mlayout.pdf, id=177, 475.97964pt x 175.63214pt> <use mlayout.pdf> [6 <./mlayou
t.pdf>] [7]

LaTeX Warning: Reference `unittests' on page 8 undefined on input line 513.

[8]

LaTeX Warning: Reference `errors' on page 9 undefined on input line 618.

[9] [10] (/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
[11]

LaTeX Warning: Reference `gttestdata' on page 12 undefined on input line 824.


LaTeX Warning: Reference `testdefinitions' on page 12 undefined on input line 8
39.


Overfull \hbox (13.93028pt too wide) in paragraph at lines 835--841
\OT1/ptm/m/n/10.95 tem-po-rary data cre-ated us-ing test runs. Af-ter start-ing
 a test suite run, the [][][][][]
[12]
Overfull \hbox (15.8892pt too wide) in paragraph at lines 866--872
[]\OT1/ptm/m/n/10.95 All pub-lic API func-tions for a given class must be de-cl
ared in a pro-to-type header file named [][][][][][][][].

LaTeX Warning: Reference `documentation' on page 13 undefined on input line 874
.

[13] [14] [15] [16] [17] [18] [19] [20] [21]
Overfull \hbox (2.08699pt too wide) in paragraph at lines 1495--1500
[]\OT1/ptm/m/n/10.95 For syn-chro-niza-tion dur-ing par-al-lel ex-e-cu-tion of 
mul-ti-ple threads, \OT1/ptm/m/it/10.95 Genome-Tools \OT1/ptm/m/n/10.95 pro-vid
es classes
[22]

LaTeX Warning: Reference `gttestdata' on page 23 undefined on input line 1595.

(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang2.sty) [23]

LaTeX Warning: Reference `gttestdata' on page 24 undefined on input line 1662.


Overfull \hbox (44.87006pt too wide) in paragraph at lines 1666--1669
[][][][]\OT1/ptm/m/n/10.95 , the path to the work-ing di-rec-tory of the test-s
uit, e.g. the di-rec-tory from which [][][][][][][]
[24] [25]

Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding):
(hyperref)                removing `\lstinline' on input line 1780.

[26] [27] [28]

LaTeX Warning: Reference `copyright' on page 29 undefined on input line 1981.

[29] (./devguide.aux)

Package rerunfilecheck Warning: File `devguide.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.


LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy
7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb></usr/share/texlive/
texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/font
s/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/tim
es/utmri8a.pfb>
Output written on devguide.pdf (29 pages, 257407 bytes).
Transcript written on devguide.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
(./devguide.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo))
(/usr/share/texlive/texmf-dist/tex/latex/a4wide/a4wide.sty
(/usr/share/texlive/texmf-dist/tex/latex/ntgclass/a4.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))))
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty)
(/usr/share/texlive/texmf-dist/tex/latex/caption/caption.sty
(/usr/share/texlive/texmf-dist/tex/latex/caption/caption3.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/mathptmx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty) (./devguide.aux)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./devguide.out) (./devguide.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omlztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omxztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) (./devguide.toc)
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4]
Overfull \hbox (5.07777pt too wide) in paragraph at lines 292--301
[]\OT1/ptm/m/n/10.95 The [][][] stores a func-tion pointer to the spe-cific fun
c-tion im-ple-ment-ing the [][][][]

Overfull \hbox (10.48648pt too wide) in paragraph at lines 307--311
[]\OT1/ptm/m/n/10.95 returns an ob-ject of the in-ter-face type, al-lo-cat-ing 
mem-ory to hold both a pointer to a [][][]
[5]
Overfull \hbox (4.09738pt too wide) in paragraph at lines 386--390
[]\OT1/ptm/m/n/10.95 a pointer to a [][][] in-ter-face im-ple-men-ta-tion, so i
t can be used safely with the [][][][]
<mlayout.pdf, id=216, 475.97964pt x 175.63214pt> <use mlayout.pdf> [6] [7 <./ml
ayout.pdf>] [8] [9] [10]
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty) [11] [12]
Overfull \hbox (13.93028pt too wide) in paragraph at lines 835--841
\OT1/ptm/m/n/10.95 tem-po-rary data cre-ated us-ing test runs. Af-ter start-ing
 a test suite run, the [][][][][]

Overfull \hbox (15.8892pt too wide) in paragraph at lines 866--872
[]\OT1/ptm/m/n/10.95 All pub-lic API func-tions for a given class must be de-cl
ared in a pro-to-type header file named [][][][][][][][].
[13] [14] [15] [16] [17] [18] [19] [20] [21]
Overfull \hbox (2.08699pt too wide) in paragraph at lines 1495--1500
[]\OT1/ptm/m/n/10.95 For syn-chro-niza-tion dur-ing par-al-lel ex-e-cu-tion of 
mul-ti-ple threads, \OT1/ptm/m/it/10.95 Genome-Tools \OT1/ptm/m/n/10.95 pro-vid
es classes
[22] [23] (/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang2.sty) [24]
Overfull \hbox (44.87006pt too wide) in paragraph at lines 1666--1669
[][][][]\OT1/ptm/m/n/10.95 , the path to the work-ing di-rec-tory of the test-s
uit, e.g. the di-rec-tory from which [][][][][][][]
[25]

Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding):
(hyperref)                removing `\lstinline' on input line 1780.

[26] [27] [28] [29] [30] (./devguide.aux)

LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy
7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb></usr/share/texlive/
texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/font
s/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/tim
es/utmri8a.pfb>
Output written on devguide.pdf (30 pages, 258173 bytes).
Transcript written on devguide.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
(./devguide.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo))
(/usr/share/texlive/texmf-dist/tex/latex/a4wide/a4wide.sty
(/usr/share/texlive/texmf-dist/tex/latex/ntgclass/a4.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))))
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty)
(/usr/share/texlive/texmf-dist/tex/latex/caption/caption.sty
(/usr/share/texlive/texmf-dist/tex/latex/caption/caption3.sty))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/mathptmx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty) (./devguide.aux)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./devguide.out) (./devguide.out)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omlztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omxztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) (./devguide.toc)
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] [2] [3] [4]
Overfull \hbox (5.07777pt too wide) in paragraph at lines 292--301
[]\OT1/ptm/m/n/10.95 The [][][] stores a func-tion pointer to the spe-cific fun
c-tion im-ple-ment-ing the [][][][]

Overfull \hbox (10.48648pt too wide) in paragraph at lines 307--311
[]\OT1/ptm/m/n/10.95 returns an ob-ject of the in-ter-face type, al-lo-cat-ing 
mem-ory to hold both a pointer to a [][][]
[5]
Overfull \hbox (4.09738pt too wide) in paragraph at lines 386--390
[]\OT1/ptm/m/n/10.95 a pointer to a [][][] in-ter-face im-ple-men-ta-tion, so i
t can be used safely with the [][][][]
<mlayout.pdf, id=216, 475.97964pt x 175.63214pt> <use mlayout.pdf> [6] [7 <./ml
ayout.pdf>] [8] [9] [10]
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty) [11] [12]
Overfull \hbox (13.93028pt too wide) in paragraph at lines 835--841
\OT1/ptm/m/n/10.95 tem-po-rary data cre-ated us-ing test runs. Af-ter start-ing
 a test suite run, the [][][][][]

Overfull \hbox (15.8892pt too wide) in paragraph at lines 866--872
[]\OT1/ptm/m/n/10.95 All pub-lic API func-tions for a given class must be de-cl
ared in a pro-to-type header file named [][][][][][][][].
[13] [14] [15] [16] [17] [18] [19] [20] [21]
Overfull \hbox (2.08699pt too wide) in paragraph at lines 1495--1500
[]\OT1/ptm/m/n/10.95 For syn-chro-niza-tion dur-ing par-al-lel ex-e-cu-tion of 
mul-ti-ple threads, \OT1/ptm/m/it/10.95 Genome-Tools \OT1/ptm/m/n/10.95 pro-vid
es classes
[22] [23] (/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang2.sty) [24]
Overfull \hbox (44.87006pt too wide) in paragraph at lines 1666--1669
[][][][]\OT1/ptm/m/n/10.95 , the path to the work-ing di-rec-tory of the test-s
uit, e.g. the di-rec-tory from which [][][][][][][]
[25]

Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding):
(hyperref)                removing `\lstinline' on input line 1780.

[26] [27] [28] [29] [30] (./devguide.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy
7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb></usr/share/texlive/
texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/font
s/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/tim
es/utmri8a.pfb>
Output written on devguide.pdf (30 pages, 258170 bytes).
Transcript written on devguide.log.
make[3]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.8+ds/doc/devguide'
bin/gt -list > /tmp/list.txt
warning: skipping tool 'mgth' in iterator (not a GtTool object)
warning: skipping tool 'mkfmindex' in iterator (not a GtTool object)
warning: skipping tool 'suffixerator' in iterator (not a GtTool object)
warning: skipping tool 'chkintegrity' in iterator (not a GtTool object)
warning: skipping tool 'chksearch' in iterator (not a GtTool object)
warning: skipping tool 'mkctxmap' in iterator (not a GtTool object)
warning: skipping tool 'mkindex' in iterator (not a GtTool object)
warning: skipping tool 'trsuftab' in iterator (not a GtTool object)
bin/gt -createman /tmp/gtmanpages
warning: skipping tool 'mgth' in iterator (not a GtTool object)
warning: skipping tool 'mkfmindex' in iterator (not a GtTool object)
warning: skipping tool 'suffixerator' in iterator (not a GtTool object)
warning: skipping tool 'chkintegrity' in iterator (not a GtTool object)
warning: skipping tool 'chksearch' in iterator (not a GtTool object)
warning: skipping tool 'mkctxmap' in iterator (not a GtTool object)
warning: skipping tool 'mkindex' in iterator (not a GtTool object)
warning: skipping tool 'trsuftab' in iterator (not a GtTool object)
asciidoc --backend=xhtml11 -a linkcss -a stylesdir=. \
  -a stylesheet=style.css -a badges -a icons \
  -f www/genometools.org/htdocs/tool_list.conf \
  --out-file www/genometools.org/htdocs/tools.html /tmp/list.txt
test -d www/genometools.org/htdocs/tools || mkdir -p www/genometools.org/htdocs/tools
rm -f www/genometools.org/htdocs/tools/*
scripts/create_html /tmp/gtmanpages www/genometools.org/htdocs/
..............................................................................................
rm -rf /tmp/list.txt /tmp/gtmanpages
make -C /<<BUILDDIR>>/genometools-1.5.8+ds/doc/manuals annotationsketch
make[3]: Entering directory '/<<BUILDDIR>>/genometools-1.5.8+ds/doc/manuals'
test -e annotationsketch-pdf.aux && mv annotationsketch-pdf.aux annotationsketch.aux
Makefile:39: recipe for target 'annotationsketch-pdf.aux' failed
make[3]: [annotationsketch-pdf.aux] Error 1 (ignored)
pdflatex annotationsketch.tex && rm annotationsketch.pdf
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./annotationsketch.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrreprt.cls
Document Class: scrreprt 2015/10/03 v3.19a KOMA-Script document class (report)
(/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrkbase.sty
(/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrbase.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrlfile.sty
Package scrlfile, 2015/10/03 v3.19a KOMA-Script package (loading files)
                  Copyright (C) Markus Kohm

))) (/usr/share/texlive/texmf-dist/tex/latex/koma-script/tocbasic.sty)
(/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrsize11pt.clo)
(/usr/share/texlive/texmf-dist/tex/latex/koma-script/typearea.sty
Package typearea, 2015/10/03 v3.19a KOMA-Script package (type area)
                  Copyright (C) Frank Neukam, 1992-1994
                  Copyright (C) Markus Kohm, 1994-

)) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg)))
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/mathptmx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/bold-extra/bold-extra.sty)
(/usr/share/texlive/texmf-dist/tex/latex/caption/caption.sty
(/usr/share/texlive/texmf-dist/tex/latex/caption/caption3.sty))
No file annotationsketch.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))

LaTeX Font Warning: Font shape `OT1/cmss/bx/it' undefined
(Font)              using `OT1/cmss/bx/n' instead on input line 56.

(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omlztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omxztmcm.fd) [1{/var/lib/texmf/
fonts/map/pdftex/updmap/pdftex.map}] [2]
chapter 1.

Class scrreprt Warning: \float@addtolists detected!
(scrreprt)              Implementation of \float@addtolist became
(scrreprt)              deprecated in KOMA-Script v3.01 2008/11/14 and
(scrreprt)              has been replaced by several more flexible
(scrreprt)              features of package `tocbasic`.
(scrreprt)              Since Version 3.12 support for deprecated
(scrreprt)              \float@addtolist interface has been
(scrreprt)              restricted to only some of the KOMA-Script
(scrreprt)              features and been removed from others.
(scrreprt)              Loading of package `scrhack' may help to
(scrreprt)              avoid this warning, if you are using a
(scrreprt)              a package that still implements the
(scrreprt)              deprecated \float@addtolist interface .


LaTeX Warning: Reference `dataflow' on page 3 undefined on input line 65.


<../../www/genometools.org/htdocs/images/dataflow.pdf, id=17, 680.33936pt x 861
.9156pt> <use ../../www/genometools.org/htdocs/images/dataflow.pdf>

LaTeX Warning: Reference `gfftree' on page 3 undefined on input line 74.


<../../www/genometools.org/htdocs/images/gfftree.pdf, id=18, 510.53029pt x 138.
67685pt> <use ../../www/genometools.org/htdocs/images/gfftree.pdf>

LaTeX Warning: Reference `diagram' on page 3 undefined on input line 84.

[3]
<../../www/genometools.org/htdocs/images/diagram.pdf, id=29, 1363.36378pt x 593
.45078pt> <use ../../www/genometools.org/htdocs/images/diagram.pdf> [4 <../../w
ww/genometools.org/htdocs/images/dataflow.pdf>] [5 <../../www/genometools.org/h
tdocs/images/gfftree.pdf> <../../www/genometools.org/htdocs/images/diagram.pdf

pdfTeX warning: /usr/bin/pdflatex (file ../../www/genometools.org/htdocs/images
/diagram.pdf): PDF inclusion: multiple pdfs with page group included in a singl
e page
>]

LaTeX Warning: Reference `collapsetypes' on page 6 undefined on input line 119.



LaTeX Warning: Reference `cnn_large' on page 6 undefined on input line 119.


<../../www/genometools.org/htdocs/images/collapse_types.pdf, id=63, 215.72322pt
 x 285.93611pt>
<use ../../www/genometools.org/htdocs/images/collapse_types.pdf>
<../../www/genometools.org/htdocs/images/cnn_large.jpg, id=64, 1589.94pt x 654.
7662pt> <use ../../www/genometools.org/htdocs/images/cnn_large.jpg> [6 <../../w
ww/genometools.org/htdocs/images/collapse_types.pdf>]
kpathsea: Running mktextfm cmttb10
mkdir: cannot create directory '././sbuild-nonexistent': Permission denied
mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input cmttb10
This is METAFONT, Version 2.7182818 (TeX Live 2015/Debian) (preloaded base=mf)

(/usr/share/texlive/texmf-dist/fonts/source/public/cm/cmttb10.mf
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/cmbase.mf)
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/roman.mf
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romanu.mf [65] [66]
[67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81]
[82] [83] [84] [85] [86] [87] [88] [89] [90])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romanl.mf [97] [98]
[99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111]
[112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/greeku.mf [0] [1]
[2] [3] [4] [5] [6] [7] [8] [9] [10])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romand.mf [48] [49]
[50] [51] [52] [53] [54] [55] [56] [57])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romanp.mf [36] [38]
[63] [15]) (/usr/share/texlive/texmf-dist/fonts/source/public/cm/romspl.mf
[16] [17] [25] [26] [27] [28])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romspu.mf [29] [30]
[31]) (/usr/share/texlive/texmf-dist/fonts/source/public/cm/punct.mf [33]
[14] [35] [37] [39] [40] [41] [42] [43] [44] [46] [47] [58] [59] [61] [64]
[91] [93] [96]) (/usr/share/texlive/texmf-dist/fonts/source/public/cm/accent.mf
[18] [19] [20] [21] [22] [23] [24] [94] [126] [127])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romsub.mf
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/sym.mf [45] [12] [11]
[60] [62] [95] [92] [124] [123] [125] [34]) [13] [32]) ) )
Font metrics written on cmttb10.tfm.
Output written on cmttb10.600gf (128 characters, 19408 bytes).
Transcript written on cmttb10.log.
mktextfm: /tmp/texfonts/tfm/public/cm/cmttb10.tfm: successfully generated.
 [7 <../../www/genometools
.org/htdocs/images/cnn_large.jpg>]

LaTeX Warning: Reference `callbacks' on page 8 undefined on input line 175.


<../../www/genometools.org/htdocs/images/callbacks.jpg, id=140, 602.25pt x 379.
4175pt> <use ../../www/genometools.org/htdocs/images/callbacks.jpg>
kpathsea: Running mktextfm cmttb10
mkdir: cannot create directory '././sbuild-nonexistent': Permission denied
mktextfm: /tmp/texfonts/tfm/public/cm/cmttb10.tfm already exists.
 [8 <../../w
ww/genometools.org/htdocs/images/callbacks.jpg>]

LaTeX Warning: Reference `tsexample1' on page 9 undefined on input line 234.

(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)
<../../www/genometools.org/htdocs/images/example_nocollapse_noselect.jpg, id=15
3, 602.25pt x 242.9075pt>
<use ../../www/genometools.org/htdocs/images/example_nocollapse_noselect.jpg>
[9] (/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)

LaTeX Warning: Reference `tsexample1' on page 10 undefined on input line 258.


LaTeX Warning: Reference `tsexample2' on page 10 undefined on input line 270.


<../../www/genometools.org/htdocs/images/example_strandselect.jpg, id=161, 602.
25pt x 319.1925pt>
<use ../../www/genometools.org/htdocs/images/example_strandselect.jpg> [10 <../
../www/genometools.org/htdocs/images/example_nocollapse_noselect.jpg>]
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang2.sty)

LaTeX Warning: Reference `tsexample3' on page 11 undefined on input line 312.


<../../www/genometools.org/htdocs/images/example_filterselect.jpg, id=177, 602.
25pt x 319.1925pt>
<use ../../www/genometools.org/htdocs/images/example_filterselect.jpg>

LaTeX Warning: Reference `ctexample1' on page 11 undefined on input line 321.

[11 <../../www/genometools.org/htdocs/images/example_strandselect.jpg>]
<../../www/genometools.org/htdocs/images/example_ct.jpg, id=204, 602.25pt x 554
.07pt> <use ../../www/genometools.org/htdocs/images/example_ct.jpg> [12 <../../
www/genometools.org/htdocs/images/example_filterselect.jpg>] [13 <../../www/gen
ometools.org/htdocs/images/example_ct.jpg>]
Overfull \hbox (4.75348pt too wide) in paragraph at lines 388--389
[][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] 

Overfull \hbox (4.75348pt too wide) in paragraph at lines 390--391
[][][][][][][][][][][][][][][][][][][][][][][][][][] 

Overfull \hbox (4.75348pt too wide) in paragraph at lines 391--392
[][][][][][][][][][][][][][] 

Overfull \hbox (4.75348pt too wide) in paragraph at lines 393--394
[][][][][][][][][][][][][][][][][][] 

Overfull \hbox (4.75348pt too wide) in paragraph at lines 394--395
[][][][][][][][][][][][][][][][][][][][][][] 

Overfull \hbox (4.75348pt too wide) in paragraph at lines 396--397
[][][][][][][][][][][][][][][][][][][][][][][][][][] 

Overfull \hbox (4.75348pt too wide) in paragraph at lines 397--398
[][][][][][][][][][][][][][][][][][][][][][] 

LaTeX Warning: Reference `ctexample2' on page 14 undefined on input line 414.


<../../www/genometools.org/htdocs/images/example_ct2.jpg, id=218, 602.25pt x 29
8.11375pt> <use ../../www/genometools.org/htdocs/images/example_ct2.jpg>
[14]

LaTeX Warning: Reference `parsed_img' on page 15 undefined on input line 429.


<../../www/genometools.org/htdocs/images/parsed.jpg, id=262, 602.25pt x 404.511
25pt> <use ../../www/genometools.org/htdocs/images/parsed.jpg>
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(../../src/examples/sketch_parsed.c [15 <../../www/genometools.org/htdocs/image
s/example_ct2.jpg>] [16 <../../www/genometools.org/htdocs/images/parsed.jpg>])
Overfull \hbox (37.5989pt too wide) in paragraph at lines 441--442
\OT1/ptm/m/n/10.95 the com-mand line \OT1/cmtt/m/n/10.95 gt gtscripts/sketch[]p
arsed.lua <style[]file> <PNG[]file> <GFF3[]file>\OT1/ptm/m/n/10.95 ) 
(../../gtscripts/sketch_parsed.lua [17]) (../../gtruby/sketch_parsed.rb
[18]) (../../gtpython/sketch_parsed.py [19])

LaTeX Warning: Reference `constructed_img' on page 20 undefined on input line 4
52.


<../../www/genometools.org/htdocs/images/constructed.jpg, id=508, 602.25pt x 14
9.55875pt> <use ../../www/genometools.org/htdocs/images/constructed.jpg>
(../../src/examples/sketch_constructed.c [20 <../../www/genometools.org/htdocs/
images/constructed.jpg>] [21])
Overfull \hbox (28.675pt too wide) in paragraph at lines 464--465
\OT1/ptm/m/n/10.95 run by the com-mand line \OT1/cmtt/m/n/10.95 gt gtscripts/sk
etch[]constructed.lua <style[]file> <PNG[]file>\OT1/ptm/m/n/10.95 ) 
(../../gtscripts/sketch_constructed.lua [22])
(../../gtruby/sketch_constructed.rb [23]) (../../gtpython/sketch_constructed.py
[24]) (./api_reference.tex [25]
chapter 2.

LaTeX Warning: Reference `GtAddIntronsStream' on page 26 undefined on input lin
e 5.


LaTeX Warning: Reference `GtAlphabet' on page 26 undefined on input line 7.


LaTeX Warning: Reference `GtAnnoDBGFFlike' on page 26 undefined on input line 9
.


LaTeX Warning: Reference `GtAnnoDBSchema' on page 26 undefined on input line 11
.


LaTeX Warning: Reference `GtArray' on page 26 undefined on input line 13.


LaTeX Warning: Reference `GtArrayInStream' on page 26 undefined on input line 1
5.


LaTeX Warning: Reference `GtArrayOutStream' on page 26 undefined on input line 
17.


LaTeX Warning: Reference `GtBEDInStream' on page 26 undefined on input line 19.



LaTeX Warning: Reference `GtBittab' on page 26 undefined on input line 21.


LaTeX Warning: Reference `GtBlock' on page 26 undefined on input line 23.


LaTeX Warning: Reference `GtCDSStream' on page 26 undefined on input line 25.


LaTeX Warning: Reference `GtCSAStream' on page 26 undefined on input line 27.


LaTeX Warning: Reference `GtCanvas' on page 26 undefined on input line 29.


LaTeX Warning: Reference `GtCanvasCairoContext' on page 26 undefined on input l
ine 31.


LaTeX Warning: Reference `GtCanvasCairoFile' on page 26 undefined on input line
 33.


LaTeX Warning: Reference `GtCheckBoundariesVisitor' on page 26 undefined on inp
ut line 35.


LaTeX Warning: Reference `GtCodonIterator' on page 26 undefined on input line 3
7.


LaTeX Warning: Reference `GtCodonIteratorEncseq' on page 26 undefined on input 
line 39.


LaTeX Warning: Reference `GtCodonIteratorSimple' on page 26 undefined on input 
line 41.


LaTeX Warning: Reference `GtColor' on page 26 undefined on input line 43.


LaTeX Warning: Reference `GtCommentNode' on page 26 undefined on input line 45.



LaTeX Warning: Reference `GtCstrTable' on page 26 undefined on input line 47.


LaTeX Warning: Reference `GtCustomTrack' on page 26 undefined on input line 49.



LaTeX Warning: Reference `GtCustomTrackGcContent' on page 26 undefined on input
 line 51.

[26]

LaTeX Warning: Reference `GtCustomTrackScriptWrapper' on page 27 undefined on i
nput line 53.


LaTeX Warning: Reference `GtDiagram' on page 27 undefined on input line 55.


LaTeX Warning: Reference `GtDiscDistri' on page 27 undefined on input line 57.


LaTeX Warning: Reference `GtDlist' on page 27 undefined on input line 59.


LaTeX Warning: Reference `GtDlistelem' on page 27 undefined on input line 61.


LaTeX Warning: Reference `GtEOFNode' on page 27 undefined on input line 63.


LaTeX Warning: Reference `GtEncseq' on page 27 undefined on input line 65.


LaTeX Warning: Reference `GtEncseqBuilder' on page 27 undefined on input line 6
7.


LaTeX Warning: Reference `GtEncseqEncoder' on page 27 undefined on input line 6
9.


LaTeX Warning: Reference `GtEncseqLoader' on page 27 undefined on input line 71
.


LaTeX Warning: Reference `GtEncseqReader' on page 27 undefined on input line 73
.


LaTeX Warning: Reference `GtError' on page 27 undefined on input line 75.


LaTeX Warning: Reference `GtExtractFeatureStream' on page 27 undefined on input
 line 77.


LaTeX Warning: Reference `GtFeatureInStream' on page 27 undefined on input line
 79.


LaTeX Warning: Reference `GtFeatureIndex' on page 27 undefined on input line 81
.


LaTeX Warning: Reference `GtFeatureIndexMemory' on page 27 undefined on input l
ine 83.


LaTeX Warning: Reference `GtFeatureNode' on page 27 undefined on input line 85.



LaTeX Warning: Reference `GtFeatureNodeIterator' on page 27 undefined on input 
line 87.


LaTeX Warning: Reference `GtFeatureOutStream' on page 27 undefined on input lin
e 89.


LaTeX Warning: Reference `GtFeatureStream' on page 27 undefined on input line 9
1.


LaTeX Warning: Reference `GtFile' on page 27 undefined on input line 93.


LaTeX Warning: Reference `GtGFF3InStream' on page 27 undefined on input line 95
.


LaTeX Warning: Reference `GtGFF3OutStream' on page 27 undefined on input line 9
7.


LaTeX Warning: Reference `GtGFF3Parser' on page 27 undefined on input line 99.


LaTeX Warning: Reference `GtGFF3Visitor' on page 27 undefined on input line 101
.


LaTeX Warning: Reference `GtGTFInStream' on page 27 undefined on input line 103
.


LaTeX Warning: Reference `GtGTFOutStream' on page 27 undefined on input line 10
5.

[27]

LaTeX Warning: Reference `GtGenomeNode' on page 28 undefined on input line 107.



LaTeX Warning: Reference `GtGraphics' on page 28 undefined on input line 109.


LaTeX Warning: Reference `GtGraphicsCairo' on page 28 undefined on input line 1
11.


LaTeX Warning: Reference `GtHashmap' on page 28 undefined on input line 113.


LaTeX Warning: Reference `GtIDToMD5Stream' on page 28 undefined on input line 1
15.


LaTeX Warning: Reference `GtImageInfo' on page 28 undefined on input line 117.


LaTeX Warning: Reference `GtInterFeatureStream' on page 28 undefined on input l
ine 119.


LaTeX Warning: Reference `GtIntervalTree' on page 28 undefined on input line 12
1.


LaTeX Warning: Reference `GtIntervalTreeNode' on page 28 undefined on input lin
e 123.


LaTeX Warning: Reference `GtLayout' on page 28 undefined on input line 125.


LaTeX Warning: Reference `GtLogger' on page 28 undefined on input line 127.


LaTeX Warning: Reference `GtMD5Encoder' on page 28 undefined on input line 129.



LaTeX Warning: Reference `GtMD5ToIDStream' on page 28 undefined on input line 1
31.


LaTeX Warning: Reference `GtMatch' on page 28 undefined on input line 133.


LaTeX Warning: Reference `GtMatchBlast' on page 28 undefined on input line 135.



LaTeX Warning: Reference `GtMatchIterator' on page 28 undefined on input line 1
37.


LaTeX Warning: Reference `GtMatchLAST' on page 28 undefined on input line 139.


LaTeX Warning: Reference `GtMatchOpen' on page 28 undefined on input line 141.


LaTeX Warning: Reference `GtMatchSW' on page 28 undefined on input line 143.


LaTeX Warning: Reference `GtMatchVisitor' on page 28 undefined on input line 14
5.


LaTeX Warning: Reference `GtMergeFeatureStream' on page 28 undefined on input l
ine 147.


LaTeX Warning: Reference `GtMergeStream' on page 28 undefined on input line 149
.


LaTeX Warning: Reference `GtMetaNode' on page 28 undefined on input line 151.


LaTeX Warning: Reference `GtMutex' on page 28 undefined on input line 153.


LaTeX Warning: Reference `GtNodeStream' on page 28 undefined on input line 155.



LaTeX Warning: Reference `GtNodeStreamClass' on page 28 undefined on input line
 157.


LaTeX Warning: Reference `GtNodeVisitor' on page 28 undefined on input line 159
.

[28]

LaTeX Warning: Reference `GtORFIterator' on page 29 undefined on input line 161
.


LaTeX Warning: Reference `GtOption' on page 29 undefined on input line 163.


LaTeX Warning: Reference `GtOptionParser' on page 29 undefined on input line 16
5.


LaTeX Warning: Reference `GtOutputFileInfo' on page 29 undefined on input line 
167.


LaTeX Warning: Reference `GtPhase' on page 29 undefined on input line 169.


LaTeX Warning: Reference `GtQueue' on page 29 undefined on input line 171.


LaTeX Warning: Reference `GtRDBMySQL' on page 29 undefined on input line 173.


LaTeX Warning: Reference `GtRDBSqlite' on page 29 undefined on input line 175.


LaTeX Warning: Reference `GtRDBVisitor' on page 29 undefined on input line 177.



LaTeX Warning: Reference `GtRWLock' on page 29 undefined on input line 179.


LaTeX Warning: Reference `GtRange' on page 29 undefined on input line 181.


LaTeX Warning: Reference `GtReadmode' on page 29 undefined on input line 183.


LaTeX Warning: Reference `GtRecMap' on page 29 undefined on input line 185.


LaTeX Warning: Reference `GtRegionMapping' on page 29 undefined on input line 1
87.


LaTeX Warning: Reference `GtRegionNode' on page 29 undefined on input line 189.



LaTeX Warning: Reference `GtScriptWrapperStream' on page 29 undefined on input 
line 191.


LaTeX Warning: Reference `GtScriptWrapperVisitor' on page 29 undefined on input
 line 193.


LaTeX Warning: Reference `GtSelectStream' on page 29 undefined on input line 19
5.


LaTeX Warning: Reference `GtSeqIterator' on page 29 undefined on input line 197
.


LaTeX Warning: Reference `GtSeqIteratorFastQ' on page 29 undefined on input lin
e 199.


LaTeX Warning: Reference `GtSeqIteratorSequenceBuffer' on page 29 undefined on 
input line 201.


LaTeX Warning: Reference `GtSequenceNode' on page 29 undefined on input line 20
3.


LaTeX Warning: Reference `GtSetSourceVisitor' on page 29 undefined on input lin
e 205.


LaTeX Warning: Reference `GtSortStream' on page 29 undefined on input line 207.



LaTeX Warning: Reference `GtSplitter' on page 29 undefined on input line 209.


LaTeX Warning: Reference `GtStatStream' on page 29 undefined on input line 211.



LaTeX Warning: Reference `GtStr' on page 29 undefined on input line 213.

[29]

LaTeX Warning: Reference `GtStrArray' on page 30 undefined on input line 215.


LaTeX Warning: Reference `GtStrand' on page 30 undefined on input line 217.


LaTeX Warning: Reference `GtStyle' on page 30 undefined on input line 219.


LaTeX Warning: Reference `GtTagValueMap' on page 30 undefined on input line 221
.


LaTeX Warning: Reference `GtTextWidthCalculator' on page 30 undefined on input 
line 223.


LaTeX Warning: Reference `GtTextWidthCalculatorCairo' on page 30 undefined on i
nput line 225.


LaTeX Warning: Reference `GtThread' on page 30 undefined on input line 227.


LaTeX Warning: Reference `GtTimer' on page 30 undefined on input line 229.


LaTeX Warning: Reference `GtTool' on page 30 undefined on input line 231.


LaTeX Warning: Reference `GtToolbox' on page 30 undefined on input line 233.


LaTeX Warning: Reference `GtTransTable' on page 30 undefined on input line 235.



LaTeX Warning: Reference `GtTranslator' on page 30 undefined on input line 237.



LaTeX Warning: Reference `GtTypeChecker' on page 30 undefined on input line 239
.


LaTeX Warning: Reference `GtTypeCheckerOBO' on page 30 undefined on input line 
241.


LaTeX Warning: Reference `GtUniqStream' on page 30 undefined on input line 243.



LaTeX Warning: Reference `GtVisitorStream' on page 30 undefined on input line 2
45.


LaTeX Warning: Reference `GtXRFChecker' on page 30 undefined on input line 247.



LaTeX Warning: Reference `Array2dim' on page 30 undefined on input line 253.


LaTeX Warning: Reference `Assert' on page 30 undefined on input line 255.


LaTeX Warning: Reference `Bsearch' on page 30 undefined on input line 257.


LaTeX Warning: Reference `BytePopcount' on page 30 undefined on input line 259.



LaTeX Warning: Reference `ByteSelect' on page 30 undefined on input line 261.


LaTeX Warning: Reference `Countingsort' on page 30 undefined on input line 263.



LaTeX Warning: Reference `Cstr' on page 30 undefined on input line 265.


LaTeX Warning: Reference `Deprecated' on page 30 undefined on input line 267.

[30]

LaTeX Warning: Reference `Endianess' on page 31 undefined on input line 269.


LaTeX Warning: Reference `FASTA' on page 31 undefined on input line 271.


LaTeX Warning: Reference `Fileutils' on page 31 undefined on input line 273.


LaTeX Warning: Reference `FunctionPointer' on page 31 undefined on input line 2
75.


LaTeX Warning: Reference `Grep' on page 31 undefined on input line 277.


LaTeX Warning: Reference `Init' on page 31 undefined on input line 279.


LaTeX Warning: Reference `Log' on page 31 undefined on input line 281.


LaTeX Warning: Reference `MD5Fingerprint' on page 31 undefined on input line 28
3.


LaTeX Warning: Reference `MemoryAllocation' on page 31 undefined on input line 
285.


LaTeX Warning: Reference `Msort' on page 31 undefined on input line 287.


LaTeX Warning: Reference `Multithread' on page 31 undefined on input line 289.


LaTeX Warning: Reference `POSIX' on page 31 undefined on input line 291.


LaTeX Warning: Reference `Parseutils' on page 31 undefined on input line 293.


LaTeX Warning: Reference `Qsort' on page 31 undefined on input line 295.


LaTeX Warning: Reference `Reverse' on page 31 undefined on input line 297.


LaTeX Warning: Reference `Strcmp' on page 31 undefined on input line 299.


LaTeX Warning: Reference `Symbol' on page 31 undefined on input line 301.


LaTeX Warning: Reference `Threads' on page 31 undefined on input line 303.


LaTeX Warning: Reference `Undef' on page 31 undefined on input line 305.


LaTeX Warning: Reference `Unused' on page 31 undefined on input line 307.


LaTeX Warning: Reference `Version' on page 31 undefined on input line 309.


LaTeX Warning: Reference `Warning' on page 31 undefined on input line 311.


LaTeX Warning: Reference `XANSI' on page 31 undefined on input line 313.


Underfull \hbox (badness 10000) in paragraph at lines 321--322
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]gfflike[]get[]all[]features([]GtF
eatureIndex *gfi, GtArray

Underfull \hbox (badness 10000) in paragraph at lines 321--322


Underfull \hbox (badness 10000) in paragraph at lines 333--334
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]dup[]feature[]stream[]new([]GtNodeStrea
m*, const char

Underfull \hbox (badness 10000) in paragraph at lines 333--334


Underfull \hbox (badness 10000) in paragraph at lines 343--344


Underfull \hbox (badness 10000) in paragraph at lines 354--355

[31]
Underfull \hbox (badness 10000) in paragraph at lines 376--377


Underfull \hbox (badness 10000) in paragraph at lines 394--395


Underfull \hbox (badness 10000) in paragraph at lines 403--404


Underfull \hbox (badness 10000) in paragraph at lines 412--413


Underfull \hbox (badness 10000) in paragraph at lines 421--422


Underfull \hbox (badness 10000) in paragraph at lines 432--433
[]\OT1/cmtt/m/n/10.95 GtAlphabet* gt[]alphabet[]new[]from[]file[]no[]suffix([]c
onst char *filename,

Underfull \hbox (badness 10000) in paragraph at lines 432--433


Underfull \hbox (badness 10000) in paragraph at lines 443--444
[]\OT1/cmtt/m/n/10.95 GtAlphabet* gt[]alphabet[]new[]from[]string([]const char 
*alphadef, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 443--444


Underfull \hbox (badness 10000) in paragraph at lines 454--455
[]\OT1/cmtt/m/n/10.95 GtAlphabet* gt[]alphabet[]new[]from[]sequence([]const GtS
trArray *filenametab,

Underfull \hbox (badness 10000) in paragraph at lines 454--455


Underfull \hbox (badness 10000) in paragraph at lines 466--467


Underfull \hbox (badness 10000) in paragraph at lines 476--477


Underfull \hbox (badness 10000) in paragraph at lines 485--486


Underfull \hbox (badness 10000) in paragraph at lines 495--496


Underfull \hbox (badness 10000) in paragraph at lines 505--506
[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]add[]mapping([]GtAlphabet *alphabet, c
onst char

Underfull \hbox (badness 10000) in paragraph at lines 505--506


Underfull \hbox (badness 10000) in paragraph at lines 515--516


Underfull \hbox (badness 10000) in paragraph at lines 524--525


Underfull \hbox (badness 10000) in paragraph at lines 534--535


Underfull \hbox (badness 10000) in paragraph at lines 543--544


Underfull \hbox (badness 10000) in paragraph at lines 552--553


Underfull \hbox (badness 10000) in paragraph at lines 561--562


Underfull \hbox (badness 10000) in paragraph at lines 570--571


Underfull \hbox (badness 10000) in paragraph at lines 580--581


Underfull \hbox (badness 10000) in paragraph at lines 591--592
[]\OT1/cmtt/m/n/10.95 int gt[]alphabet[]to[]file([]const GtAlphabet *alphabet, 
const char

Underfull \hbox (badness 10000) in paragraph at lines 591--592


Underfull \hbox (badness 10000) in paragraph at lines 601--602


Underfull \hbox (badness 10000) in paragraph at lines 612--613
[]\OT1/cmtt/m/n/10.95 GtUchar gt[]alphabet[]pretty[]symbol([]const GtAlphabet *
alphabet, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 612--613


Underfull \hbox (badness 10000) in paragraph at lines 623--624
[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]echo[]pretty[]symbol([]const GtAlphabe
t *alphabet, FILE

Underfull \hbox (badness 10000) in paragraph at lines 623--624


Underfull \hbox (badness 10000) in paragraph at lines 633--634


Underfull \hbox (badness 10000) in paragraph at lines 645--646


Underfull \hbox (badness 10000) in paragraph at lines 656--657


Underfull \hbox (badness 10000) in paragraph at lines 665--666


Underfull \hbox (badness 10000) in paragraph at lines 675--676


Underfull \hbox (badness 10000) in paragraph at lines 685--686
[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]encode[]seq([]const GtAlphabet *alphab
et, GtUchar *out,

Underfull \hbox (badness 10000) in paragraph at lines 685--686


Underfull \hbox (badness 10000) in paragraph at lines 698--699
[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]decode[]seq[]to[]fp([]const GtAlphabet
 *alphabet, FILE *fpout,

Underfull \hbox (badness 10000) in paragraph at lines 698--699


Underfull \hbox (badness 10000) in paragraph at lines 713--714
[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]decode[]seq[]to[]cstr([]const GtAlphab
et *alphabet, char

Underfull \hbox (badness 10000) in paragraph at lines 713--714


Underfull \hbox (badness 10000) in paragraph at lines 728--729
[]\OT1/cmtt/m/n/10.95 GtStr* gt[]alphabet[]decode[]seq[]to[]str([]const GtAlpha
bet *alphabet, const

Underfull \hbox (badness 10000) in paragraph at lines 728--729


Underfull \hbox (badness 10000) in paragraph at lines 738--739

[32] [33] [34]
Underfull \hbox (badness 10000) in paragraph at lines 757--758


Underfull \hbox (badness 10000) in paragraph at lines 775--776
[]\OT1/cmtt/m/n/10.95 GtFeatureIndex* gt[]anno[]db[]schema[]get[]feature[]index
([]GtAnnoDBSchema

Underfull \hbox (badness 10000) in paragraph at lines 775--776


Underfull \hbox (badness 10000) in paragraph at lines 786--787

[35]
Underfull \hbox (badness 10000) in paragraph at lines 803--804


Underfull \hbox (badness 10000) in paragraph at lines 812--813


Underfull \hbox (badness 10000) in paragraph at lines 822--823


Underfull \hbox (badness 10000) in paragraph at lines 831--832


Underfull \hbox (badness 10000) in paragraph at lines 841--842


Underfull \hbox (badness 10000) in paragraph at lines 850--851


Underfull \hbox (badness 10000) in paragraph at lines 859--860


Underfull \hbox (badness 10000) in paragraph at lines 868--869


Underfull \hbox (badness 10000) in paragraph at lines 878--879


Underfull \hbox (badness 10000) in paragraph at lines 889--890


Underfull \hbox (badness 10000) in paragraph at lines 901--902


Underfull \hbox (badness 10000) in paragraph at lines 911--912


Underfull \hbox (badness 10000) in paragraph at lines 922--923


Underfull \hbox (badness 10000) in paragraph at lines 934--935


Underfull \hbox (badness 10000) in paragraph at lines 943--944


Underfull \hbox (badness 5563) in paragraph at lines 947--949
[]\OT1/ptm/m/n/10.95 Set the size of \OT1/cmtt/m/n/10.95 array \OT1/ptm/m/n/10.
95 to \OT1/cmtt/m/n/10.95 size\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 size \OT
1/ptm/m/n/10.95 must be smaller or equal than

Underfull \hbox (badness 10000) in paragraph at lines 953--954


Underfull \hbox (badness 10000) in paragraph at lines 962--963


Underfull \hbox (badness 10000) in paragraph at lines 971--972


Underfull \hbox (badness 10000) in paragraph at lines 981--982


Underfull \hbox (badness 10000) in paragraph at lines 990--991


Underfull \hbox (badness 10000) in paragraph at lines 1000--1001
[]\OT1/cmtt/m/n/10.95 void gt[]array[]sort[]with[]data([]GtArray *array, GtComp
areWithData compar,

Underfull \hbox (badness 10000) in paragraph at lines 1000--1001


Underfull \hbox (badness 10000) in paragraph at lines 1011--1012
[]\OT1/cmtt/m/n/10.95 void gt[]array[]sort[]stable[]with[]data([]GtArray *array
, GtCompareWithData

Underfull \hbox (badness 10000) in paragraph at lines 1011--1012


Underfull \hbox (badness 10000) in paragraph at lines 1021--1022


Underfull \hbox (badness 10000) in paragraph at lines 1032--1033

[36] [37]
Overfull \hbox (7.61789pt too wide) in paragraph at lines 1043--1046
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. \OT1/cmtt/m/n/10.95 GtArrayOutStream \OT1/ptm/m/n/10.95 tak
es an ar-ray of \OT1/cmtt/m/n/10.95 GtGenomeNodes

Underfull \hbox (badness 10000) in paragraph at lines 1052--1053
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]in[]stream[]new([]GtArray *nodes
, GtUword *progress,

Underfull \hbox (badness 10000) in paragraph at lines 1052--1053


Underfull \hbox (badness 10000) in paragraph at lines 1074--1075
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]out[]stream[]new([]GtNodeStream 
*in[]stream, GtArray

Underfull \hbox (badness 10000) in paragraph at lines 1074--1075


Underfull \hbox (badness 10000) in paragraph at lines 1086--1087
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]out[]stream[]all[]new([]GtNodeSt
ream *in[]stream, GtArray

Underfull \hbox (badness 10000) in paragraph at lines 1086--1087

[38]
Underfull \hbox (badness 10000) in paragraph at lines 1103--1104


Underfull \hbox (badness 10000) in paragraph at lines 1115--1116
[]\OT1/cmtt/m/n/10.95 void gt[]bed[]in[]stream[]set[]feature[]type([]GtBEDInStr
eam *bed[]in[]stream, const

Underfull \hbox (badness 10000) in paragraph at lines 1115--1116


Underfull \hbox (badness 10000) in paragraph at lines 1127--1128
[]\OT1/cmtt/m/n/10.95 void gt[]bed[]in[]stream[]set[]thick[]feature[]type([]GtB
EDInStream *bed[]in[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 1127--1128


Underfull \hbox (badness 10000) in paragraph at lines 1138--1139
[]\OT1/cmtt/m/n/10.95 void gt[]bed[]in[]stream[]set[]block[]type([]GtBEDInStrea
m *bed[]in[]stream, const

Underfull \hbox (badness 10000) in paragraph at lines 1138--1139


Underfull \hbox (badness 10000) in paragraph at lines 1155--1156


Underfull \hbox (badness 10000) in paragraph at lines 1165--1166


Underfull \hbox (badness 10000) in paragraph at lines 1174--1175


Underfull \hbox (badness 10000) in paragraph at lines 1183--1184


Underfull \hbox (badness 10000) in paragraph at lines 1192--1193


Underfull \hbox (badness 10000) in paragraph at lines 1202--1203
[]\OT1/cmtt/m/n/10.95 void gt[]bittab[]and([]GtBittab *bittab[]a, const GtBitta
b *bittab[]b, const

Underfull \hbox (badness 10000) in paragraph at lines 1202--1203


Underfull \hbox (badness 10000) in paragraph at lines 1212--1213
[]\OT1/cmtt/m/n/10.95 void gt[]bittab[]or([]GtBittab *bittab[]a, const GtBittab
 *bittab[]b, const

Underfull \hbox (badness 10000) in paragraph at lines 1212--1213


Underfull \hbox (badness 10000) in paragraph at lines 1222--1223
[]\OT1/cmtt/m/n/10.95 void gt[]bittab[]nand([]GtBittab *bittab[]a, const GtBitt
ab *bittab[]b, const

Underfull \hbox (badness 10000) in paragraph at lines 1222--1223


Underfull \hbox (badness 10000) in paragraph at lines 1231--1232


Underfull \hbox (badness 10000) in paragraph at lines 1240--1241


Underfull \hbox (badness 10000) in paragraph at lines 1249--1250


Underfull \hbox (badness 10000) in paragraph at lines 1258--1259


Underfull \hbox (badness 10000) in paragraph at lines 1267--1268


Underfull \hbox (badness 10000) in paragraph at lines 1276--1277


Underfull \hbox (badness 10000) in paragraph at lines 1285--1286


Underfull \hbox (badness 10000) in paragraph at lines 1294--1295


Underfull \hbox (badness 10000) in paragraph at lines 1303--1304


Underfull \hbox (badness 10000) in paragraph at lines 1312--1313


Underfull \hbox (badness 10000) in paragraph at lines 1321--1322


Underfull \hbox (badness 10000) in paragraph at lines 1330--1331


Underfull \hbox (badness 10000) in paragraph at lines 1340--1341


Underfull \hbox (badness 10000) in paragraph at lines 1349--1350


Underfull \hbox (badness 10000) in paragraph at lines 1358--1359

[39] [40]
Underfull \hbox (badness 10000) in paragraph at lines 1377--1378


Underfull \hbox (badness 10000) in paragraph at lines 1386--1387


Underfull \hbox (badness 10000) in paragraph at lines 1395--1396


Underfull \hbox (badness 10000) in paragraph at lines 1405--1406


Underfull \hbox (badness 10000) in paragraph at lines 1414--1415


Underfull \hbox (badness 10000) in paragraph at lines 1423--1424


Underfull \hbox (badness 10000) in paragraph at lines 1432--1433


Underfull \hbox (badness 10000) in paragraph at lines 1441--1442


Underfull \hbox (badness 10000) in paragraph at lines 1450--1451


Underfull \hbox (badness 10000) in paragraph at lines 1459--1460


Underfull \hbox (badness 10000) in paragraph at lines 1468--1469


Underfull \hbox (badness 10000) in paragraph at lines 1477--1478


Underfull \hbox (badness 10000) in paragraph at lines 1486--1487


Underfull \hbox (badness 10000) in paragraph at lines 1495--1496


Underfull \hbox (badness 10000) in paragraph at lines 1504--1505


Underfull \hbox (badness 10000) in paragraph at lines 1513--1514


Underfull \hbox (badness 10000) in paragraph at lines 1522--1523


Underfull \hbox (badness 10000) in paragraph at lines 1531--1532

[41]
Underfull \hbox (badness 10000) in paragraph at lines 1553--1554
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]cds[]stream[]new([]GtNodeStream *in[]st
ream, GtRegionMapping

Underfull \hbox (badness 10000) in paragraph at lines 1553--1554
\OT1/cmtt/m/n/10.95 *region[]mapping, unsigned int minorflen, const char *sourc
e, bool

Underfull \hbox (badness 10000) in paragraph at lines 1553--1554

[42]
Underfull \hbox (badness 10000) in paragraph at lines 1581--1582
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]csa[]stream[]new([]GtNodeStream *in[]st
ream, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 1581--1582


Underfull \hbox (badness 10000) in paragraph at lines 1601--1602


Underfull \hbox (badness 10000) in paragraph at lines 1610--1611


Underfull \hbox (badness 10000) in paragraph at lines 1633--1634
[]\OT1/cmtt/m/n/10.95 GtCanvas* gt[]canvas[]cairo[]context[]new([]GtStyle *styl
e, cairo[]t *context,

Underfull \hbox (badness 10000) in paragraph at lines 1633--1634
\OT1/cmtt/m/n/10.95 double offsetpos, GtUword width, GtUword height, GtImageInf
o *image[]info,

Underfull \hbox (badness 10000) in paragraph at lines 1633--1634

[43]
Underfull \hbox (badness 10000) in paragraph at lines 1658--1659
[]\OT1/cmtt/m/n/10.95 GtCanvas* gt[]canvas[]cairo[]file[]new([]GtStyle *style, 
GtGraphicsOutType

Underfull \hbox (badness 10000) in paragraph at lines 1658--1659
\OT1/cmtt/m/n/10.95 output[]type, GtUword width, GtUword height, GtImageInfo *i
mage[]info,

Underfull \hbox (badness 10000) in paragraph at lines 1658--1659


Underfull \hbox (badness 10000) in paragraph at lines 1673--1674
[]\OT1/cmtt/m/n/10.95 int gt[]canvas[]cairo[]file[]to[]file([]GtCanvasCairoFile
 *canvas, const char

Underfull \hbox (badness 10000) in paragraph at lines 1673--1674


Underfull \hbox (badness 10000) in paragraph at lines 1684--1685
[]\OT1/cmtt/m/n/10.95 int gt[]canvas[]cairo[]file[]to[]stream([]GtCanvasCairoFi
le *canvas, GtStr

Underfull \hbox (badness 10000) in paragraph at lines 1684--1685


Underfull \hbox (badness 10000) in paragraph at lines 1700--1701


Underfull \hbox (badness 10000) in paragraph at lines 1717--1718
[]\OT1/cmtt/m/n/10.95 GtUword gt[]codon[]iterator[]current[]position([]GtCodonI
terator

Underfull \hbox (badness 10000) in paragraph at lines 1717--1718


Underfull \hbox (badness 10000) in paragraph at lines 1728--1729


Underfull \hbox (badness 10000) in paragraph at lines 1738--1739


Underfull \hbox (badness 10000) in paragraph at lines 1751--1752
[]\OT1/cmtt/m/n/10.95 GtCodonIteratorStatus gt[]codon[]iterator[]next([]GtCodon
Iterator

Underfull \hbox (badness 10000) in paragraph at lines 1751--1752
\OT1/cmtt/m/n/10.95 *codon[]iterator, char *n1, char *n2, char *n3, unsigned in
t *frame,

Underfull \hbox (badness 10000) in paragraph at lines 1751--1752


Underfull \hbox (badness 10000) in paragraph at lines 1770--1771

[44]
Underfull \hbox (badness 10000) in paragraph at lines 1784--1785
[]\OT1/cmtt/m/n/10.95 GtCodonIterator* gt[]codon[]iterator[]encseq[]new([]GtEnc
seq *encseq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 1784--1785


Underfull \hbox (badness 10000) in paragraph at lines 1799--1800
[]\OT1/cmtt/m/n/10.95 GtCodonIterator* gt[]codon[]iterator[]encseq[]new[]with[]
readmode([]GtEncseq

Underfull \hbox (badness 10000) in paragraph at lines 1799--1800
\OT1/cmtt/m/n/10.95 *encseq, GtUword startpos, GtUword length, GtReadmode readm
ode, GtError

Underfull \hbox (badness 10000) in paragraph at lines 1799--1800


Underfull \hbox (badness 10000) in paragraph at lines 1815--1816
[]\OT1/cmtt/m/n/10.95 GtCodonIterator* gt[]codon[]iterator[]simple[]new([]const
 char *seq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 1815--1816

[45]
Underfull \hbox (badness 10000) in paragraph at lines 1832--1833
[]\OT1/cmtt/m/n/10.95 GtColor* gt[]color[]new([]double red, double green, doubl
e blue, double

Underfull \hbox (badness 10000) in paragraph at lines 1832--1833


Underfull \hbox (badness 10000) in paragraph at lines 1844--1845
[]\OT1/cmtt/m/n/10.95 void gt[]color[]set([]GtColor *color, double red, double 
green, double blue,

Underfull \hbox (badness 10000) in paragraph at lines 1844--1845


Underfull \hbox (badness 10000) in paragraph at lines 1855--1856


Underfull \hbox (badness 10000) in paragraph at lines 1864--1865


Underfull \hbox (badness 10000) in paragraph at lines 1881--1882


Underfull \hbox (badness 10000) in paragraph at lines 1893--1894


Underfull \hbox (badness 10000) in paragraph at lines 1902--1903


Underfull \hbox (badness 10000) in paragraph at lines 1914--1915

[46]
Underfull \hbox (badness 10000) in paragraph at lines 1931--1932


Underfull \hbox (badness 10000) in paragraph at lines 1940--1941


Underfull \hbox (badness 10000) in paragraph at lines 1949--1950


Underfull \hbox (badness 10000) in paragraph at lines 1959--1960


Underfull \hbox (badness 10000) in paragraph at lines 1969--1970


Underfull \hbox (badness 10000) in paragraph at lines 1978--1979


Underfull \hbox (badness 10000) in paragraph at lines 1987--1988


Underfull \hbox (badness 10000) in paragraph at lines 2006--2007


Underfull \hbox (badness 10000) in paragraph at lines 2015--2016

[47]
Underfull \hbox (badness 10000) in paragraph at lines 2038--2039
[]\OT1/cmtt/m/n/10.95 GtCustomTrack* gt[]custom[]track[]gc[]content[]new([]cons
t char *seq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 2038--2039


Underfull \hbox (badness 10000) in paragraph at lines 2068--2069
[]\OT1/cmtt/m/n/10.95 GtCustomTrack* gt[]custom[]track[]script[]wrapper[]new([]
GtCtScriptRenderFunc

Underfull \hbox (badness 10000) in paragraph at lines 2068--2069
\OT1/cmtt/m/n/10.95 render[]func, GtCtScriptGetHeightFunc get[]height[]func,

Underfull \hbox (badness 10000) in paragraph at lines 2068--2069


Underfull \hbox (badness 10000) in paragraph at lines 2090--2091
[]\OT1/cmtt/m/n/10.95 GtDiagram* gt[]diagram[]new([]GtFeatureIndex *feature[]in
dex, const char

Underfull \hbox (badness 10000) in paragraph at lines 2090--2091


Underfull \hbox (badness 10000) in paragraph at lines 2103--2104
[]\OT1/cmtt/m/n/10.95 GtDiagram* gt[]diagram[]new[]from[]array([]GtArray *featu
res, const GtRange

Underfull \hbox (badness 10000) in paragraph at lines 2103--2104


Underfull \hbox (badness 10000) in paragraph at lines 2115--2116


Underfull \hbox (badness 10000) in paragraph at lines 2125--2126
[]\OT1/cmtt/m/n/10.95 void gt[]diagram[]set[]track[]selector[]func([]GtDiagram*
, GtTrackSelectorFunc,

Underfull \hbox (badness 10000) in paragraph at lines 2125--2126


Underfull \hbox (badness 10000) in paragraph at lines 2136--2137


Underfull \hbox (badness 10000) in paragraph at lines 2146--2147


Underfull \hbox (badness 10000) in paragraph at lines 2155--2156

[48]
Underfull \hbox (badness 10000) in paragraph at lines 2174--2175


Underfull \hbox (badness 10000) in paragraph at lines 2184--2185


Underfull \hbox (badness 10000) in paragraph at lines 2193--2194


Underfull \hbox (badness 10000) in paragraph at lines 2203--2204
[]\OT1/cmtt/m/n/10.95 void gt[]disc[]distri[]add[]multi([]GtDiscDistri *d, GtUw
ord key, GtUint64

Underfull \hbox (badness 10000) in paragraph at lines 2203--2204


Underfull \hbox (badness 10000) in paragraph at lines 2212--2213


Underfull \hbox (badness 10000) in paragraph at lines 2221--2222


Underfull \hbox (badness 10000) in paragraph at lines 2233--2234
[]\OT1/cmtt/m/n/10.95 void gt[]disc[]distri[]foreach([]const GtDiscDistri *d, G
tDiscDistriIterFunc

Underfull \hbox (badness 10000) in paragraph at lines 2233--2234


Underfull \hbox (badness 10000) in paragraph at lines 2246--2247
[]\OT1/cmtt/m/n/10.95 void gt[]disc[]distri[]foreach[]in[]reverse[]order([]cons
t GtDiscDistri *d,

Underfull \hbox (badness 10000) in paragraph at lines 2246--2247

[49]
Underfull \hbox (badness 10000) in paragraph at lines 2263--2264


Underfull \hbox (badness 10000) in paragraph at lines 2273--2274


Underfull \hbox (badness 10000) in paragraph at lines 2284--2285


Underfull \hbox (badness 10000) in paragraph at lines 2293--2294


Underfull \hbox (badness 10000) in paragraph at lines 2302--2303


Underfull \hbox (badness 10000) in paragraph at lines 2312--2313


Underfull \hbox (badness 10000) in paragraph at lines 2321--2322


Underfull \hbox (badness 10000) in paragraph at lines 2331--2332


Underfull \hbox (badness 10000) in paragraph at lines 2340--2341


Underfull \hbox (badness 10000) in paragraph at lines 2349--2350

[50]
Underfull \hbox (badness 10000) in paragraph at lines 2360--2361


Underfull \hbox (badness 10000) in paragraph at lines 2370--2371


Underfull \hbox (badness 10000) in paragraph at lines 2380--2381


Underfull \hbox (badness 10000) in paragraph at lines 2397--2398


Underfull \hbox (badness 10000) in paragraph at lines 2406--2407

[51]
Underfull \hbox (badness 10000) in paragraph at lines 2442--2443


Underfull \hbox (badness 10000) in paragraph at lines 2452--2453


Underfull \hbox (badness 10000) in paragraph at lines 2462--2463


Underfull \hbox (badness 10000) in paragraph at lines 2473--2474
[]\OT1/cmtt/m/n/10.95 GtUchar gt[]encseq[]get[]encoded[]char([]const GtEncseq *
encseq, GtUword pos,

Underfull \hbox (badness 10000) in paragraph at lines 2473--2474


Underfull \hbox (badness 10000) in paragraph at lines 2485--2486
[]\OT1/cmtt/m/n/10.95 char gt[]encseq[]get[]decoded[]char([]const GtEncseq *enc
seq, GtUword pos,

Underfull \hbox (badness 10000) in paragraph at lines 2485--2486


Underfull \hbox (badness 10000) in paragraph at lines 2497--2498
[]\OT1/cmtt/m/n/10.95 bool gt[]encseq[]position[]is[]separator([]const GtEncseq
 *encseq, GtUword pos,

Underfull \hbox (badness 10000) in paragraph at lines 2497--2498


Underfull \hbox (badness 10000) in paragraph at lines 2509--2510
[]\OT1/cmtt/m/n/10.95 bool gt[]encseq[]position[]is[]wildcard([]const GtEncseq 
*encseq, GtUword pos,

Underfull \hbox (badness 10000) in paragraph at lines 2509--2510


Underfull \hbox (badness 10000) in paragraph at lines 2519--2520


Underfull \hbox (badness 10000) in paragraph at lines 2530--2531
[]\OT1/cmtt/m/n/10.95 GtEncseqReader* gt[]encseq[]create[]reader[]with[]readmod
e([]const GtEncseq

Underfull \hbox (badness 10000) in paragraph at lines 2530--2531


Underfull \hbox (badness 10000) in paragraph at lines 2546--2547
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]extract[]encoded([]const GtEncseq *encse
q, GtUchar *buffer,

Underfull \hbox (badness 10000) in paragraph at lines 2546--2547


Underfull \hbox (badness 10000) in paragraph at lines 2561--2562
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]extract[]decoded([]const GtEncseq *encse
q, char *buffer,

Underfull \hbox (badness 10000) in paragraph at lines 2561--2562


Underfull \hbox (badness 10000) in paragraph at lines 2576--2577


Underfull \hbox (badness 10000) in paragraph at lines 2586--2587


Underfull \hbox (badness 10000) in paragraph at lines 2595--2596


Underfull \hbox (badness 10000) in paragraph at lines 2604--2605


Underfull \hbox (badness 10000) in paragraph at lines 2613--2614


Underfull \hbox (badness 10000) in paragraph at lines 2622--2623


Underfull \hbox (badness 10000) in paragraph at lines 2632--2633


Underfull \hbox (badness 10000) in paragraph at lines 2643--2644


Underfull \hbox (badness 10000) in paragraph at lines 2655--2656
[]\OT1/cmtt/m/n/10.95 const char* gt[]encseq[]description([]const GtEncseq *enc
seq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 2655--2656


Underfull \hbox (badness 10000) in paragraph at lines 2668--2669


Underfull \hbox (badness 10000) in paragraph at lines 2678--2679


Underfull \hbox (badness 10000) in paragraph at lines 2688--2689
[]\OT1/cmtt/m/n/10.95 GtUint64 gt[]encseq[]effective[]filelength([]const GtEncs
eq *encseq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 2688--2689


Underfull \hbox (badness 10000) in paragraph at lines 2699--2700


Underfull \hbox (badness 10000) in paragraph at lines 2710--2711


Underfull \hbox (badness 10000) in paragraph at lines 2721--2722
[]\OT1/cmtt/m/n/10.95 GtUword gt[]encseq[]filenum[]first[]seqnum([]const GtEncs
eq *encseq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 2721--2722


Underfull \hbox (badness 10000) in paragraph at lines 2731--2732


Underfull \hbox (badness 10000) in paragraph at lines 2740--2741


Underfull \hbox (badness 10000) in paragraph at lines 2751--2752


Underfull \hbox (badness 10000) in paragraph at lines 2761--2762


Underfull \hbox (badness 10000) in paragraph at lines 2771--2772


Underfull \hbox (badness 10000) in paragraph at lines 2781--2782


Underfull \hbox (badness 10000) in paragraph at lines 2790--2791

[52] [53] [54]
Underfull \hbox (badness 10000) in paragraph at lines 2807--2808


Underfull \hbox (badness 10000) in paragraph at lines 2817--2818


Underfull \hbox (badness 10000) in paragraph at lines 2829--2830


Underfull \hbox (badness 10000) in paragraph at lines 2841--2842


Underfull \hbox (badness 10000) in paragraph at lines 2852--2853


Underfull \hbox (badness 10000) in paragraph at lines 2864--2865


Underfull \hbox (badness 10000) in paragraph at lines 2874--2875


Underfull \hbox (badness 10000) in paragraph at lines 2883--2884


Underfull \hbox (badness 10000) in paragraph at lines 2892--2893


Underfull \hbox (badness 10000) in paragraph at lines 2901--2902


Underfull \hbox (badness 10000) in paragraph at lines 2910--2911


Underfull \hbox (badness 10000) in paragraph at lines 2919--2920


Underfull \hbox (badness 10000) in paragraph at lines 2929--2930


Underfull \hbox (badness 10000) in paragraph at lines 2941--2942
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]cstr([]GtEncseqBuilder *eb
, const char *str,

Underfull \hbox (badness 10000) in paragraph at lines 2941--2942


Underfull \hbox (badness 10000) in paragraph at lines 2956--2957
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]str([]GtEncseqBuilder *eb,
 GtStr *str, const

Underfull \hbox (badness 10000) in paragraph at lines 2956--2957


Underfull \hbox (badness 10000) in paragraph at lines 2973--2974
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]encoded([]GtEncseqBuilder 
*eb, const GtUchar

Underfull \hbox (badness 10000) in paragraph at lines 2973--2974


Underfull \hbox (badness 10000) in paragraph at lines 2990--2991
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]encoded[]own([]GtEncseqBui
lder *eb, const GtUchar

Underfull \hbox (badness 10000) in paragraph at lines 2990--2991


Underfull \hbox (badness 10000) in paragraph at lines 3007--3008
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]multiple[]encoded([]GtEncs
eqBuilder *eb, const

Underfull \hbox (badness 10000) in paragraph at lines 3007--3008


Underfull \hbox (badness 10000) in paragraph at lines 3019--3020


Underfull \hbox (badness 10000) in paragraph at lines 3029--3030


Underfull \hbox (badness 10000) in paragraph at lines 3042--3043


Underfull \hbox (badness 10000) in paragraph at lines 3052--3053

[55] [56]
Underfull \hbox (badness 10000) in paragraph at lines 3070--3071


Underfull \hbox (badness 10000) in paragraph at lines 3079--3080


Underfull \hbox (badness 10000) in paragraph at lines 3089--3090


Underfull \hbox (badness 10000) in paragraph at lines 3100--3101
[]\OT1/cmtt/m/n/10.95 int gt[]encseq[]encoder[]use[]representation([]GtEncseqEn
coder *ee, const char

Underfull \hbox (badness 10000) in paragraph at lines 3100--3101


Underfull \hbox (badness 10000) in paragraph at lines 3111--3112


Underfull \hbox (badness 10000) in paragraph at lines 3122--3123
[]\OT1/cmtt/m/n/10.95 int gt[]encseq[]encoder[]use[]symbolmap[]file([]GtEncseqE
ncoder *ee, const char

Underfull \hbox (badness 10000) in paragraph at lines 3122--3123


Underfull \hbox (badness 10000) in paragraph at lines 3134--3135


Underfull \hbox (badness 10000) in paragraph at lines 3144--3145


Underfull \hbox (badness 10000) in paragraph at lines 3154--3155


Underfull \hbox (badness 10000) in paragraph at lines 3166--3167


Underfull \hbox (badness 10000) in paragraph at lines 3179--3180


Underfull \hbox (badness 10000) in paragraph at lines 3191--3192


Underfull \hbox (badness 10000) in paragraph at lines 3204--3205


Underfull \hbox (badness 10000) in paragraph at lines 3215--3216


Underfull \hbox (badness 3039) in paragraph at lines 3219--3224
[]\OT1/ptm/m/n/10.95 Enables sup-port for loss-less re-pro-duc-tion of the orig
-i-nal se-quence, re-gard-less

Underfull \hbox (badness 1655) in paragraph at lines 3219--3224
\OT1/ptm/m/n/10.95 of al-pha-bet trans-for-ma-tions that may ap-ply. En-coded s
e-quences cre-ated with-

Underfull \hbox (badness 2359) in paragraph at lines 3219--3224
\OT1/ptm/m/n/10.95 out this sup-port will not be able to be loaded via a \OT1/c
mtt/m/n/10.95 GtEncseqLoader \OT1/ptm/m/n/10.95 with

Underfull \hbox (badness 10000) in paragraph at lines 3228--3229


Underfull \hbox (badness 10000) in paragraph at lines 3238--3239


Underfull \hbox (badness 10000) in paragraph at lines 3249--3250


Underfull \hbox (badness 10000) in paragraph at lines 3259--3260


Underfull \hbox (badness 10000) in paragraph at lines 3268--3269


Underfull \hbox (badness 10000) in paragraph at lines 3278--3279


Underfull \hbox (badness 10000) in paragraph at lines 3288--3289


Underfull \hbox (badness 10000) in paragraph at lines 3297--3298


Underfull \hbox (badness 10000) in paragraph at lines 3307--3308


Underfull \hbox (badness 10000) in paragraph at lines 3317--3318


Underfull \hbox (badness 10000) in paragraph at lines 3326--3327


Underfull \hbox (badness 10000) in paragraph at lines 3336--3337


Underfull \hbox (badness 10000) in paragraph at lines 3346--3347


Underfull \hbox (badness 10000) in paragraph at lines 3355--3356


Underfull \hbox (badness 10000) in paragraph at lines 3365--3366


Underfull \hbox (badness 10000) in paragraph at lines 3374--3375


Underfull \hbox (badness 10000) in paragraph at lines 3383--3384


Underfull \hbox (badness 10000) in paragraph at lines 3392--3393


Underfull \hbox (badness 10000) in paragraph at lines 3401--3402


Underfull \hbox (badness 10000) in paragraph at lines 3411--3412


Underfull \hbox (badness 10000) in paragraph at lines 3423--3424
[]\OT1/cmtt/m/n/10.95 int gt[]encseq[]encoder[]encode([]GtEncseqEncoder *ee, Gt
StrArray *seqfiles,

Underfull \hbox (badness 10000) in paragraph at lines 3423--3424


Underfull \hbox (badness 10000) in paragraph at lines 3434--3435

[57] [58] [59]
Underfull \hbox (badness 10000) in paragraph at lines 3451--3452


Underfull \hbox (badness 10000) in paragraph at lines 3460--3461


Underfull \hbox (badness 10000) in paragraph at lines 3472--3473


Underfull \hbox (badness 10000) in paragraph at lines 3481--3482


Underfull \hbox (badness 10000) in paragraph at lines 3494--3495


Underfull \hbox (badness 10000) in paragraph at lines 3507--3508


Underfull \hbox (badness 10000) in paragraph at lines 3520--3521


Underfull \hbox (badness 10000) in paragraph at lines 3533--3534


Underfull \hbox (badness 10000) in paragraph at lines 3547--3548


Underfull \hbox (badness 10000) in paragraph at lines 3560--3561


Underfull \hbox (badness 10000) in paragraph at lines 3573--3574


Underfull \hbox (badness 10000) in paragraph at lines 3584--3585


Underfull \hbox (badness 10000) in paragraph at lines 3594--3595


Underfull \hbox (badness 10000) in paragraph at lines 3604--3605


Underfull \hbox (badness 10000) in paragraph at lines 3613--3614


Underfull \hbox (badness 10000) in paragraph at lines 3623--3624


Underfull \hbox (badness 10000) in paragraph at lines 3633--3634


Underfull \hbox (badness 10000) in paragraph at lines 3642--3643


Underfull \hbox (badness 10000) in paragraph at lines 3652--3653


Underfull \hbox (badness 10000) in paragraph at lines 3662--3663


Underfull \hbox (badness 10000) in paragraph at lines 3671--3672


Underfull \hbox (badness 10000) in paragraph at lines 3681--3682


Underfull \hbox (badness 10000) in paragraph at lines 3691--3692


Underfull \hbox (badness 10000) in paragraph at lines 3703--3704
[]\OT1/cmtt/m/n/10.95 GtEncseq* gt[]encseq[]loader[]load([]GtEncseqLoader *el, 
const char

Underfull \hbox (badness 10000) in paragraph at lines 3703--3704


Underfull \hbox (badness 10000) in paragraph at lines 3715--3716

[60] [61] [62]
Underfull \hbox (badness 10000) in paragraph at lines 3735--3736
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]reader[]reinit[]with[]readmode([]GtEncse
qReader *esr, const

Underfull \hbox (badness 10000) in paragraph at lines 3735--3736


Underfull \hbox (badness 10000) in paragraph at lines 3739--3741
[]\OT1/ptm/m/n/10.95 Reinitializes the given \OT1/cmtt/m/n/10.95 esr \OT1/ptm/m
/n/10.95 with the val-ues as de-scribed in

Underfull \hbox (badness 10000) in paragraph at lines 3745--3746


Underfull \hbox (badness 10000) in paragraph at lines 3755--3756


Underfull \hbox (badness 10000) in paragraph at lines 3765--3766

[63]
Underfull \hbox (badness 10000) in paragraph at lines 3791--3792


Underfull \hbox (badness 10000) in paragraph at lines 3800--3801


Underfull \hbox (badness 10000) in paragraph at lines 3812--3813


Underfull \hbox (badness 10000) in paragraph at lines 3822--3823


Underfull \hbox (badness 10000) in paragraph at lines 3832--3833


Underfull \hbox (badness 10000) in paragraph at lines 3841--3842


Underfull \hbox (badness 10000) in paragraph at lines 3850--3851


Underfull \hbox (badness 10000) in paragraph at lines 3859--3860


Underfull \hbox (badness 10000) in paragraph at lines 3868--3869


Underfull \hbox (badness 10000) in paragraph at lines 3890--3891
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]extract[]feature[]stream[]new([]GtNodeS
tream *in[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 3890--3891
\OT1/cmtt/m/n/10.95 GtRegionMapping *region[]Mapping, const char *type, bool jo
in, bool

Underfull \hbox (badness 10000) in paragraph at lines 3890--3891

[64]
Underfull \hbox (badness 10000) in paragraph at lines 3909--3910


Underfull \hbox (badness 10000) in paragraph at lines 3919--3920


Underfull \hbox (badness 10000) in paragraph at lines 3944--3945
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]add[]region[]node([]GtFeatureInde
x *feature[]index,

Underfull \hbox (badness 10000) in paragraph at lines 3944--3945


Underfull \hbox (badness 10000) in paragraph at lines 3955--3956
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]add[]feature[]node([]GtFeatureInd
ex *feature[]index,

Underfull \hbox (badness 10000) in paragraph at lines 3955--3956


Underfull \hbox (badness 10000) in paragraph at lines 3967--3968
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]remove[]node([]GtFeatureIndex *fe
ature[]index,

Underfull \hbox (badness 10000) in paragraph at lines 3967--3968


Underfull \hbox (badness 10000) in paragraph at lines 3977--3978
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]add[]gff3file([]GtFeatureIndex *f
eature[]index, const

Underfull \hbox (badness 10000) in paragraph at lines 3977--3978


Underfull \hbox (badness 10000) in paragraph at lines 3989--3990
[]\OT1/cmtt/m/n/10.95 GtArray* gt[]feature[]index[]get[]features[]for[]seqid([]
GtFeatureIndex*, const

Underfull \hbox (badness 10000) in paragraph at lines 3989--3990


Underfull \hbox (badness 10000) in paragraph at lines 4004--4005
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]get[]features[]for[]range([]GtFea
tureIndex *feature[]index,

Underfull \hbox (badness 10000) in paragraph at lines 4004--4005


Underfull \hbox (badness 10000) in paragraph at lines 4016--4017
[]\OT1/cmtt/m/n/10.95 char* gt[]feature[]index[]get[]first[]seqid([]const GtFea
tureIndex

Underfull \hbox (badness 10000) in paragraph at lines 4016--4017


Underfull \hbox (badness 10000) in paragraph at lines 4026--4027
[]\OT1/cmtt/m/n/10.95 GtStrArray* gt[]feature[]index[]get[]seqids([]const GtFea
tureIndex

Underfull \hbox (badness 10000) in paragraph at lines 4026--4027


Underfull \hbox (badness 10000) in paragraph at lines 4039--4040
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]get[]range[]for[]seqid([]GtFeatur
eIndex *feature[]index,

Underfull \hbox (badness 10000) in paragraph at lines 4039--4040


Underfull \hbox (badness 10000) in paragraph at lines 4053--4054
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]get[]orig[]range[]for[]seqid([]Gt
FeatureIndex

Underfull \hbox (badness 10000) in paragraph at lines 4053--4054


Underfull \hbox (badness 10000) in paragraph at lines 4067--4068
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]has[]seqid([]const GtFeatureIndex
 *feature[]index, bool

Underfull \hbox (badness 10000) in paragraph at lines 4067--4068


Underfull \hbox (badness 10000) in paragraph at lines 4077--4078


Underfull \hbox (badness 10000) in paragraph at lines 4088--4089

[65] [66]
Underfull \hbox (badness 10000) in paragraph at lines 4107--4108


Overfull \hbox (13.12596pt too wide) in paragraph at lines 4118--4119
[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]index[]memory[]get[]node[]by[
]ptr([]GtFeatureIndexMemory*,

Underfull \hbox (badness 10000) in paragraph at lines 4118--4119


Overfull \hbox (26.19778pt too wide) in paragraph at lines 4129--4148
\OT1/ptm/m/n/10.95 with the \OT1/cmtt/m/n/10.95 Parent \OT1/ptm/m/n/10.95 and \
OT1/cmtt/m/n/10.95 ID \OT1/ptm/m/n/10.95 at-tributes) are re-al-ized in the C A
PI with the \OT1/cmtt/m/n/10.95 gt[]feature[]node[]add[]child()

Underfull \hbox (badness 10000) in paragraph at lines 4155--4156
[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]feature[]node[]new([]GtStr *seqid, cons
t char *type, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 4155--4156


Underfull \hbox (badness 10000) in paragraph at lines 4170--4171
[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]feature[]node[]new[]pseudo([]GtStr *seq
id, GtUword start,

Underfull \hbox (badness 10000) in paragraph at lines 4170--4171


Underfull \hbox (badness 10000) in paragraph at lines 4184--4185
[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]feature[]node[]new[]pseudo[]template([]
GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4184--4185


Underfull \hbox (badness 10000) in paragraph at lines 4195--4196


Underfull \hbox (badness 10000) in paragraph at lines 4205--4206
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]add[]child([]GtFeatureNode *paren
t, GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4205--4206


Underfull \hbox (badness 10000) in paragraph at lines 4215--4216


Underfull \hbox (badness 10000) in paragraph at lines 4226--4227
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]source([]GtFeatureNode *feat
ure[]node, GtStr

Underfull \hbox (badness 10000) in paragraph at lines 4226--4227


Underfull \hbox (badness 10000) in paragraph at lines 4236--4237


Underfull \hbox (badness 10000) in paragraph at lines 4246--4247


Underfull \hbox (badness 10000) in paragraph at lines 4257--4258
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]type([]GtFeatureNode *featur
e[]node, const char

Underfull \hbox (badness 10000) in paragraph at lines 4257--4258


Underfull \hbox (badness 10000) in paragraph at lines 4267--4268
[]\OT1/cmtt/m/n/10.95 bool gt[]feature[]node[]has[]type([]GtFeatureNode *featur
e[]node, const char

Underfull \hbox (badness 10000) in paragraph at lines 4267--4268


Underfull \hbox (badness 10000) in paragraph at lines 4277--4278
[]\OT1/cmtt/m/n/10.95 GtUword gt[]feature[]node[]number[]of[]children([]const G
tFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4277--4278


Underfull \hbox (badness 10000) in paragraph at lines 4289--4290
[]\OT1/cmtt/m/n/10.95 GtUword gt[]feature[]node[]number[]of[]children[]of[]type
([]const GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4289--4290


Underfull \hbox (badness 10000) in paragraph at lines 4300--4301


Underfull \hbox (badness 10000) in paragraph at lines 4310--4311


Underfull \hbox (badness 10000) in paragraph at lines 4321--4322


Underfull \hbox (badness 10000) in paragraph at lines 4330--4331


Underfull \hbox (badness 10000) in paragraph at lines 4339--4340


Underfull \hbox (badness 10000) in paragraph at lines 4350--4351
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]strand([]GtFeatureNode *feat
ure[]node, GtStrand

Underfull \hbox (badness 10000) in paragraph at lines 4350--4351


Underfull \hbox (badness 10000) in paragraph at lines 4359--4360


Underfull \hbox (badness 10000) in paragraph at lines 4370--4371


Underfull \hbox (badness 10000) in paragraph at lines 4380--4381
[]\OT1/cmtt/m/n/10.95 const char* gt[]feature[]node[]get[]attribute([]const GtF
eatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4380--4381


Underfull \hbox (badness 10000) in paragraph at lines 4392--4393
[]\OT1/cmtt/m/n/10.95 GtStrArray* gt[]feature[]node[]get[]attribute[]list([]con
st GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4392--4393


Underfull \hbox (badness 10000) in paragraph at lines 4404--4405
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]add[]attribute([]GtFeatureNode *f
eature[]node, const char

Underfull \hbox (badness 10000) in paragraph at lines 4404--4405


Underfull \hbox (badness 10000) in paragraph at lines 4418--4419
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]attribute([]GtFeatureNode* f
eature[]node, const char

Underfull \hbox (badness 10000) in paragraph at lines 4418--4419


Underfull \hbox (badness 10000) in paragraph at lines 4432--4433
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]remove[]attribute([]GtFeatureNode
* feature[]node, const

Underfull \hbox (badness 10000) in paragraph at lines 4432--4433


Underfull \hbox (badness 10000) in paragraph at lines 4445--4446
[]\OT1/cmtt/m/n/10.95 void GtFeatureNodeAttributeIterFunc([]const char *attr[]n
ame, const char

Underfull \hbox (badness 10000) in paragraph at lines 4445--4446


Underfull \hbox (badness 10000) in paragraph at lines 4449--4452
[]\OT1/ptm/m/n/10.95 Delivers the key (in \OT1/cmtt/m/n/10.95 attr[]name\OT1/pt
m/m/n/10.95 )and value (in \OT1/cmtt/m/n/10.95 attr[]value\OT1/ptm/m/n/10.95 ) 
of an at-

Underfull \hbox (badness 8094) in paragraph at lines 4449--4452
\OT1/ptm/m/n/10.95 tribute. The \OT1/cmtt/m/n/10.95 data \OT1/ptm/m/n/10.95 pa-
ram-e-ter car-ries over ar-bi-trary user data from the

Underfull \hbox (badness 10000) in paragraph at lines 4458--4459
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]foreach[]attribute([]GtFeatureNod
e *feature[]node,

Underfull \hbox (badness 10000) in paragraph at lines 4458--4459


Underfull \hbox (badness 10000) in paragraph at lines 4468--4469


Underfull \hbox (badness 10000) in paragraph at lines 4477--4478


Underfull \hbox (badness 10000) in paragraph at lines 4487--4488
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]make[]multi[]representative([]GtF
eatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4487--4488


Underfull \hbox (badness 10000) in paragraph at lines 4500--4501
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]multi[]representative([]GtFe
atureNode *feature[]node,

Underfull \hbox (badness 10000) in paragraph at lines 4500--4501


Underfull \hbox (badness 10000) in paragraph at lines 4510--4511


Underfull \hbox (badness 10000) in paragraph at lines 4521--4522
[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]node[]get[]multi[]representat
ive([]GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4521--4522


Underfull \hbox (badness 10000) in paragraph at lines 4531--4532
[]\OT1/cmtt/m/n/10.95 bool gt[]feature[]node[]is[]similar([]const GtFeatureNode
 *feature[]node[]a, const

Underfull \hbox (badness 10000) in paragraph at lines 4531--4532


Underfull \hbox (badness 10000) in paragraph at lines 4542--4543


Underfull \hbox (badness 10000) in paragraph at lines 4551--4552


Underfull \hbox (badness 10000) in paragraph at lines 4560--4561


Underfull \hbox (badness 10000) in paragraph at lines 4569--4570


Underfull \hbox (badness 10000) in paragraph at lines 4579--4580
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]remove[]leaf([]GtFeatureNode *tre
e, GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4579--4580


Underfull \hbox (badness 10000) in paragraph at lines 4592--4593


Underfull \hbox (badness 10000) in paragraph at lines 4604--4605

[67] [68] [69] [70]
Underfull \hbox (badness 10000) in paragraph at lines 4617--4618
[]\OT1/cmtt/m/n/10.95 GtFeatureNodeIterator* gt[]feature[]node[]iterator[]new([
]const GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4617--4618


Underfull \hbox (badness 10000) in paragraph at lines 4629--4630
[]\OT1/cmtt/m/n/10.95 GtFeatureNodeIterator* gt[]feature[]node[]iterator[]new[]
direct([]const

Underfull \hbox (badness 10000) in paragraph at lines 4629--4630


Underfull \hbox (badness 10000) in paragraph at lines 4640--4641
[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]node[]iterator[]next([]GtFeat
ureNodeIterator

Underfull \hbox (badness 10000) in paragraph at lines 4640--4641


Underfull \hbox (badness 10000) in paragraph at lines 4651--4652
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]iterator[]delete([]GtFeatureNodeI
terator

Underfull \hbox (badness 10000) in paragraph at lines 4651--4652

[71]
Underfull \hbox (badness 10000) in paragraph at lines 4662--4663
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]feature[]out[]stream[]new([]GtNodeStrea
m*, GtFeatureIndex

Underfull \hbox (badness 10000) in paragraph at lines 4662--4663


Underfull \hbox (badness 10000) in paragraph at lines 4674--4675


Underfull \hbox (badness 1509) in paragraph at lines 4678--4681
\OT1/cmtt/m/n/10.95 fi\OT1/ptm/m/n/10.95 . Note: The \OT1/cmtt/m/n/10.95 GtFeat
ureStream \OT1/ptm/m/n/10.95 class is now dep-re-cated. Please use the

Underfull \hbox (badness 10000) in paragraph at lines 4694--4695


Underfull \hbox (badness 10000) in paragraph at lines 4707--4708


Underfull \hbox (badness 10000) in paragraph at lines 4716--4717


Underfull \hbox (badness 10000) in paragraph at lines 4725--4726


Underfull \hbox (badness 10000) in paragraph at lines 4734--4735


Underfull \hbox (badness 10000) in paragraph at lines 4744--4745


Underfull \hbox (badness 10000) in paragraph at lines 4754--4755


Underfull \hbox (badness 10000) in paragraph at lines 4763--4764


Underfull \hbox (badness 10000) in paragraph at lines 4773--4774


Underfull \hbox (badness 10000) in paragraph at lines 4782--4783


Underfull \hbox (badness 10000) in paragraph at lines 4791--4792


Underfull \hbox (badness 10000) in paragraph at lines 4800--4801

[72]
Underfull \hbox (badness 10000) in paragraph at lines 4818--4819
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]gff3[]in[]stream[]new[]unsorted([]int n
um[]of[]files, const char

Underfull \hbox (badness 10000) in paragraph at lines 4818--4819


Underfull \hbox (badness 10000) in paragraph at lines 4830--4831


Underfull \hbox (badness 10000) in paragraph at lines 4842--4843


Underfull \hbox (badness 10000) in paragraph at lines 4853--4854


Underfull \hbox (badness 10000) in paragraph at lines 4864--4865


Underfull \hbox (badness 10000) in paragraph at lines 4874--4875


Underfull \hbox (badness 10000) in paragraph at lines 4884--4885


Underfull \hbox (badness 10000) in paragraph at lines 4896--4897
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]in[]stream[]set[]type[]checker([]GtNodeStr
eam *gff3[]in[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 4896--4897

[73]
Underfull \hbox (badness 10000) in paragraph at lines 4915--4916
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]gff3[]out[]stream[]new([]GtNodeStream *
in[]stream, GtFile

Underfull \hbox (badness 10000) in paragraph at lines 4915--4916


Underfull \hbox (badness 10000) in paragraph at lines 4927--4928
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]out[]stream[]set[]fasta[]width([]GtGFF3Out
Stream *gff3[]out[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 4927--4928


Underfull \hbox (badness 10000) in paragraph at lines 4939--4940
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]out[]stream[]retain[]id[]attributes([]GtGF
F3OutStream

Underfull \hbox (badness 10000) in paragraph at lines 4939--4940

[74]
Underfull \hbox (badness 10000) in paragraph at lines 4963--4964


Underfull \hbox (badness 10000) in paragraph at lines 4974--4975


Underfull \hbox (badness 10000) in paragraph at lines 4985--4986


Underfull \hbox (badness 10000) in paragraph at lines 4997--4998
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]parser[]do[]not[]check[]region[]boundaries
([]GtGFF3Parser

Underfull \hbox (badness 10000) in paragraph at lines 4997--4998


Underfull \hbox (badness 10000) in paragraph at lines 5008--5009


Underfull \hbox (badness 10000) in paragraph at lines 5018--5019
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]parser[]set[]type[]checker([]GtGFF3Parser 
*gff3[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 5018--5019


Underfull \hbox (badness 10000) in paragraph at lines 5028--5029
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]parser[]set[]xrf[]checker([]GtGFF3Parser *
gff3[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 5028--5029


Underfull \hbox (badness 10000) in paragraph at lines 5037--5038


Underfull \hbox (badness 10000) in paragraph at lines 5054--5055
[]\OT1/cmtt/m/n/10.95 int gt[]gff3[]parser[]parse[]genome[]nodes([]GtGFF3Parser
 *gff3[]parser, int

Underfull \hbox (badness 10000) in paragraph at lines 5054--5055
\OT1/cmtt/m/n/10.95 *status[]code, GtQueue *genome[]nodes, GtCstrTable *used[]t
ypes, GtStr

Underfull \hbox (badness 10000) in paragraph at lines 5054--5055


Underfull \hbox (badness 10000) in paragraph at lines 5073--5074


Underfull \hbox (badness 10000) in paragraph at lines 5082--5083

[75]
Underfull \hbox (badness 10000) in paragraph at lines 5100--5101


Underfull \hbox (badness 10000) in paragraph at lines 5112--5113
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]visitor[]set[]fasta[]width([]GtGFF3Visitor
 *gff3[]visitor, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 5112--5113


Underfull \hbox (badness 10000) in paragraph at lines 5124--5125

[76]
Underfull \hbox (badness 10000) in paragraph at lines 5144--5145


Underfull \hbox (badness 10000) in paragraph at lines 5163--5164
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]gtf[]out[]stream[]new([]GtNodeStream *i
n[]stream, GtFile

Underfull \hbox (badness 10000) in paragraph at lines 5163--5164


Underfull \hbox (badness 10000) in paragraph at lines 5182--5183


Underfull \hbox (badness 10000) in paragraph at lines 5192--5193


Underfull \hbox (badness 10000) in paragraph at lines 5202--5203


Underfull \hbox (badness 10000) in paragraph at lines 5212--5213


Underfull \hbox (badness 10000) in paragraph at lines 5222--5223


Underfull \hbox (badness 10000) in paragraph at lines 5232--5233


Underfull \hbox (badness 10000) in paragraph at lines 5242--5243


Underfull \hbox (badness 10000) in paragraph at lines 5253--5254


Underfull \hbox (badness 10000) in paragraph at lines 5264--5265
[]\OT1/cmtt/m/n/10.95 void gt[]genome[]node[]set[]range([]GtGenomeNode *genome[
]node, const GtRange

Underfull \hbox (badness 10000) in paragraph at lines 5264--5265


Underfull \hbox (badness 10000) in paragraph at lines 5275--5276
[]\OT1/cmtt/m/n/10.95 void gt[]genome[]node[]add[]user[]data([]GtGenomeNode *ge
nome[]node, const char

Underfull \hbox (badness 10000) in paragraph at lines 5275--5276


Underfull \hbox (badness 10000) in paragraph at lines 5286--5287
[]\OT1/cmtt/m/n/10.95 void* gt[]genome[]node[]get[]user[]data([]const GtGenomeN
ode *genome[]node, const

Underfull \hbox (badness 10000) in paragraph at lines 5286--5287


Underfull \hbox (badness 10000) in paragraph at lines 5296--5297
[]\OT1/cmtt/m/n/10.95 void gt[]genome[]node[]release[]user[]data([]GtGenomeNode
 *genome[]node, const

Underfull \hbox (badness 10000) in paragraph at lines 5296--5297


Underfull \hbox (badness 10000) in paragraph at lines 5307--5308
[]\OT1/cmtt/m/n/10.95 int gt[]genome[]node[]cmp([]GtGenomeNode *genome[]node[]a
, GtGenomeNode

Underfull \hbox (badness 10000) in paragraph at lines 5307--5308


Underfull \hbox (badness 1424) in paragraph at lines 5311--5313
[]\OT1/ptm/m/n/10.95 Compare \OT1/cmtt/m/n/10.95 genome[]node[]a \OT1/ptm/m/n/1
0.95 with \OT1/cmtt/m/n/10.95 genome[]node[]b \OT1/ptm/m/n/10.95 and re-turn th
e re-sult (sim-i-lar to

Underfull \hbox (badness 10000) in paragraph at lines 5317--5318


Underfull \hbox (badness 10000) in paragraph at lines 5326--5327


Underfull \hbox (badness 10000) in paragraph at lines 5336--5337
[]\OT1/cmtt/m/n/10.95 int gt[]genome[]node[]accept([]GtGenomeNode *genome[]node
, GtNodeVisitor

Underfull \hbox (badness 10000) in paragraph at lines 5336--5337


Underfull \hbox (badness 10000) in paragraph at lines 5346--5347

[77] [78]
Underfull \hbox (badness 10000) in paragraph at lines 5366--5367


Underfull \hbox (badness 10000) in paragraph at lines 5376--5377
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]text[]clip([]GtGraphics*, double
 x, double y, const

Underfull \hbox (badness 10000) in paragraph at lines 5376--5377


Underfull \hbox (badness 10000) in paragraph at lines 5386--5387


Underfull \hbox (badness 10000) in paragraph at lines 5396--5397
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]text[]centered([]GtGraphics*, do
uble x, double y,

Underfull \hbox (badness 10000) in paragraph at lines 5396--5397


Underfull \hbox (badness 10000) in paragraph at lines 5407--5408
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]text[]right([]GtGraphics*, doubl
e x, double y, const

Underfull \hbox (badness 10000) in paragraph at lines 5407--5408


Underfull \hbox (badness 10000) in paragraph at lines 5418--5419
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]colored[]text([]GtGraphics*, dou
ble x, double y,

Underfull \hbox (badness 10000) in paragraph at lines 5418--5419


Underfull \hbox (badness 10000) in paragraph at lines 5428--5429


Underfull \hbox (badness 10000) in paragraph at lines 5437--5438


Underfull \hbox (badness 10000) in paragraph at lines 5447--5448


Underfull \hbox (badness 10000) in paragraph at lines 5457--5458
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]set[]font([]GtGraphics *g, const char 
*family, FontSlant

Underfull \hbox (badness 10000) in paragraph at lines 5457--5458


Underfull \hbox (badness 10000) in paragraph at lines 5470--5471


Underfull \hbox (badness 10000) in paragraph at lines 5479--5480


Underfull \hbox (badness 10000) in paragraph at lines 5489--5490
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]set[]margins([]GtGraphics*, double mar
gin[]x, double

Underfull \hbox (badness 10000) in paragraph at lines 5489--5490


Underfull \hbox (badness 10000) in paragraph at lines 5501--5502


Underfull \hbox (badness 10000) in paragraph at lines 5510--5511


Underfull \hbox (badness 10000) in paragraph at lines 5521--5522
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]horizontal[]line([]GtGraphics *g
, double x, double y,

Underfull \hbox (badness 10000) in paragraph at lines 5521--5522


Underfull \hbox (badness 10000) in paragraph at lines 5533--5534
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]vertical[]line([]GtGraphics *g, 
double x, double y,

Underfull \hbox (badness 10000) in paragraph at lines 5533--5534


Underfull \hbox (badness 10000) in paragraph at lines 5545--5546
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]line([]GtGraphics *g, double x, 
double y, double xto,

Underfull \hbox (badness 10000) in paragraph at lines 5545--5546


Underfull \hbox (badness 10000) in paragraph at lines 5559--5560
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]box([]GtGraphics*, double x, dou
ble y, double width,

Underfull \hbox (badness 10000) in paragraph at lines 5559--5560
\OT1/cmtt/m/n/10.95 double height, GtColor fill[]color, ArrowStatus arrow[]stat
us, double

Underfull \hbox (badness 10000) in paragraph at lines 5559--5560


Underfull \hbox (badness 10000) in paragraph at lines 5579--5580
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]dashes([]GtGraphics*, double x, 
double y, double

Underfull \hbox (badness 10000) in paragraph at lines 5579--5580
\OT1/cmtt/m/n/10.95 width, double height, ArrowStatus arrow[]status, double arr
ow[]width,

Underfull \hbox (badness 10000) in paragraph at lines 5579--5580


Underfull \hbox (badness 10000) in paragraph at lines 5597--5598
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]caret([]GtGraphics*, double x, d
ouble y, double

Underfull \hbox (badness 10000) in paragraph at lines 5597--5598
\OT1/cmtt/m/n/10.95 width, double height, ArrowStatus arrow[]status, double arr
ow[]width,

Underfull \hbox (badness 10000) in paragraph at lines 5597--5598


Underfull \hbox (badness 10000) in paragraph at lines 5616--5617
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]rectangle([]GtGraphics*, double 
x, double y, bool

Underfull \hbox (badness 10000) in paragraph at lines 5616--5617
\OT1/cmtt/m/n/10.95 filled, GtColor fill[]color, bool stroked, GtColor stroke[]
color, double

Underfull \hbox (badness 10000) in paragraph at lines 5616--5617


Underfull \hbox (badness 10000) in paragraph at lines 5630--5631
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]arrowhead([]GtGraphics*, double 
x, double y, GtColor,

Underfull \hbox (badness 10000) in paragraph at lines 5630--5631


Underfull \hbox (badness 10000) in paragraph at lines 5643--5644
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]curve[]data([]GtGraphics *g, dou
ble x, double y,

Underfull \hbox (badness 10000) in paragraph at lines 5643--5644
\OT1/cmtt/m/n/10.95 GtColor color, double data[], GtUword ndata, GtRange valran
ge, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 5643--5644


Underfull \hbox (badness 10000) in paragraph at lines 5657--5658
[]\OT1/cmtt/m/n/10.95 int gt[]graphics[]save[]to[]file([]const GtGraphics*, con
st char *filename,

Underfull \hbox (badness 10000) in paragraph at lines 5657--5658


Underfull \hbox (badness 10000) in paragraph at lines 5666--5667


Underfull \hbox (badness 10000) in paragraph at lines 5675--5676

[79] [80] [81]
Underfull \hbox (badness 10000) in paragraph at lines 5694--5695
[]\OT1/cmtt/m/n/10.95 GtGraphics* gt[]graphics[]cairo[]new([]GtGraphicsOutType 
type, unsigned int

Underfull \hbox (badness 10000) in paragraph at lines 5694--5695


Underfull \hbox (badness 10000) in paragraph at lines 5707--5708
[]\OT1/cmtt/m/n/10.95 GtGraphics* gt[]graphics[]cairo[]new[]from[]context([]cai
ro[]t *context, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 5707--5708


Underfull \hbox (badness 10000) in paragraph at lines 5722--5723
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]cairo[]draw[]curve[]data([]GtGraphics 
*gg, double x, double y,

Underfull \hbox (badness 10000) in paragraph at lines 5722--5723
\OT1/cmtt/m/n/10.95 GtColor color, double data[], GtUword ndata, GtRange valran
ge, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 5722--5723

[82]
Underfull \hbox (badness 10000) in paragraph at lines 5743--5744


Underfull \hbox (badness 10000) in paragraph at lines 5757--5758
[]\OT1/cmtt/m/n/10.95 GtHashmap* gt[]hashmap[]new([]GtHashType keyhashtype, GtF
ree keyfree, GtFree

Underfull \hbox (badness 10000) in paragraph at lines 5757--5758


Underfull \hbox (badness 10000) in paragraph at lines 5773--5774


Underfull \hbox (badness 10000) in paragraph at lines 5782--5783


Underfull \hbox (badness 10000) in paragraph at lines 5792--5793


Underfull \hbox (badness 10000) in paragraph at lines 5802--5803


Underfull \hbox (badness 10000) in paragraph at lines 5813--5814
[]\OT1/cmtt/m/n/10.95 int gt[]hashmap[]foreach[]ordered([]GtHashmap *hashmap, G
tHashmapVisitFunc

Underfull \hbox (badness 10000) in paragraph at lines 5813--5814


Underfull \hbox (badness 10000) in paragraph at lines 5824--5825
[]\OT1/cmtt/m/n/10.95 int gt[]hashmap[]foreach([]GtHashmap *hashmap, GtHashmapV
isitFunc func, void

Underfull \hbox (badness 10000) in paragraph at lines 5824--5825


Underfull \hbox (badness 10000) in paragraph at lines 5836--5837
[]\OT1/cmtt/m/n/10.95 int gt[]hashmap[]foreach[]in[]key[]order([]GtHashmap *has
hmap, GtHashmapVisitFunc

Underfull \hbox (badness 10000) in paragraph at lines 5836--5837


Underfull \hbox (badness 2875) in paragraph at lines 5840--5843
[]\OT1/ptm/m/n/10.95 Iterate over \OT1/cmtt/m/n/10.95 hashmap \OT1/ptm/m/n/10.9
5 in ei-ther al-pha-bet-i-cal or-der (if \OT1/cmtt/m/n/10.95 GtHashType \OT1/pt
m/m/n/10.95 was spec-i-

Underfull \hbox (badness 1762) in paragraph at lines 5840--5843
\OT1/ptm/m/n/10.95 fied as \OT1/cmtt/m/n/10.95 GT[]HASH[]STRING\OT1/ptm/m/n/10.
95 ) or nu-mer-i-cal or-der (if \OT1/cmtt/m/n/10.95 GtHashType \OT1/ptm/m/n/10.
95 was spec-i-fied as

Underfull \hbox (badness 10000) in paragraph at lines 5847--5848


Underfull \hbox (badness 10000) in paragraph at lines 5857--5858

[83]
Underfull \hbox (badness 10000) in paragraph at lines 5876--5877
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]id[]to[]md5[]stream[]new([]GtNodeStream
 *in[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 5876--5877

[84]
Underfull \hbox (badness 10000) in paragraph at lines 5902--5903


Underfull \hbox (badness 10000) in paragraph at lines 5911--5912


Underfull \hbox (badness 10000) in paragraph at lines 5920--5921


Underfull \hbox (badness 10000) in paragraph at lines 5930--5931
[]\OT1/cmtt/m/n/10.95 const GtRecMap* gt[]image[]info[]get[]rec[]map([]GtImageI
nfo *image[]info, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 5930--5931


Underfull \hbox (badness 10000) in paragraph at lines 5939--5940


Overfull \hbox (1.94502pt too wide) in paragraph at lines 5949--5951
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. A \OT1/cmtt/m/n/10.95 GtInterFeatureStream \OT1/ptm/m/n/10.
95 in-serts new fea-ture nodes

Underfull \hbox (badness 10000) in paragraph at lines 5958--5959
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]inter[]feature[]stream[]new([]GtNodeStr
eam *in[]stream, const

Underfull \hbox (badness 10000) in paragraph at lines 5958--5959


Underfull \hbox (badness 10000) in paragraph at lines 5978--5979


Underfull \hbox (badness 10000) in paragraph at lines 5989--5990


Overfull \hbox (10.59654pt too wide) in paragraph at lines 6000--6001
[]\OT1/cmtt/m/n/10.95 GtIntervalTreeNode* gt[]interval[]tree[]find[]first[]over
lapping([]GtIntervalTree*,

Underfull \hbox (badness 10000) in paragraph at lines 6000--6001


Underfull \hbox (badness 10000) in paragraph at lines 6011--6012
[]\OT1/cmtt/m/n/10.95 void gt[]interval[]tree[]insert([]GtIntervalTree *tree, G
tIntervalTreeNode

Underfull \hbox (badness 10000) in paragraph at lines 6011--6012


Underfull \hbox (badness 10000) in paragraph at lines 6023--6024
[]\OT1/cmtt/m/n/10.95 void gt[]interval[]tree[]find[]all[]overlapping([]GtInter
valTree*, GtUword start,

Underfull \hbox (badness 10000) in paragraph at lines 6023--6024


Underfull \hbox (badness 10000) in paragraph at lines 6037--6038
[]\OT1/cmtt/m/n/10.95 void gt[]interval[]tree[]iterate[]overlapping([]GtInterva
lTree *it,

Underfull \hbox (badness 10000) in paragraph at lines 6037--6038


Underfull \hbox (badness 10000) in paragraph at lines 6050--6051
[]\OT1/cmtt/m/n/10.95 int gt[]interval[]tree[]traverse([]GtIntervalTree*, GtInt
ervalTreeIteratorFunc

Underfull \hbox (badness 10000) in paragraph at lines 6050--6051


Underfull \hbox (badness 10000) in paragraph at lines 6062--6063


Underfull \hbox (badness 10000) in paragraph at lines 6076--6077

[85]
Underfull \hbox (badness 10000) in paragraph at lines 6091--6092
[]\OT1/cmtt/m/n/10.95 GtIntervalTreeNode* gt[]interval[]tree[]node[]new([]void 
*data, GtUword low,

Underfull \hbox (badness 10000) in paragraph at lines 6091--6092


Underfull \hbox (badness 10000) in paragraph at lines 6102--6103

[86]
Underfull \hbox (badness 10000) in paragraph at lines 6124--6125
[]\OT1/cmtt/m/n/10.95 GtLayout* gt[]layout[]new([]GtDiagram *diagram, unsigned 
int width, GtStyle*,

Underfull \hbox (badness 10000) in paragraph at lines 6124--6125


Underfull \hbox (badness 10000) in paragraph at lines 6139--6140
[]\OT1/cmtt/m/n/10.95 GtLayout* gt[]layout[]new[]with[]twc([]GtDiagram*, unsign
ed int width,

Underfull \hbox (badness 10000) in paragraph at lines 6139--6140


Underfull \hbox (badness 10000) in paragraph at lines 6151--6152
[]\OT1/cmtt/m/n/10.95 void gt[]layout[]set[]track[]ordering[]func([]GtLayout *l
ayout,

Underfull \hbox (badness 10000) in paragraph at lines 6151--6152


Underfull \hbox (badness 10000) in paragraph at lines 6166--6167


Underfull \hbox (badness 10000) in paragraph at lines 6179--6180


Underfull \hbox (badness 10000) in paragraph at lines 6188--6189

[87]
Underfull \hbox (badness 10000) in paragraph at lines 6199--6200


Underfull \hbox (badness 10000) in paragraph at lines 6211--6212


Underfull \hbox (badness 10000) in paragraph at lines 6220--6221


Underfull \hbox (badness 10000) in paragraph at lines 6229--6230


Underfull \hbox (badness 10000) in paragraph at lines 6238--6239


Underfull \hbox (badness 10000) in paragraph at lines 6247--6248


Underfull \hbox (badness 10000) in paragraph at lines 6256--6257


Underfull \hbox (badness 10000) in paragraph at lines 6265--6266


Underfull \hbox (badness 10000) in paragraph at lines 6274--6275


Underfull \hbox (badness 10000) in paragraph at lines 6283--6284


Underfull \hbox (badness 10000) in paragraph at lines 6292--6293


Underfull \hbox (badness 10000) in paragraph at lines 6309--6310


Underfull \hbox (badness 10000) in paragraph at lines 6319--6320
[]\OT1/cmtt/m/n/10.95 void gt[]md5[]encoder[]add[]block([]GtMD5Encoder *enc, co
nst char *message,

Underfull \hbox (badness 10000) in paragraph at lines 6319--6320


Underfull \hbox (badness 10000) in paragraph at lines 6330--6331
[]\OT1/cmtt/m/n/10.95 void gt[]md5[]encoder[]finish([]GtMD5Encoder *enc, unsign
ed char *output, char

Underfull \hbox (badness 10000) in paragraph at lines 6330--6331


Underfull \hbox (badness 10000) in paragraph at lines 6341--6342


Underfull \hbox (badness 10000) in paragraph at lines 6351--6352

[88]
Underfull \hbox (badness 10000) in paragraph at lines 6369--6370
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]md5[]to[]id[]stream[]new([]GtNodeStream
 *in[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 6369--6370


Underfull \hbox (badness 10000) in paragraph at lines 6391--6392


Underfull \hbox (badness 10000) in paragraph at lines 6402--6403
[]\OT1/cmtt/m/n/10.95 void gt[]match[]set[]seqid1[]nt([]GtMatch *match, const c
har *seqid, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 6402--6403


Underfull \hbox (badness 10000) in paragraph at lines 6413--6414


Underfull \hbox (badness 10000) in paragraph at lines 6424--6425
[]\OT1/cmtt/m/n/10.95 void gt[]match[]set[]seqid2[]nt([]GtMatch *match, const c
har *seqid, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 6424--6425


Underfull \hbox (badness 10000) in paragraph at lines 6435--6436


Underfull \hbox (badness 10000) in paragraph at lines 6445--6446


Underfull \hbox (badness 10000) in paragraph at lines 6456--6457


Underfull \hbox (badness 10000) in paragraph at lines 6467--6468


Underfull \hbox (badness 10000) in paragraph at lines 6477--6478


Underfull \hbox (badness 10000) in paragraph at lines 6490--6491


Underfull \hbox (badness 10000) in paragraph at lines 6503--6504


Underfull \hbox (badness 10000) in paragraph at lines 6512--6513

[89] [90]
Underfull \hbox (badness 10000) in paragraph at lines 6533--6534
[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]blast[]new([]char *seqid1, char *seqi
d2, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 6533--6534
\OT1/cmtt/m/n/10.95 start[]seq1, GtUword start[]seq2, GtUword end[]seq1, GtUwor
d end[]seq2,

Underfull \hbox (badness 10000) in paragraph at lines 6533--6534
\OT1/cmtt/m/n/10.95 double evalue, float bitscore, GtUword ali[]l, double simil
arity,

Underfull \hbox (badness 10000) in paragraph at lines 6533--6534


Underfull \hbox (badness 10000) in paragraph at lines 6546--6547


Underfull \hbox (badness 10000) in paragraph at lines 6555--6556


Underfull \hbox (badness 10000) in paragraph at lines 6564--6565


Underfull \hbox (badness 10000) in paragraph at lines 6573--6574


Underfull \hbox (badness 10000) in paragraph at lines 6582--6583


Underfull \hbox (badness 10000) in paragraph at lines 6591--6592


Underfull \hbox (badness 10000) in paragraph at lines 6600--6601


Underfull \hbox (badness 10000) in paragraph at lines 6609--6610


Underfull \hbox (badness 10000) in paragraph at lines 6621--6622
[]\OT1/cmtt/m/n/10.95 GtMatchIteratorStatus gt[]match[]iterator[]next([]GtMatch
Iterator *mp, GtMatch

Underfull \hbox (badness 10000) in paragraph at lines 6621--6622


Underfull \hbox (badness 10000) in paragraph at lines 6635--6636

[91]
Underfull \hbox (badness 10000) in paragraph at lines 6661--6662
[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]last[]new([]const char *seqid1, const
 char *seqid2,

Underfull \hbox (badness 10000) in paragraph at lines 6661--6662
\OT1/cmtt/m/n/10.95 GtUword score, GtUword seqno1, GtUword seqno2, GtUword star
t[]seq1,

Underfull \hbox (badness 10000) in paragraph at lines 6661--6662
\OT1/cmtt/m/n/10.95 GtUword start[]seq2, GtUword end[]seq1, GtUword end[]seq2, 
GtMatchDirection

Underfull \hbox (badness 10000) in paragraph at lines 6661--6662


Underfull \hbox (badness 10000) in paragraph at lines 6671--6672


Underfull \hbox (badness 10000) in paragraph at lines 6680--6681


Underfull \hbox (badness 10000) in paragraph at lines 6689--6690


Underfull \hbox (badness 10000) in paragraph at lines 6713--6714
[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]open[]new([]char *seqid1, char *seqid
2, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 6713--6714
\OT1/cmtt/m/n/10.95 start[]seq1, GtUword start[]seq2, GtUword end[]seq1, GtUwor
d end[]seq2,

Underfull \hbox (badness 10000) in paragraph at lines 6713--6714


Underfull \hbox (badness 10000) in paragraph at lines 6724--6725


Underfull \hbox (badness 10000) in paragraph at lines 6733--6734

[92]
Underfull \hbox (badness 10000) in paragraph at lines 6760--6761
[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]sw[]new([]const char *seqid1, const c
har *seqid2,

Underfull \hbox (badness 10000) in paragraph at lines 6760--6761
\OT1/cmtt/m/n/10.95 GtUword seqno1, GtUword seqno2, GtUword length, GtUword edi
st, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 6760--6761
\OT1/cmtt/m/n/10.95 start[]seq1, GtUword start[]seq2, GtUword end[]seq1, GtUwor
d end[]seq2,

Underfull \hbox (badness 10000) in paragraph at lines 6760--6761


Underfull \hbox (badness 10000) in paragraph at lines 6772--6773


Underfull \hbox (badness 10000) in paragraph at lines 6781--6782


Underfull \hbox (badness 10000) in paragraph at lines 6790--6791


Underfull \hbox (badness 10000) in paragraph at lines 6799--6800


Underfull \hbox (badness 10000) in paragraph at lines 6819--6820
[]\OT1/cmtt/m/n/10.95 int gt[]match[]visitor[]visit[]match[]blast([]GtMatchVisi
tor *match[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 6819--6820


Underfull \hbox (badness 10000) in paragraph at lines 6830--6831
[]\OT1/cmtt/m/n/10.95 int gt[]match[]visitor[]visit[]match[]open([]GtMatchVisit
or *match[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 6830--6831


Underfull \hbox (badness 10000) in paragraph at lines 6839--6840

[93]
Underfull \hbox (badness 10000) in paragraph at lines 6856--6857


Underfull \hbox (badness 10000) in paragraph at lines 6875--6876


Underfull \hbox (badness 10000) in paragraph at lines 6895--6896
[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]meta[]node[]new([]const char *meta[]dir
ective, const char

Underfull \hbox (badness 10000) in paragraph at lines 6895--6896


Underfull \hbox (badness 10000) in paragraph at lines 6909--6910


Underfull \hbox (badness 10000) in paragraph at lines 6918--6919


Underfull \hbox (badness 10000) in paragraph at lines 6927--6928


Underfull \hbox (badness 10000) in paragraph at lines 6939--6940

[94]
Underfull \hbox (badness 10000) in paragraph at lines 6956--6957


Underfull \hbox (badness 10000) in paragraph at lines 6965--6966


Underfull \hbox (badness 10000) in paragraph at lines 6974--6975


Underfull \hbox (badness 10000) in paragraph at lines 6983--6984


Underfull \hbox (badness 10000) in paragraph at lines 7000--7001


Underfull \hbox (badness 10000) in paragraph at lines 7011--7012
[]\OT1/cmtt/m/n/10.95 int gt[]node[]stream[]next([]GtNodeStream *node[]stream, 
GtGenomeNode

Underfull \hbox (badness 10000) in paragraph at lines 7011--7012


Underfull \hbox (badness 1655) in paragraph at lines 7015--7021
\OT1/ptm/m/n/10.95 (trans-fers own-er-ship to \OT1/cmtt/m/n/10.95 genome[]node\
OT1/ptm/m/n/10.95 ). If no er-ror oc-curs, 0 is re-turned and

Underfull \hbox (badness 10000) in paragraph at lines 7025--7026


Underfull \hbox (badness 3240) in paragraph at lines 7029--7036
\OT1/ptm/m/n/10.95 is ex-hausted (0 is re-turned) or an er-ror oc-curs (-1 is r
e-turned and \OT1/cmtt/m/n/10.95 err \OT1/ptm/m/n/10.95 is

Underfull \hbox (badness 4266) in paragraph at lines 7029--7036
\OT1/ptm/m/n/10.95 set). All re-trieved \OT1/cmtt/m/n/10.95 GtGenomeNode\OT1/pt
m/m/n/10.95 s are deleted au-to-mat-i-cally with calls to

Underfull \hbox (badness 2828) in paragraph at lines 7029--7036
\OT1/cmtt/m/n/10.95 gt[]genome[]node[]delete()\OT1/ptm/m/n/10.95 . This method 
is ba-si-cally a con-ve-nience method

Underfull \hbox (badness 10000) in paragraph at lines 7040--7041


Underfull \hbox (badness 10000) in paragraph at lines 7049--7050


Underfull \hbox (badness 10000) in paragraph at lines 7059--7060


Underfull \hbox (badness 10000) in paragraph at lines 7069--7070


Underfull \hbox (badness 10000) in paragraph at lines 7081--7082
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]node[]stream[]create([]const GtNodeStre
amClass

Underfull \hbox (badness 10000) in paragraph at lines 7081--7082


Underfull \hbox (badness 10000) in paragraph at lines 7097--7098
[]\OT1/cmtt/m/n/10.95 void* gt[]node[]stream[]cast([]const GtNodeStreamClass *n
ode[]stream[]class,

Underfull \hbox (badness 10000) in paragraph at lines 7097--7098

[95]
Underfull \hbox (badness 10000) in paragraph at lines 7113--7114
[]\OT1/cmtt/m/n/10.95 const GtNodeStreamClass* gt[]node[]stream[]class[]new([]s
ize[]t size,

Underfull \hbox (badness 10000) in paragraph at lines 7113--7114

[96]
Underfull \hbox (badness 10000) in paragraph at lines 7135--7136
[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]comment[]node([]GtNodeVisit
or *node[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 7135--7136


Underfull \hbox (badness 10000) in paragraph at lines 7146--7147
[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]feature[]node([]GtNodeVisit
or *node[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 7146--7147


Underfull \hbox (badness 10000) in paragraph at lines 7157--7158
[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]meta[]node([]GtNodeVisitor 
*node[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 7157--7158


Underfull \hbox (badness 10000) in paragraph at lines 7168--7169
[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]region[]node([]GtNodeVisito
r *node[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 7168--7169


Underfull \hbox (badness 10000) in paragraph at lines 7179--7180
[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]sequence[]node([]GtNodeVisi
tor *node[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 7179--7180


Underfull \hbox (badness 10000) in paragraph at lines 7188--7189


Underfull \hbox (badness 10000) in paragraph at lines 7207--7208
[]\OT1/cmtt/m/n/10.95 GtORFIterator* gt[]orf[]iterator[]new([]GtCodonIterator *
ci, GtTranslator

Underfull \hbox (badness 10000) in paragraph at lines 7207--7208


Underfull \hbox (badness 10000) in paragraph at lines 7220--7221
[]\OT1/cmtt/m/n/10.95 GtORFIteratorStatus gt[]orf[]iterator[]next([]GtORFIterat
or *orf[]iterator,

Underfull \hbox (badness 10000) in paragraph at lines 7220--7221


Underfull \hbox (badness 10000) in paragraph at lines 7237--7238

[97]
Underfull \hbox (badness 10000) in paragraph at lines 7259--7260
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]bool([]const char *option[]str
ing, const char

Underfull \hbox (badness 10000) in paragraph at lines 7259--7260


Underfull \hbox (badness 2856) in paragraph at lines 7263--7265
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7271--7272
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]double([]const char *option[]s
tring, const char

Underfull \hbox (badness 10000) in paragraph at lines 7271--7272


Underfull \hbox (badness 2856) in paragraph at lines 7275--7277
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7284--7285
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]double[]min([]const char *opti
on[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7284--7285


Underfull \hbox (badness 2856) in paragraph at lines 7288--7291
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7300--7301
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]double[]min[]max([]const char 
*option[]string,

Underfull \hbox (badness 10000) in paragraph at lines 7300--7301
\OT1/cmtt/m/n/10.95 const char *description, double *value, double default[]val
ue, double

Underfull \hbox (badness 10000) in paragraph at lines 7300--7301


Underfull \hbox (badness 2856) in paragraph at lines 7304--7308
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7315--7316
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]probability([]const char *opti
on[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7315--7316


Underfull \hbox (badness 2856) in paragraph at lines 7319--7323
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7329--7330
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int([]const char *option[]stri
ng, const char

Underfull \hbox (badness 10000) in paragraph at lines 7329--7330


Underfull \hbox (badness 2856) in paragraph at lines 7333--7335
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7341--7342
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int[]min([]const char *option[
]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7341--7342


Underfull \hbox (badness 2856) in paragraph at lines 7345--7348
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7354--7355
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int[]max([]const char *option[
]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7354--7355


Underfull \hbox (badness 2856) in paragraph at lines 7358--7361
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7368--7369
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int[]min[]max([]const char *op
tion[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7368--7369
\OT1/cmtt/m/n/10.95 *description, int *value, int default[]value, int minimum[]
value, int

Underfull \hbox (badness 10000) in paragraph at lines 7368--7369


Underfull \hbox (badness 2856) in paragraph at lines 7372--7376
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7383--7384
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint([]const char *option[]str
ing, const char

Underfull \hbox (badness 10000) in paragraph at lines 7383--7384


Underfull \hbox (badness 2856) in paragraph at lines 7387--7389
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7397--7398
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint[]min([]const char *option
[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7397--7398
\OT1/cmtt/m/n/10.95 *description, unsigned int *value, unsigned int default[]va
lue, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 7397--7398


Underfull \hbox (badness 2856) in paragraph at lines 7401--7404
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7412--7413
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint[]max([]const char *option
[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7412--7413
\OT1/cmtt/m/n/10.95 *description, unsigned int *value, unsigned int default[]va
lue, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 7412--7413


Underfull \hbox (badness 2856) in paragraph at lines 7416--7419
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7428--7429
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint[]min[]max([]const char *o
ption[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7428--7429
\OT1/cmtt/m/n/10.95 *description, unsigned int *value, unsigned int default[]va
lue, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 7428--7429


Underfull \hbox (badness 2856) in paragraph at lines 7432--7436
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7442--7443
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]word([]const char *option[]str
ing, const char

Underfull \hbox (badness 10000) in paragraph at lines 7442--7443


Underfull \hbox (badness 2856) in paragraph at lines 7446--7448
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7455--7456
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uword([]const char *option[]st
ring, const char

Underfull \hbox (badness 10000) in paragraph at lines 7455--7456


Underfull \hbox (badness 2856) in paragraph at lines 7459--7461
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7469--7470
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uword[]min([]const char *optio
n[]string, const

Underfull \hbox (badness 10000) in paragraph at lines 7469--7470
\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

Underfull \hbox (badness 10000) in paragraph at lines 7469--7470


Underfull \hbox (badness 2856) in paragraph at lines 7473--7476
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7485--7486
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uword[]min[]max([]const char *
option[]string, const

Underfull \hbox (badness 10000) in paragraph at lines 7485--7486
\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

Underfull \hbox (badness 10000) in paragraph at lines 7485--7486


Underfull \hbox (badness 2856) in paragraph at lines 7489--7493
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7499--7500
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]long([]const char *option[]str
ing, const char

Underfull \hbox (badness 10000) in paragraph at lines 7499--7500


Underfull \hbox (badness 10000) in paragraph at lines 7511--7512
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]ulong([]const char *option[]st
ring, const char

Underfull \hbox (badness 10000) in paragraph at lines 7511--7512


Underfull \hbox (badness 10000) in paragraph at lines 7524--7525
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]ulong[]min([]const char *optio
n[]string, const

Underfull \hbox (badness 10000) in paragraph at lines 7524--7525
\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

Underfull \hbox (badness 10000) in paragraph at lines 7524--7525


Underfull \hbox (badness 10000) in paragraph at lines 7538--7539
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]ulong[]min[]max([]const char *
option[]string, const

Underfull \hbox (badness 10000) in paragraph at lines 7538--7539
\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

Underfull \hbox (badness 10000) in paragraph at lines 7538--7539


Underfull \hbox (badness 10000) in paragraph at lines 7549--7550
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]range([]const char *option[]st
ring, const char

Underfull \hbox (badness 10000) in paragraph at lines 7549--7550


Underfull \hbox (badness 2856) in paragraph at lines 7553--7557
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7566--7567
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]range[]min[]max([]const char *
option[]string, const

Underfull \hbox (badness 10000) in paragraph at lines 7566--7567
\OT1/cmtt/m/n/10.95 char *description, GtRange *value, GtRange *default[]value,
 GtUword

Underfull \hbox (badness 10000) in paragraph at lines 7566--7567


Underfull \hbox (badness 2856) in paragraph at lines 7570--7575
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7581--7582
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]string([]const char *option[]s
tring, const char

Underfull \hbox (badness 10000) in paragraph at lines 7581--7582


Underfull \hbox (badness 2856) in paragraph at lines 7585--7587
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7593--7594
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]string[]array([]const char *op
tion[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7593--7594


Underfull \hbox (badness 2856) in paragraph at lines 7597--7599
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7606--7607
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]choice([]const char *option[]s
tring, const char

Underfull \hbox (badness 10000) in paragraph at lines 7606--7607
\OT1/cmtt/m/n/10.95 *description, GtStr *value, const char *default[]value, con
st char

Underfull \hbox (badness 10000) in paragraph at lines 7606--7607


Underfull \hbox (badness 10000) in paragraph at lines 7610--7613
[]\OT1/ptm/m/n/10.95 Return a \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.95 w
ith the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/cmtt/
m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7619--7620
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]filename([]const char *option[
]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7619--7620


Underfull \hbox (badness 10000) in paragraph at lines 7632--7633
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]filename[]array([]const char *
option[]string, const

Underfull \hbox (badness 10000) in paragraph at lines 7632--7633


Underfull \hbox (badness 2856) in paragraph at lines 7636--7638
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7642--7643


Underfull \hbox (badness 10000) in paragraph at lines 7652--7653


Underfull \hbox (badness 10000) in paragraph at lines 7662--7663


Underfull \hbox (badness 10000) in paragraph at lines 7673--7674


Underfull \hbox (badness 10000) in paragraph at lines 7682--7683


Underfull \hbox (badness 10000) in paragraph at lines 7691--7692


Underfull \hbox (badness 10000) in paragraph at lines 7701--7702
[]\OT1/cmtt/m/n/10.95 void gt[]option[]is[]mandatory[]either([]GtOption *option
[]a, const GtOption

Underfull \hbox (badness 10000) in paragraph at lines 7701--7702


Underfull \hbox (badness 10000) in paragraph at lines 7712--7713
[]\OT1/cmtt/m/n/10.95 void gt[]option[]is[]mandatory[]either[]3([]GtOption *opt
ion[]a, const GtOption

Underfull \hbox (badness 10000) in paragraph at lines 7712--7713


Underfull \hbox (badness 10000) in paragraph at lines 7725--7726
[]\OT1/cmtt/m/n/10.95 void gt[]option[]is[]mandatory[]either[]4([]GtOption *opt
ion[]a, const GtOption

Underfull \hbox (badness 10000) in paragraph at lines 7725--7726


Underfull \hbox (badness 10000) in paragraph at lines 7735--7736


Underfull \hbox (badness 10000) in paragraph at lines 7744--7745


Underfull \hbox (badness 10000) in paragraph at lines 7753--7754


Underfull \hbox (badness 10000) in paragraph at lines 7764--7765
[]\OT1/cmtt/m/n/10.95 void gt[]option[]imply[]either[]2([]GtOption *option[]a, 
const GtOption

Underfull \hbox (badness 10000) in paragraph at lines 7764--7765


Underfull \hbox (badness 10000) in paragraph at lines 7776--7777
[]\OT1/cmtt/m/n/10.95 void gt[]option[]imply[]either[]3([]GtOption *option[]a, 
const GtOption

Underfull \hbox (badness 10000) in paragraph at lines 7776--7777


Underfull \hbox (badness 10000) in paragraph at lines 7785--7786


Underfull \hbox (badness 10000) in paragraph at lines 7794--7795


Underfull \hbox (badness 10000) in paragraph at lines 7803--7804


Underfull \hbox (badness 10000) in paragraph at lines 7812--7813


Underfull \hbox (badness 10000) in paragraph at lines 7821--7822


Underfull \hbox (badness 10000) in paragraph at lines 7833--7834
[]\OT1/cmtt/m/n/10.95 int gt[]option[]parse[]spacespec([]GtUword *maximumspace,
 const char *optname,

Underfull \hbox (badness 10000) in paragraph at lines 7833--7834

[98] [99] [100] [101] [102]
Underfull \hbox (badness 10000) in paragraph at lines 7850--7851


Underfull \hbox (badness 10000) in paragraph at lines 7860--7861
[]\OT1/cmtt/m/n/10.95 GtOptionParser* gt[]option[]parser[]new([]const char *syn
opsis, const char

Underfull \hbox (badness 10000) in paragraph at lines 7860--7861


Underfull \hbox (badness 10000) in paragraph at lines 7874--7875
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]add[]option([]GtOptionParser *op
tion[]parser, GtOption

Underfull \hbox (badness 10000) in paragraph at lines 7874--7875


Underfull \hbox (badness 10000) in paragraph at lines 7884--7885
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]parser[]get[]option([]GtOptionParse
r *option[]parser, const

Underfull \hbox (badness 10000) in paragraph at lines 7884--7885


Underfull \hbox (badness 1496) in paragraph at lines 7888--7890
[]\OT1/ptm/m/n/10.95 Return the \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.95
 ob-ject if an op-tion named \OT1/cmtt/m/n/10.95 option[]string \OT1/ptm/m/n/10
.95 is present in

Underfull \hbox (badness 10000) in paragraph at lines 7894--7895


Underfull \hbox (badness 10000) in paragraph at lines 7906--7907
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]comment[]func([]GtOptionPar
ser *option[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 7906--7907


Underfull \hbox (badness 10000) in paragraph at lines 7917--7918
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]version[]func([]GtOptionPar
ser *option[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 7917--7918


Underfull \hbox (badness 10000) in paragraph at lines 7929--7930
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]mail[]address([]GtOptionPar
ser*, const char

Underfull \hbox (badness 10000) in paragraph at lines 7929--7930


Underfull \hbox (badness 10000) in paragraph at lines 7943--7944
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]register[]hook([]GtOptionParser 
*option[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 7943--7944


Underfull \hbox (badness 10000) in paragraph at lines 7957--7958
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]min[]args([]GtOptionParser 
*option[]parser, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 7957--7958


Underfull \hbox (badness 10000) in paragraph at lines 7968--7969
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]max[]args([]GtOptionParser 
*option[]parser, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 7968--7969


Underfull \hbox (badness 10000) in paragraph at lines 7980--7981
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]min[]max[]args([]GtOptionPa
rser *option[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 7980--7981


Underfull \hbox (badness 5446) in paragraph at lines 7984--7986
[]\OT1/ptm/m/n/10.95 The \OT1/cmtt/m/n/10.95 minimum \OT1/ptm/m/n/10.95 and \OT
1/cmtt/m/n/10.95 maximum \OT1/ptm/m/n/10.95 num-ber of ad-di-tional com-mand li
ne ar-gu-ments

Underfull \hbox (badness 10000) in paragraph at lines 7994--7995
[]\OT1/cmtt/m/n/10.95 GtOPrval gt[]option[]parser[]parse([]GtOptionParser *opti
on[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 7994--7995
\OT1/cmtt/m/n/10.95 int *parsed[]args, int argc, const char **argv, GtShowVersi
onFunc

Underfull \hbox (badness 10000) in paragraph at lines 7994--7995


Underfull \hbox (badness 10000) in paragraph at lines 8007--8008


Underfull \hbox (badness 10000) in paragraph at lines 8017--8018

[103] [104]
Underfull \hbox (badness 10000) in paragraph at lines 8033--8034


Underfull \hbox (badness 10000) in paragraph at lines 8044--8045
[]\OT1/cmtt/m/n/10.95 void gt[]output[]file[]info[]register[]options([]GtOutput
FileInfo

Underfull \hbox (badness 10000) in paragraph at lines 8044--8045


Underfull \hbox (badness 10000) in paragraph at lines 8057--8058

[105]
Underfull \hbox (badness 10000) in paragraph at lines 8075--8076


Underfull \hbox (badness 10000) in paragraph at lines 8084--8085


Underfull \hbox (badness 10000) in paragraph at lines 8102--8103


Underfull \hbox (badness 10000) in paragraph at lines 8111--8112


Underfull \hbox (badness 10000) in paragraph at lines 8120--8121


Underfull \hbox (badness 10000) in paragraph at lines 8130--8131


Underfull \hbox (badness 10000) in paragraph at lines 8139--8140


Underfull \hbox (badness 10000) in paragraph at lines 8150--8151


Underfull \hbox (badness 10000) in paragraph at lines 8159--8160

[106]
Underfull \hbox (badness 10000) in paragraph at lines 8179--8180
[]\OT1/cmtt/m/n/10.95 GtRDB* gt[]rdb[]mysql[]new([]const char *server, unsigned
 int port, const char

Underfull \hbox (badness 10000) in paragraph at lines 8179--8180


Underfull \hbox (badness 10000) in paragraph at lines 8200--8201


Underfull \hbox (badness 10000) in paragraph at lines 8218--8219
[]\OT1/cmtt/m/n/10.95 int gt[]rdb[]visitor[]visit[]sqlite([]GtRDBVisitor *rdbv,
 GtRDBSqlite *rdbs,

Underfull \hbox (badness 10000) in paragraph at lines 8218--8219


Underfull \hbox (badness 10000) in paragraph at lines 8229--8230
[]\OT1/cmtt/m/n/10.95 int gt[]rdb[]visitor[]visit[]mysql([]GtRDBVisitor *rdbv, 
GtRDBMySQL *rdbm,

Underfull \hbox (badness 10000) in paragraph at lines 8229--8230


Underfull \hbox (badness 10000) in paragraph at lines 8239--8240

[107]
Underfull \hbox (badness 10000) in paragraph at lines 8255--8256


Underfull \hbox (badness 10000) in paragraph at lines 8264--8265


Underfull \hbox (badness 10000) in paragraph at lines 8273--8274


Underfull \hbox (badness 10000) in paragraph at lines 8282--8283


Underfull \hbox (badness 10000) in paragraph at lines 8291--8292


Underfull \hbox (badness 10000) in paragraph at lines 8308--8309


Underfull \hbox (badness 10000) in paragraph at lines 8321--8322
[]\OT1/cmtt/m/n/10.95 int gt[]range[]compare[]with[]delta([]const GtRange *rang
e[]a, const GtRange

Underfull \hbox (badness 10000) in paragraph at lines 8321--8322


Underfull \hbox (badness 10000) in paragraph at lines 8334--8335


Underfull \hbox (badness 10000) in paragraph at lines 8345--8346
[]\OT1/cmtt/m/n/10.95 bool gt[]range[]overlap[]delta([]const GtRange *range[]a,
 const GtRange

Underfull \hbox (badness 10000) in paragraph at lines 8345--8346


Underfull \hbox (badness 10000) in paragraph at lines 8355--8356


Underfull \hbox (badness 10000) in paragraph at lines 8364--8365


Underfull \hbox (badness 10000) in paragraph at lines 8373--8374


Underfull \hbox (badness 10000) in paragraph at lines 8382--8383


Underfull \hbox (badness 10000) in paragraph at lines 8391--8392

[108]
Overfull \hbox (37.97119pt too wide) in paragraph at lines 8401--8403
\OT1/ptm/m/n/10.95 This enum type de-fines the pos-si-ble reamodes, namely \OT1
/cmtt/m/n/10.95 GT[]READMODE[]FORWARD\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/n/10.95 G
T[]READMODE[]REVERSE\OT1/ptm/m/n/10.95 ,

Underfull \hbox (badness 10000) in paragraph at lines 8408--8409


Underfull \hbox (badness 10000) in paragraph at lines 8417--8418


Underfull \hbox (badness 2626) in paragraph at lines 8421--8424
[]\OT1/ptm/m/n/10.95 Returns the \OT1/cmtt/m/n/10.95 GtReadmode \OT1/ptm/m/n/10
.95 for the de-scrip-tion \OT1/cmtt/m/n/10.95 string\OT1/ptm/m/n/10.95 , which 
must be one of

Underfull \hbox (badness 10000) in paragraph at lines 8428--8429


Underfull \hbox (badness 10000) in paragraph at lines 8450--8451
[]\OT1/cmtt/m/n/10.95 GtRecMap* gt[]rec[]map[]new([]double nw[]x, double nw[]y,
 double se[]x, double

Underfull \hbox (badness 10000) in paragraph at lines 8450--8451


Underfull \hbox (badness 10000) in paragraph at lines 8459--8460


Underfull \hbox (badness 10000) in paragraph at lines 8468--8469


Underfull \hbox (badness 10000) in paragraph at lines 8477--8478


Underfull \hbox (badness 10000) in paragraph at lines 8486--8487


Underfull \hbox (badness 10000) in paragraph at lines 8495--8496


Underfull \hbox (badness 10000) in paragraph at lines 8504--8505


Underfull \hbox (badness 10000) in paragraph at lines 8513--8514


Underfull \hbox (badness 10000) in paragraph at lines 8523--8524

[109]
Underfull \hbox (badness 10000) in paragraph at lines 8541--8542
[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]mapping([]GtSt
r *mapping[]filename,

Underfull \hbox (badness 10000) in paragraph at lines 8541--8542


Underfull \hbox (badness 2735) in paragraph at lines 8545--8548
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtRegionMapping \OT1/ptm/
m/n/10.95 ob-ject for the map-ping file with the given

Underfull \hbox (badness 10000) in paragraph at lines 8553--8554
[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]seqfiles([]GtS
trArray

Underfull \hbox (badness 10000) in paragraph at lines 8553--8554


Underfull \hbox (badness 10000) in paragraph at lines 8557--8563
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtRegionMapping \OT1/ptm/
m/n/10.95 ob-ject for the se-quence files given in

Underfull \hbox (badness 1189) in paragraph at lines 8557--8563
\OT1/cmtt/m/n/10.95 sequence[]filenames\OT1/ptm/m/n/10.95 . If \OT1/cmtt/m/n/10
.95 matchdesc \OT1/ptm/m/n/10.95 is \OT1/cmtt/m/n/10.95 true\OT1/ptm/m/n/10.95 
, the se-quence de-scrip-tions from

Underfull \hbox (badness 10000) in paragraph at lines 8568--8569
[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]encseq([]GtEnc
seq *encseq, bool

Underfull \hbox (badness 10000) in paragraph at lines 8568--8569


Underfull \hbox (badness 10000) in paragraph at lines 8579--8580
[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]rawseq([]const
 char *rawseq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 8579--8580


Underfull \hbox (badness 10000) in paragraph at lines 8589--8590


Underfull \hbox (badness 10000) in paragraph at lines 8602--8603
[]\OT1/cmtt/m/n/10.95 int gt[]region[]mapping[]get[]sequence([]GtRegionMapping 
*region[]mapping, char

Underfull \hbox (badness 10000) in paragraph at lines 8602--8603


Underfull \hbox (badness 10000) in paragraph at lines 8618--8619
[]\OT1/cmtt/m/n/10.95 int gt[]region[]mapping[]get[]sequence[]length([]GtRegion
Mapping *region[]mapping,

Underfull \hbox (badness 10000) in paragraph at lines 8618--8619


Underfull \hbox (badness 10000) in paragraph at lines 8633--8634
[]\OT1/cmtt/m/n/10.95 int gt[]region[]mapping[]get[]description([]GtRegionMappi
ng *region[]mapping,

Underfull \hbox (badness 10000) in paragraph at lines 8633--8634


Underfull \hbox (badness 10000) in paragraph at lines 8649--8650
[]\OT1/cmtt/m/n/10.95 const char* gt[]region[]mapping[]get[]md5[]fingerprint([]
GtRegionMapping

Underfull \hbox (badness 10000) in paragraph at lines 8649--8650
\OT1/cmtt/m/n/10.95 *region[]mapping, GtStr *seqid, const GtRange *range, GtUwo
rd *offset,

Underfull \hbox (badness 10000) in paragraph at lines 8649--8650


Underfull \hbox (badness 10000) in paragraph at lines 8661--8662

[110] [111]
Overfull \hbox (1.85855pt too wide) in paragraph at lines 8671--8673
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtGenomeNode \OT1/ptm/m/n
/10.95 in-ter-face. Re-gion nodes cor-re-spond to the \OT1/cmtt/m/n/10.95 ##seq
uence-region

Underfull \hbox (badness 10000) in paragraph at lines 8679--8680
[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]region[]node[]new([]GtStr *seqid, GtUwo
rd start, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 8679--8680


Underfull \hbox (badness 10000) in paragraph at lines 8692--8693


Underfull \hbox (badness 10000) in paragraph at lines 8704--8705


Underfull \hbox (badness 10000) in paragraph at lines 8725--8726
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]script[]wrapper[]stream[]new([]GtScript
WrapperStreamNextFunc,

Underfull \hbox (badness 10000) in paragraph at lines 8725--8726

[112]
Overfull \hbox (52.44699pt too wide) in paragraph at lines 8747--8748
[]\OT1/cmtt/m/n/10.95 GtNodeVisitor* gt[]script[]wrapper[]visitor[]new([]GtScri
ptWrapperVisitorCommentNodeFunc,

Overfull \hbox (18.64471pt too wide) in paragraph at lines 8747--8748
\OT1/cmtt/m/n/10.95 GtScriptWrapperVisitorFeatureNodeFunc, GtScriptWrapperVisit
orRegionNodeFunc,

Overfull \hbox (12.89603pt too wide) in paragraph at lines 8747--8748
\OT1/cmtt/m/n/10.95 GtScriptWrapperVisitorSequenceNodeFunc, GtScriptWrapperVisi
torMetaNodeFunc,

Underfull \hbox (badness 10000) in paragraph at lines 8747--8748


Underfull \hbox (badness 10000) in paragraph at lines 8780--8781
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]select[]stream[]new([]GtNodeStream *in[
]stream, GtStr

Underfull \hbox (badness 10000) in paragraph at lines 8780--8781
\OT1/cmtt/m/n/10.95 *seqid, GtStr *source, const GtRange *contain[]range, const
 GtRange

Underfull \hbox (badness 10000) in paragraph at lines 8780--8781
\OT1/cmtt/m/n/10.95 *overlap[]range, GtStrand strand, GtStrand targetstrand, bo
ol has[]CDS,

Underfull \hbox (badness 10000) in paragraph at lines 8780--8781
\OT1/cmtt/m/n/10.95 GtUword max[]gene[]length, GtUword max[]gene[]num, double m
in[]gene[]score,

Underfull \hbox (badness 10000) in paragraph at lines 8780--8781
\OT1/cmtt/m/n/10.95 double max[]gene[]score, double min[]average[]splice[]site[
]prob, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 8780--8781


Underfull \hbox (badness 10000) in paragraph at lines 8823--8824
[]\OT1/cmtt/m/n/10.95 void gt[]select[]stream[]set[]drophandler([]GtSelectStrea
m *sstr,

Underfull \hbox (badness 10000) in paragraph at lines 8823--8824

[113]
Underfull \hbox (badness 10000) in paragraph at lines 8837--8838
[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]set[]symbolmap([]GtSeqIterator*, 
const GtUchar

Underfull \hbox (badness 10000) in paragraph at lines 8837--8838


Underfull \hbox (badness 10000) in paragraph at lines 8848--8849


Underfull \hbox (badness 10000) in paragraph at lines 8862--8863
[]\OT1/cmtt/m/n/10.95 int gt[]seq[]iterator[]next([]GtSeqIterator *seqit, const
 GtUchar **sequence,

Underfull \hbox (badness 10000) in paragraph at lines 8862--8863


Underfull \hbox (badness 10000) in paragraph at lines 8876--8877
[]\OT1/cmtt/m/n/10.95 const GtUint64* gt[]seq[]iterator[]getcurrentcounter([]Gt
SeqIterator*,

Underfull \hbox (badness 10000) in paragraph at lines 8876--8877


Underfull \hbox (badness 10000) in paragraph at lines 8885--8886


Underfull \hbox (badness 10000) in paragraph at lines 8895--8896
[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]set[]quality[]buffer([]GtSeqItera
tor *seqit, const

Underfull \hbox (badness 10000) in paragraph at lines 8895--8896


Underfull \hbox (badness 10000) in paragraph at lines 8906--8907

[114]
Underfull \hbox (badness 10000) in paragraph at lines 8918--8919
[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]fastq[]new([]const GtSt
rArray *filenametab,

Underfull \hbox (badness 10000) in paragraph at lines 8918--8919


Underfull \hbox (badness 10000) in paragraph at lines 8929--8930
[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]fastq[]new[]colorspace(
[]const GtStrArray

Underfull \hbox (badness 10000) in paragraph at lines 8929--8930


Underfull \hbox (badness 10000) in paragraph at lines 8939--8940


Overfull \hbox (28.76239pt too wide) in paragraph at lines 8949--8950
[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]fastq[]relax[]check[]of[]quality[
]description([]GtSeqIteratorFastQ

Underfull \hbox (badness 10000) in paragraph at lines 8949--8950

[115]
Underfull \hbox (badness 10000) in paragraph at lines 8963--8964
[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]sequence[]buffer[]new([
]const GtStrArray

Underfull \hbox (badness 10000) in paragraph at lines 8963--8964


Underfull \hbox (badness 10000) in paragraph at lines 8984--8985
[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]sequence[]node[]new([]const char *descr
iption, GtStr

Underfull \hbox (badness 10000) in paragraph at lines 8984--8985


Underfull \hbox (badness 2698) in paragraph at lines 8988--8990
[]\OT1/ptm/m/n/10.95 Create a new \OT1/cmtt/m/n/10.95 GtSequenceNode* \OT1/ptm/
m/n/10.95 rep-re-sent-ing a FASTA en-try with the given

Underfull \hbox (badness 10000) in paragraph at lines 8996--8997
[]\OT1/cmtt/m/n/10.95 const char* gt[]sequence[]node[]get[]description([]const 
GtSequenceNode

Underfull \hbox (badness 10000) in paragraph at lines 8996--8997


Underfull \hbox (badness 10000) in paragraph at lines 9006--9007
[]\OT1/cmtt/m/n/10.95 const char* gt[]sequence[]node[]get[]sequence([]const GtS
equenceNode

Underfull \hbox (badness 10000) in paragraph at lines 9006--9007


Underfull \hbox (badness 10000) in paragraph at lines 9017--9018
[]\OT1/cmtt/m/n/10.95 GtUword gt[]sequence[]node[]get[]sequence[]length([]const
 GtSequenceNode

Underfull \hbox (badness 10000) in paragraph at lines 9017--9018


Underfull \hbox (badness 10000) in paragraph at lines 9026--9027


Underfull \hbox (badness 10000) in paragraph at lines 9038--9039

[116]
Overfull \hbox (58.46886pt too wide) in paragraph at lines 9049--9052
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeVisitor \OT1/ptm/m/
n/10.95 in-ter-face. Used with the \OT1/cmtt/m/n/10.95 GtVisitorStream \OT1/ptm
/m/n/10.95 class, a \OT1/cmtt/m/n/10.95 GtSetSourceVisitor

Underfull \hbox (badness 10000) in paragraph at lines 9057--9058


Underfull \hbox (badness 10000) in paragraph at lines 9075--9076


Underfull \hbox (badness 10000) in paragraph at lines 9094--9095


Underfull \hbox (badness 10000) in paragraph at lines 9104--9105
[]\OT1/cmtt/m/n/10.95 void gt[]splitter[]split([]GtSplitter *splitter, char *st
ring, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 9104--9105


Underfull \hbox (badness 10000) in paragraph at lines 9115--9116
[]\OT1/cmtt/m/n/10.95 void gt[]splitter[]split[]non[]empty([]GtSplitter *s, cha
r *string, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 9115--9116


Underfull \hbox (badness 10000) in paragraph at lines 9126--9127


Underfull \hbox (badness 10000) in paragraph at lines 9136--9137


Underfull \hbox (badness 10000) in paragraph at lines 9145--9146


Underfull \hbox (badness 10000) in paragraph at lines 9154--9155


Underfull \hbox (badness 10000) in paragraph at lines 9163--9164

[117]
Overfull \hbox (31.52028pt too wide) in paragraph at lines 9173--9176
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. A \OT1/cmtt/m/n/10.95 GtStatStream \OT1/ptm/m/n/10.95 gath-
ers statis-tics about the \OT1/cmtt/m/n/10.95 GtGenomeNode

Underfull \hbox (badness 10000) in paragraph at lines 9188--9189
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]stat[]stream[]new([]GtNodeStream *in[]s
tream, bool

Underfull \hbox (badness 10000) in paragraph at lines 9188--9189
\OT1/cmtt/m/n/10.95 gene[]length[]distribution, bool gene[]score[]distribution,
 bool

Underfull \hbox (badness 10000) in paragraph at lines 9188--9189
\OT1/cmtt/m/n/10.95 exon[]length[]distribution, bool exon[]number[]distribution
, bool

Underfull \hbox (badness 10000) in paragraph at lines 9188--9189
\OT1/cmtt/m/n/10.95 intron[]length[]distribution, bool cds[]length[]distributio
n, bool

Underfull \hbox (badness 10000) in paragraph at lines 9188--9189


Underfull \hbox (badness 3668) in paragraph at lines 9192--9200
\OT1/ptm/m/n/10.95 ment equals \OT1/cmtt/m/n/10.95 true\OT1/ptm/m/n/10.95 : \OT
1/cmtt/m/n/10.95 gene[]length[]distribution\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/n/1
0.95 gene[]score[]distribution\OT1/ptm/m/n/10.95 ,

Underfull \hbox (badness 10000) in paragraph at lines 9192--9200
\OT1/cmtt/m/n/10.95 exon[]length[]distribution\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/
n/10.95 exon[]number[]distribution\OT1/ptm/m/n/10.95 ,

Underfull \hbox (badness 10000) in paragraph at lines 9205--9206

[118]
Underfull \hbox (badness 10000) in paragraph at lines 9221--9222


Underfull \hbox (badness 10000) in paragraph at lines 9230--9231


Underfull \hbox (badness 10000) in paragraph at lines 9239--9240


Underfull \hbox (badness 10000) in paragraph at lines 9248--9249


Underfull \hbox (badness 10000) in paragraph at lines 9258--9259


Underfull \hbox (badness 10000) in paragraph at lines 9268--9269


Underfull \hbox (badness 10000) in paragraph at lines 9277--9278


Underfull \hbox (badness 10000) in paragraph at lines 9286--9287


Underfull \hbox (badness 10000) in paragraph at lines 9295--9296


Underfull \hbox (badness 10000) in paragraph at lines 9305--9306


Underfull \hbox (badness 10000) in paragraph at lines 9314--9315


Underfull \hbox (badness 10000) in paragraph at lines 9323--9324


Underfull \hbox (badness 10000) in paragraph at lines 9333--9334


Underfull \hbox (badness 10000) in paragraph at lines 9342--9343


Underfull \hbox (badness 10000) in paragraph at lines 9351--9352


Underfull \hbox (badness 10000) in paragraph at lines 9360--9361


Underfull \hbox (badness 5667) in paragraph at lines 9364--9366
[]\OT1/ptm/m/n/10.95 Set length of \OT1/cmtt/m/n/10.95 str \OT1/ptm/m/n/10.95 t
o \OT1/cmtt/m/n/10.95 length\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 length \OT
1/ptm/m/n/10.95 must be smaller or equal than

Underfull \hbox (badness 10000) in paragraph at lines 9370--9371


Underfull \hbox (badness 10000) in paragraph at lines 9379--9380


Underfull \hbox (badness 10000) in paragraph at lines 9388--9389


Underfull \hbox (badness 10000) in paragraph at lines 9397--9398

[119]
Underfull \hbox (badness 10000) in paragraph at lines 9414--9415


Underfull \hbox (badness 10000) in paragraph at lines 9423--9424


Underfull \hbox (badness 10000) in paragraph at lines 9432--9433


Underfull \hbox (badness 10000) in paragraph at lines 9442--9443
[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]add[]cstr[]nt([]GtStrArray *str[]arr
ay, const char *cstr,

Underfull \hbox (badness 10000) in paragraph at lines 9442--9443


Underfull \hbox (badness 10000) in paragraph at lines 9452--9453


Underfull \hbox (badness 10000) in paragraph at lines 9462--9463


Underfull \hbox (badness 10000) in paragraph at lines 9473--9474
[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]set[]cstr([]GtStrArray *str[]array, 
GtUword strnum, const

Underfull \hbox (badness 10000) in paragraph at lines 9473--9474


Underfull \hbox (badness 10000) in paragraph at lines 9483--9484
[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]set([]GtStrArray *str[]array, GtUwor
d strnum, const GtStr

Underfull \hbox (badness 10000) in paragraph at lines 9483--9484


Underfull \hbox (badness 10000) in paragraph at lines 9492--9493


Underfull \hbox (badness 2564) in paragraph at lines 9496--9498
[]\OT1/ptm/m/n/10.95 Set the size of \OT1/cmtt/m/n/10.95 str[]array \OT1/ptm/m/
n/10.95 to \OT1/cmtt/m/n/10.95 size\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 siz
e \OT1/ptm/m/n/10.95 must be smaller or equal than

Underfull \hbox (badness 10000) in paragraph at lines 9502--9503


Underfull \hbox (badness 10000) in paragraph at lines 9511--9512


Underfull \hbox (badness 10000) in paragraph at lines 9520--9521

[120]
Overfull \hbox (21.75429pt too wide) in paragraph at lines 9530--9533
\OT1/ptm/m/n/10.95 This enum type de-fines the pos-si-ble strands. The fol-low-
ing strands are de-fined: \OT1/cmtt/m/n/10.95 GT[]STRAND[]FORWARD\OT1/ptm/m/n/1
0.95 ,

Underfull \hbox (badness 10000) in paragraph at lines 9538--9539


Underfull \hbox (badness 10000) in paragraph at lines 9547--9548


Underfull \hbox (badness 10000) in paragraph at lines 9551--9553
[]\OT1/ptm/m/n/10.95 Map \OT1/cmtt/m/n/10.95 strand[]char \OT1/ptm/m/n/10.95 to
 the cor-re-spond-ing strand enum type. Re-turns

Underfull \hbox (badness 10000) in paragraph at lines 9568--9569


Underfull \hbox (badness 10000) in paragraph at lines 9577--9578


Underfull \hbox (badness 10000) in paragraph at lines 9586--9587


Underfull \hbox (badness 10000) in paragraph at lines 9595--9596


Underfull \hbox (badness 10000) in paragraph at lines 9604--9605


Underfull \hbox (badness 10000) in paragraph at lines 9613--9614


Underfull \hbox (badness 10000) in paragraph at lines 9622--9623


Underfull \hbox (badness 10000) in paragraph at lines 9632--9633


Underfull \hbox (badness 10000) in paragraph at lines 9642--9643


Underfull \hbox (badness 10000) in paragraph at lines 9652--9653


Underfull \hbox (badness 10000) in paragraph at lines 9662--9663
[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]color([]GtStyle*, const char *sectio
n, const char *key,

Underfull \hbox (badness 10000) in paragraph at lines 9662--9663


Underfull \hbox (badness 10000) in paragraph at lines 9674--9675
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]color([]const GtStyle 
*style, const char

Underfull \hbox (badness 10000) in paragraph at lines 9674--9675
\OT1/cmtt/m/n/10.95 *section, const char *key, GtColor *result, GtFeatureNode *
fn, GtError

Underfull \hbox (badness 10000) in paragraph at lines 9674--9675


Underfull \hbox (badness 10000) in paragraph at lines 9700--9701
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]color[]with[]track([]c
onst GtStyle *style,

Underfull \hbox (badness 10000) in paragraph at lines 9700--9701
\OT1/cmtt/m/n/10.95 const char *section, const char *key, GtColor *result, GtFe
atureNode

Underfull \hbox (badness 10000) in paragraph at lines 9700--9701


Underfull \hbox (badness 10000) in paragraph at lines 9711--9712
[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]str([]GtStyle*, const char *section,
 const char *key,

Underfull \hbox (badness 10000) in paragraph at lines 9711--9712


Underfull \hbox (badness 10000) in paragraph at lines 9722--9723
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]str([]const GtStyle *s
tyle, const char

Underfull \hbox (badness 10000) in paragraph at lines 9722--9723
\OT1/cmtt/m/n/10.95 *section, const char *key, GtStr *result, GtFeatureNode *fn
, GtError

Underfull \hbox (badness 10000) in paragraph at lines 9722--9723


Underfull \hbox (badness 10000) in paragraph at lines 9747--9748
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]str[]with[]track([]con
st GtStyle *style, const

Underfull \hbox (badness 10000) in paragraph at lines 9747--9748
\OT1/cmtt/m/n/10.95 char *section, const char *key, GtStr *result, GtFeatureNod
e *fn, const

Underfull \hbox (badness 10000) in paragraph at lines 9747--9748


Underfull \hbox (badness 10000) in paragraph at lines 9758--9759
[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]num([]GtStyle*, const char *section,
 const char *key,

Underfull \hbox (badness 10000) in paragraph at lines 9758--9759


Underfull \hbox (badness 10000) in paragraph at lines 9769--9770
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]num([]const GtStyle *s
tyle, const char

Underfull \hbox (badness 10000) in paragraph at lines 9769--9770
\OT1/cmtt/m/n/10.95 *section, const char *key, double *result, GtFeatureNode *f
n, GtError

Underfull \hbox (badness 10000) in paragraph at lines 9769--9770


Underfull \hbox (badness 10000) in paragraph at lines 9794--9795
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]num[]with[]track([]con
st GtStyle *style, const

Underfull \hbox (badness 10000) in paragraph at lines 9794--9795
\OT1/cmtt/m/n/10.95 char *section, const char *key, double *result, GtFeatureNo
de *fn, const

Underfull \hbox (badness 10000) in paragraph at lines 9794--9795


Underfull \hbox (badness 10000) in paragraph at lines 9805--9806
[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]bool([]GtStyle*, const char *section
, const char *key,

Underfull \hbox (badness 10000) in paragraph at lines 9805--9806


Underfull \hbox (badness 10000) in paragraph at lines 9816--9817
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]bool([]const GtStyle *
style, const char

Underfull \hbox (badness 10000) in paragraph at lines 9816--9817
\OT1/cmtt/m/n/10.95 *section, const char *key, bool *result, GtFeatureNode *fn,
 GtError

Underfull \hbox (badness 10000) in paragraph at lines 9816--9817


Underfull \hbox (badness 10000) in paragraph at lines 9841--9842
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]bool[]with[]track([]co
nst GtStyle *style,

Underfull \hbox (badness 10000) in paragraph at lines 9841--9842
\OT1/cmtt/m/n/10.95 const char *section, const char *key, bool *result, GtFeatu
reNode *fn,

Underfull \hbox (badness 10000) in paragraph at lines 9841--9842


Underfull \hbox (badness 10000) in paragraph at lines 9852--9853


Underfull \hbox (badness 10000) in paragraph at lines 9861--9862

[121] [122] [123] [124]
Underfull \hbox (badness 10000) in paragraph at lines 9885--9886
[]\OT1/cmtt/m/n/10.95 void GtTagValueMapIteratorFunc([]const char *tag, const c
har *value, void

Underfull \hbox (badness 10000) in paragraph at lines 9885--9886


Underfull \hbox (badness 10000) in paragraph at lines 9895--9896


Underfull \hbox (badness 10000) in paragraph at lines 9907--9908
[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]add([]GtTagValueMap *tag[]value
[]map, const char *tag,

Underfull \hbox (badness 10000) in paragraph at lines 9907--9908


Underfull \hbox (badness 10000) in paragraph at lines 9918--9919
[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]set([]GtTagValueMap *tag[]value
[]map, const char *tag,

Underfull \hbox (badness 10000) in paragraph at lines 9918--9919


Underfull \hbox (badness 10000) in paragraph at lines 9928--9929
[]\OT1/cmtt/m/n/10.95 const char* gt[]tag[]value[]map[]get([]const GtTagValueMa
p tag[]value[]map, const

Underfull \hbox (badness 10000) in paragraph at lines 9928--9929


Underfull \hbox (badness 10000) in paragraph at lines 9938--9939


Underfull \hbox (badness 10000) in paragraph at lines 9948--9949
[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]remove([]GtTagValueMap *tag[]va
lue[]map, const char

Underfull \hbox (badness 10000) in paragraph at lines 9948--9949


Underfull \hbox (badness 10000) in paragraph at lines 9961--9962
[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]foreach([]const GtTagValueMap t
ag[]value[]map,

Underfull \hbox (badness 10000) in paragraph at lines 9961--9962


Underfull \hbox (badness 10000) in paragraph at lines 9971--9972


Underfull \hbox (badness 10000) in paragraph at lines 9980--9981

[125]
Overfull \hbox (6.45749pt too wide) in paragraph at lines 9999--10000
[]\OT1/cmtt/m/n/10.95 GtTextWidthCalculator* gt[]text[]width[]calculator[]ref([
]GtTextWidthCalculator*[]) 

Underfull \hbox (badness 10000) in paragraph at lines 9999--10000


Underfull \hbox (badness 10000) in paragraph at lines 10010--10011
[]\OT1/cmtt/m/n/10.95 double gt[]text[]width[]calculator[]get[]text[]width([]Gt
TextWidthCalculator*,

Underfull \hbox (badness 10000) in paragraph at lines 10010--10011


Underfull \hbox (badness 10000) in paragraph at lines 10021--10022


Overfull \hbox (83.5338pt too wide) in paragraph at lines 10031--10037
\OT1/cmtt/m/n/10.95 cairo[]t \OT1/ptm/m/n/10.95 and which should be used later 
via a \OT1/cmtt/m/n/10.95 GtCanvasCairoContext\OT1/ptm/m/n/10.95 , cre-ate a \O
T1/cmtt/m/n/10.95 GtTextWidthCalculatorCairo

Underfull \hbox (badness 10000) in paragraph at lines 10043--10044
[]\OT1/cmtt/m/n/10.95 GtTextWidthCalculator* gt[]text[]width[]calculator[]cairo
[]new([]cairo[]t*,

Underfull \hbox (badness 10000) in paragraph at lines 10043--10044


Underfull \hbox (badness 10000) in paragraph at lines 10062--10063


Underfull \hbox (badness 10000) in paragraph at lines 10071--10072


Underfull \hbox (badness 10000) in paragraph at lines 10082--10083


Underfull \hbox (badness 10000) in paragraph at lines 10091--10092

[126]
Underfull \hbox (badness 10000) in paragraph at lines 10109--10110


Underfull \hbox (badness 10000) in paragraph at lines 10118--10119


Underfull \hbox (badness 10000) in paragraph at lines 10127--10128


Underfull \hbox (badness 10000) in paragraph at lines 10136--10137


Underfull \hbox (badness 10000) in paragraph at lines 10145--10146


Underfull \hbox (badness 3168) in paragraph at lines 10149--10153
[]\OT1/ptm/m/n/10.95 Output the cur-rent state of \OT1/cmtt/m/n/10.95 timer \OT
1/ptm/m/n/10.95 in the for-mat ""GT[]WD".pointer \OT1/cmtt/m/n/10.95 fp \OT1/pt
m/m/n/10.95 (see

Underfull \hbox (badness 10000) in paragraph at lines 10157--10158


Underfull \hbox (badness 10000) in paragraph at lines 10169--10170


Underfull \hbox (badness 10000) in paragraph at lines 10178--10179


Underfull \hbox (badness 10000) in paragraph at lines 10182--10186
[]\OT1/ptm/m/n/10.95 Output the cur-rent state of \OT1/cmtt/m/n/10.95 timer \OT
1/ptm/m/n/10.95 on \OT1/cmtt/m/n/10.95 fp \OT1/ptm/m/n/10.95 since the last cal
l of

Underfull \hbox (badness 1292) in paragraph at lines 10182--10186
\OT1/cmtt/m/n/10.95 gt[]timer[]show[]progress() \OT1/ptm/m/n/10.95 or the last 
start of \OT1/cmtt/m/n/10.95 timer\OT1/ptm/m/n/10.95 , along with the cur-rent

Underfull \hbox (badness 10000) in paragraph at lines 10191--10192
[]\OT1/cmtt/m/n/10.95 void gt[]timer[]show[]progress[]formatted([]GtTimer *time
r, FILE *fp, const

Underfull \hbox (badness 10000) in paragraph at lines 10191--10192


Underfull \hbox (badness 10000) in paragraph at lines 10202--10203
[]\OT1/cmtt/m/n/10.95 void gt[]timer[]show[]progress[]va([]GtTimer *timer, FILE
 *fp, const char

Underfull \hbox (badness 10000) in paragraph at lines 10202--10203


Underfull \hbox (badness 10000) in paragraph at lines 10212--10213


Underfull \hbox (badness 10000) in paragraph at lines 10221--10222


Underfull \hbox (badness 10000) in paragraph at lines 10231--10232


Underfull \hbox (badness 10000) in paragraph at lines 10240--10241

[127]
Underfull \hbox (badness 10000) in paragraph at lines 10257--10258


Underfull \hbox (badness 10000) in paragraph at lines 10267--10268


Underfull \hbox (badness 10000) in paragraph at lines 10277--10278


Underfull \hbox (badness 10000) in paragraph at lines 10289--10290
[]\OT1/cmtt/m/n/10.95 int GtToolArgumentsCheck([]int rest[]argc, void *tool[]ar
guments, GtError

Underfull \hbox (badness 10000) in paragraph at lines 10289--10290


Underfull \hbox (badness 10000) in paragraph at lines 10303--10304
[]\OT1/cmtt/m/n/10.95 int GtToolRunner([]int argc, const char **argv, int parse
d[]args, void

Underfull \hbox (badness 10000) in paragraph at lines 10303--10304


Underfull \hbox (badness 10000) in paragraph at lines 10319--10320


Underfull \hbox (badness 10000) in paragraph at lines 10332--10333
[]\OT1/cmtt/m/n/10.95 GtTool* gt[]tool[]new([]GtToolArgumentsNew tool[]argument
s[]new,

Underfull \hbox (badness 10000) in paragraph at lines 10332--10333
\OT1/cmtt/m/n/10.95 GtToolArgumentsDelete tool[]arguments[]delete, GtToolOption
ParserNew

Underfull \hbox (badness 10000) in paragraph at lines 10332--10333
\OT1/cmtt/m/n/10.95 tool[]option[]parser[]new, GtToolArgumentsCheck tool[]argum
ents[]check,

Underfull \hbox (badness 10000) in paragraph at lines 10332--10333


Underfull \hbox (badness 10000) in paragraph at lines 10348--10349


Underfull \hbox (badness 10000) in paragraph at lines 10367--10368

[128]
Underfull \hbox (badness 10000) in paragraph at lines 10384--10385


Underfull \hbox (badness 10000) in paragraph at lines 10394--10395
[]\OT1/cmtt/m/n/10.95 void gt[]toolbox[]add[]tool([]GtToolbox *toolbox, const c
har *toolname, GtTool

Underfull \hbox (badness 10000) in paragraph at lines 10394--10395


Underfull \hbox (badness 10000) in paragraph at lines 10404--10405
[]\OT1/cmtt/m/n/10.95 void gt[]toolbox[]add[]hidden[]tool([]GtToolbox *toolbox,
 const char *toolname,

Underfull \hbox (badness 10000) in paragraph at lines 10404--10405


Underfull \hbox (badness 10000) in paragraph at lines 10414--10415


Underfull \hbox (badness 10000) in paragraph at lines 10424--10425


Underfull \hbox (badness 10000) in paragraph at lines 10434--10435

[129]
Underfull \hbox (badness 10000) in paragraph at lines 10445--10446


Underfull \hbox (badness 2035) in paragraph at lines 10449--10453
[]\OT1/ptm/m/n/10.95 Returns a \OT1/cmtt/m/n/10.95 GtStrArray \OT1/ptm/m/n/10.9
5 of trans-la-tion scheme de-scrip-tions, each of the for-mat

Underfull \hbox (badness 10000) in paragraph at lines 10457--10458


Underfull \hbox (badness 10000) in paragraph at lines 10470--10471


Underfull \hbox (badness 10000) in paragraph at lines 10479--10480


Underfull \hbox (badness 10000) in paragraph at lines 10490--10491
[]\OT1/cmtt/m/n/10.95 int gt[]trans[]table[]translate[]codon([]const GtTransTab
le *tt, char c1, char

Underfull \hbox (badness 10000) in paragraph at lines 10490--10491


Underfull \hbox (badness 10000) in paragraph at lines 10502--10503

[130]
Underfull \hbox (badness 10000) in paragraph at lines 10520--10521
[]\OT1/cmtt/m/n/10.95 GtTranslator* gt[]translator[]new[]with[]table([]GtTransT
able *tt,

Underfull \hbox (badness 10000) in paragraph at lines 10520--10521


Underfull \hbox (badness 10000) in paragraph at lines 10531--10532


Underfull \hbox (badness 10000) in paragraph at lines 10543--10544
[]\OT1/cmtt/m/n/10.95 void gt[]translator[]set[]codon[]iterator([]GtTranslator 
*translator,

Underfull \hbox (badness 10000) in paragraph at lines 10543--10544


Underfull \hbox (badness 10000) in paragraph at lines 10554--10555
[]\OT1/cmtt/m/n/10.95 void gt[]translator[]set[]translation[]table([]GtTranslat
or *translator,

Underfull \hbox (badness 10000) in paragraph at lines 10554--10555


Underfull \hbox (badness 10000) in paragraph at lines 10567--10568
[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]next([]GtTranslator *t
ranslator, char

Underfull \hbox (badness 10000) in paragraph at lines 10567--10568


Underfull \hbox (badness 10000) in paragraph at lines 10584--10585
[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]find[]startcodon([]GtT
ranslator

Underfull \hbox (badness 10000) in paragraph at lines 10584--10585


Underfull \hbox (badness 10000) in paragraph at lines 10602--10603
[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]find[]stopcodon([]GtTr
anslator *translator,

Underfull \hbox (badness 10000) in paragraph at lines 10602--10603


Underfull \hbox (badness 10000) in paragraph at lines 10621--10622
[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]find[]codon([]GtTransl
ator *translator,

Underfull \hbox (badness 10000) in paragraph at lines 10621--10622


Underfull \hbox (badness 10000) in paragraph at lines 10636--10637

[131]
Underfull \hbox (badness 10000) in paragraph at lines 10653--10654


Underfull \hbox (badness 10000) in paragraph at lines 10662--10663


Underfull \hbox (badness 10000) in paragraph at lines 10672--10673
[]\OT1/cmtt/m/n/10.95 bool gt[]type[]checker[]is[]valid([]GtTypeChecker *type[]
checker, const char

Underfull \hbox (badness 10000) in paragraph at lines 10672--10673


Underfull \hbox (badness 10000) in paragraph at lines 10684--10685
[]\OT1/cmtt/m/n/10.95 bool gt[]type[]checker[]is[]partof([]GtTypeChecker *type[
]checker, const char

Underfull \hbox (badness 10000) in paragraph at lines 10684--10685


Underfull \hbox (badness 10000) in paragraph at lines 10695--10696
[]\OT1/cmtt/m/n/10.95 bool gt[]type[]checker[]is[]a([]GtTypeChecker *type[]chec
ker, const char

Underfull \hbox (badness 10000) in paragraph at lines 10695--10696


Underfull \hbox (badness 10000) in paragraph at lines 10704--10705

[132]
Underfull \hbox (badness 10000) in paragraph at lines 10721--10722
[]\OT1/cmtt/m/n/10.95 GtTypeChecker* gt[]type[]checker[]obo[]new([]const char *
obo[]file[]path, GtError

Underfull \hbox (badness 10000) in paragraph at lines 10721--10722


Underfull \hbox (badness 10000) in paragraph at lines 10740--10741


Underfull \hbox (badness 10000) in paragraph at lines 10764--10765
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]visitor[]stream[]new([]GtNodeStream *in
[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 10764--10765

[133]
Underfull \hbox (badness 10000) in paragraph at lines 10783--10784


Underfull \hbox (badness 10000) in paragraph at lines 10793--10794


Underfull \hbox (badness 10000) in paragraph at lines 10803--10804
[]\OT1/cmtt/m/n/10.95 bool gt[]xrf[]checker[]is[]valid([]GtXRFChecker *xrf[]che
cker, const char *value,

Underfull \hbox (badness 10000) in paragraph at lines 10803--10804


Underfull \hbox (badness 10000) in paragraph at lines 10814--10815


Underfull \hbox (badness 10000) in paragraph at lines 10825--10826


Underfull \hbox (badness 10000) in paragraph at lines 10837--10838


Underfull \hbox (badness 10000) in paragraph at lines 10850--10851


Underfull \hbox (badness 10000) in paragraph at lines 10859--10860


Underfull \hbox (badness 10000) in paragraph at lines 10871--10872

[134]
Underfull \hbox (badness 10000) in paragraph at lines 10886--10887
[]\OT1/cmtt/m/n/10.95 void* gt[]bsearch[]data([]const void *key, const void *ba
se, size[]t nmemb,

Underfull \hbox (badness 10000) in paragraph at lines 10886--10887


Underfull \hbox (badness 10000) in paragraph at lines 10897--10898
[]\OT1/cmtt/m/n/10.95 void gt[]bsearch[]all([]GtArray *members, const void *key
, const void *base,

Underfull \hbox (badness 10000) in paragraph at lines 10897--10898


Underfull \hbox (badness 10000) in paragraph at lines 10910--10911
[]\OT1/cmtt/m/n/10.95 void gt[]bsearch[]all[]mark([]GtArray *members, const voi
d *key, const

Underfull \hbox (badness 10000) in paragraph at lines 10910--10911
\OT1/cmtt/m/n/10.95 void *base, size[]t nmemb, size[]t size, GtCompareWithData,
 void *data,

Underfull \hbox (badness 10000) in paragraph at lines 10910--10911


Underfull \hbox (badness 10000) in paragraph at lines 10923--10924


Underfull \hbox (badness 10000) in paragraph at lines 10935--10936


Underfull \hbox (badness 10000) in paragraph at lines 10950--10951
[]\OT1/cmtt/m/n/10.95 void gt[]countingsort([]void *out, const void *in, size[]
t elem[]size, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 10950--10951


Underfull \hbox (badness 10000) in paragraph at lines 10966--10967
[]\OT1/cmtt/m/n/10.95 GtUword gt[]countingsort[]get[]max([]const void *in, size
[]t elem[]size, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 10966--10967

[135]
Underfull \hbox (badness 10000) in paragraph at lines 10977--10978


Underfull \hbox (badness 10000) in paragraph at lines 10987--10988


Underfull \hbox (badness 10000) in paragraph at lines 10999--11000


Underfull \hbox (badness 10000) in paragraph at lines 11010--11011


Underfull \hbox (badness 10000) in paragraph at lines 11019--11020


Underfull \hbox (badness 10000) in paragraph at lines 11029--11030


Underfull \hbox (badness 10000) in paragraph at lines 11039--11040


Underfull \hbox (badness 10000) in paragraph at lines 11050--11051

[136]
Underfull \hbox (badness 10000) in paragraph at lines 11063--11064


Underfull \hbox (badness 10000) in paragraph at lines 11075--11076
[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry([]const char *description, co
nst char *sequence,

Underfull \hbox (badness 10000) in paragraph at lines 11075--11076


Underfull \hbox (badness 10000) in paragraph at lines 11087--11088
[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry[]nt([]const char *description
, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 11087--11088
\OT1/cmtt/m/n/10.95 description[]length, const char *sequence, GtUword sequence
[]length,

Underfull \hbox (badness 10000) in paragraph at lines 11087--11088


Underfull \hbox (badness 3364) in paragraph at lines 11091--11096
[]\OT1/ptm/m/n/10.95 Print a fasta en-try with op-tional \OT1/cmtt/m/n/10.95 de
scription \OT1/ptm/m/n/10.95 and manda-tory \OT1/cmtt/m/n/10.95 sequence \OT1/p
tm/m/n/10.95 to

Underfull \hbox (badness 10000) in paragraph at lines 11102--11103
[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry[]str([]const char *descriptio
n, const char

Underfull \hbox (badness 10000) in paragraph at lines 11102--11103


Underfull \hbox (badness 10000) in paragraph at lines 11117--11118
[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry[]nt[]str([]const char *descri
ption, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 11117--11118
\OT1/cmtt/m/n/10.95 description[]length, const char *sequence, GtUword sequence
[]length,

Underfull \hbox (badness 10000) in paragraph at lines 11117--11118


Underfull \hbox (badness 3364) in paragraph at lines 11121--11126
[]\OT1/ptm/m/n/10.95 Print a fasta en-try with op-tional \OT1/cmtt/m/n/10.95 de
scription \OT1/ptm/m/n/10.95 and manda-tory \OT1/cmtt/m/n/10.95 sequence \OT1/p
tm/m/n/10.95 to

Underfull \hbox (badness 10000) in paragraph at lines 11132--11133


Underfull \hbox (badness 10000) in paragraph at lines 11144--11145


Underfull \hbox (badness 10000) in paragraph at lines 11153--11154


Underfull \hbox (badness 10000) in paragraph at lines 11163--11164


Underfull \hbox (badness 10000) in paragraph at lines 11173--11174


Underfull \hbox (badness 10000) in paragraph at lines 11182--11183


Underfull \hbox (badness 10000) in paragraph at lines 11191--11192


Overfull \hbox (183.05757pt too wide) in paragraph at lines 11195--11197
[]\OT1/ptm/m/n/10.95 Find \OT1/cmtt/m/n/10.95 file \OT1/ptm/m/n/10.95 in $\OML/
ztmcm/m/it/10.95 PATH; ifithasnodirname\OT1/ztmcm/m/n/10.95 ; \OML/ztmcm/m/it/1
0.95 set[]todirnameotherwise:Sets[]totheemptystringif[]couldnotbefoundin$\OT1/p
tm/m/n/10.95 PATH. 

Underfull \hbox (badness 10000) in paragraph at lines 11202--11203
[]\OT1/cmtt/m/n/10.95 int gt[]file[]find[]in[]env([]GtStr *path, const char *fi
le, const char *env,

Underfull \hbox (badness 10000) in paragraph at lines 11202--11203


Underfull \hbox (badness 10000) in paragraph at lines 11206--11210
[]\OT1/ptm/m/n/10.95 Find \OT1/cmtt/m/n/10.95 file \OT1/ptm/m/n/10.95 in the ':
'-separated di-rec-tory list (on Win-

Underfull \hbox (badness 10000) in paragraph at lines 11206--11210
\OT1/ptm/m/n/10.95 dows ';'-separated) spec-i-fied in en-vi-ron-ment vari-able

Overfull \hbox (105.20361pt too wide) in paragraph at lines 11206--11210
[]\OML/ztmcm/m/it/10.95 ; ifithasnodirname\OT1/ztmcm/m/n/10.95 ; \OML/ztmcm/m/i
t/10.95 set[]todirnameotherwise:Sets[]totheemptystringif[]couldnotbefoundin$\OT
1/cmtt/m/n/10.95 env\OT1/ptm/m/n/10.95 . 

Underfull \hbox (badness 10000) in paragraph at lines 11214--11215


Underfull \hbox (badness 10000) in paragraph at lines 11225--11226


Underfull \hbox (badness 5091) in paragraph at lines 11229--11231
[]\OT1/ptm/m/n/10.95 Return the (es-ti-mated) to-tal size of all files given in
 \OT1/cmtt/m/n/10.95 filenames\OT1/ptm/m/n/10.95 . Uses

Underfull \hbox (badness 10000) in paragraph at lines 11236--11237
[]\OT1/cmtt/m/n/10.95 int gt[]files[]guess[]if[]protein[]sequences([]const GtSt
rArray *filenames,

Underfull \hbox (badness 10000) in paragraph at lines 11236--11237


Underfull \hbox (badness 10000) in paragraph at lines 11250--11251


Overfull \hbox (344.88547pt too wide) in paragraph at lines 11254--11257
[]\OT1/ptm/m/n/10.95 Find reg-u-lar ex-e-cutable \OT1/cmtt/m/n/10.95 file \OT1/
ptm/m/n/10.95 in $\OML/ztmcm/m/it/10.95 PATH; ifithasnodirname\OT1/ztmcm/m/n/10
.95 ; \OML/ztmcm/m/it/10.95 set[]todirnameotherwise:Sets[]totheemptystringifreg
ularexecutable[]couldnotbefoundin$\OT1/ptm/m/n/10.95 PATH. 

Underfull \hbox (badness 10000) in paragraph at lines 11261--11262


Underfull \hbox (badness 10000) in paragraph at lines 11270--11271

[137] [138]
Underfull \hbox (badness 10000) in paragraph at lines 11282--11283


Underfull \hbox (badness 10000) in paragraph at lines 11295--11296


Underfull \hbox (badness 10000) in paragraph at lines 11304--11305


Underfull \hbox (badness 10000) in paragraph at lines 11315--11316


Underfull \hbox (badness 10000) in paragraph at lines 11325--11326
[]\OT1/cmtt/m/n/10.95 int gt[]grep[]nt([]bool *match, const char *pattern, cons
t char *line, size[]t

Underfull \hbox (badness 10000) in paragraph at lines 11325--11326


Underfull \hbox (badness 10000) in paragraph at lines 11337--11338


Underfull \hbox (badness 10000) in paragraph at lines 11347--11348


Underfull \hbox (badness 10000) in paragraph at lines 11356--11357

[139]
Underfull \hbox (badness 10000) in paragraph at lines 11369--11370


Underfull \hbox (badness 10000) in paragraph at lines 11378--11379


Underfull \hbox (badness 10000) in paragraph at lines 11387--11388


Underfull \hbox (badness 10000) in paragraph at lines 11398--11399


Underfull \hbox (badness 2065) in paragraph at lines 11402--11406
[]\OT1/ptm/m/n/10.95 Prints the log mes-sage ob-tained from for-mat and fol-low
-ing pa-ram-e-ter ac-cord-

Underfull \hbox (badness 4660) in paragraph at lines 11402--11406
\OT1/ptm/m/n/10.95 ing to if log-ging is en-abled ana-log to\OT1/cmtt/m/n/10.95
 gt[]log[]log()\OT1/ptm/m/n/10.95 . But in con-trast to

Underfull \hbox (badness 10000) in paragraph at lines 11410--11411


Underfull \hbox (badness 10000) in paragraph at lines 11419--11420


Underfull \hbox (badness 10000) in paragraph at lines 11430--11431


Underfull \hbox (badness 10000) in paragraph at lines 11443--11444


Underfull \hbox (badness 10000) in paragraph at lines 11454--11455


Underfull \hbox (badness 10000) in paragraph at lines 11465--11466


Underfull \hbox (badness 10000) in paragraph at lines 11476--11477


Underfull \hbox (badness 10000) in paragraph at lines 11486--11487

[140]
Underfull \hbox (badness 10000) in paragraph at lines 11497--11498


Underfull \hbox (badness 10000) in paragraph at lines 11509--11510
[]\OT1/cmtt/m/n/10.95 void gt[]msort[]r([]void *base, size[]t nmemb, size[]t si
ze, void *comparinfo,

Underfull \hbox (badness 10000) in paragraph at lines 11509--11510


Underfull \hbox (badness 10000) in paragraph at lines 11521--11522


Underfull \hbox (badness 10000) in paragraph at lines 11534--11535


Underfull \hbox (badness 2762) in paragraph at lines 11538--11548
[]\OT1/ptm/m/n/10.95 This mod-ule im-ple-ments the func-tion\OT1/cmtt/m/n/10.95
 gt[]basename() \OT1/ptm/m/n/10.95 ac-cord-ing to the spec-i-fi-

Underfull \hbox (badness 2951) in paragraph at lines 11538--11548
\OT1/ptm/m/n/10.95 ca-tions in http://www.unix-systems.org/onlinepubs/7908799/x
sh/basename.html and
[141]
Underfull \hbox (badness 10000) in paragraph at lines 11554--11555


Underfull \hbox (badness 10000) in paragraph at lines 11564--11565


Underfull \hbox (badness 10000) in paragraph at lines 11574--11575


Underfull \hbox (badness 10000) in paragraph at lines 11584--11585


Underfull \hbox (badness 10000) in paragraph at lines 11594--11595


Underfull \hbox (badness 10000) in paragraph at lines 11605--11606
[]\OT1/cmtt/m/n/10.95 int gt[]parse[]range([]GtRange *rng, const char *start, c
onst char *end,

Underfull \hbox (badness 10000) in paragraph at lines 11605--11606


Underfull \hbox (badness 10000) in paragraph at lines 11619--11620
[]\OT1/cmtt/m/n/10.95 int gt[]parse[]range[]tidy([]GtRange *rng, const char *st
art, const char *end,

Underfull \hbox (badness 10000) in paragraph at lines 11619--11620

[142]
Underfull \hbox (badness 10000) in paragraph at lines 11633--11634
[]\OT1/cmtt/m/n/10.95 void gt[]qsort[]r([]void *a, size[]t n, size[]t es, void 
*data,

Underfull \hbox (badness 10000) in paragraph at lines 11633--11634


Underfull \hbox (badness 10000) in paragraph at lines 11637--11639
[]\OT1/ptm/m/n/10.95 Like \OT1/cmtt/m/n/10.95 qsort(3)\OT1/ptm/m/n/10.95 , but 
al-lows an ad-di-tional \OT1/cmtt/m/n/10.95 data \OT1/ptm/m/n/10.95 pointer pas
sed to the

Underfull \hbox (badness 10000) in paragraph at lines 11645--11646


Underfull \hbox (badness 10000) in paragraph at lines 11656--11657


Underfull \hbox (badness 10000) in paragraph at lines 11669--11670


Underfull \hbox (badness 10000) in paragraph at lines 11686--11687


Underfull \hbox (badness 10000) in paragraph at lines 11697--11698


Underfull \hbox (badness 10000) in paragraph at lines 11706--11707


Underfull \hbox (badness 10000) in paragraph at lines 11715--11716


Underfull \hbox (badness 10000) in paragraph at lines 11724--11725


Underfull \hbox (badness 10000) in paragraph at lines 11733--11734


Underfull \hbox (badness 10000) in paragraph at lines 11742--11743


Underfull \hbox (badness 10000) in paragraph at lines 11751--11752


Underfull \hbox (badness 10000) in paragraph at lines 11760--11761


Underfull \hbox (badness 10000) in paragraph at lines 11769--11770


Underfull \hbox (badness 10000) in paragraph at lines 11778--11779


Underfull \hbox (badness 10000) in paragraph at lines 11787--11788

[143]
Underfull \hbox (badness 10000) in paragraph at lines 11798--11799


Underfull \hbox (badness 10000) in paragraph at lines 11812--11813
[]\OT1/cmtt/m/n/10.95 const char* gt[]version[]check([]unsigned int required[]m
ajor, unsigned int

Underfull \hbox (badness 10000) in paragraph at lines 11812--11813


Underfull \hbox (badness 10000) in paragraph at lines 11826--11827

[144]
Underfull \hbox (badness 10000) in paragraph at lines 11837--11838


Underfull \hbox (badness 10000) in paragraph at lines 11846--11847


Underfull \hbox (badness 10000) in paragraph at lines 11855--11856


Underfull \hbox (badness 10000) in paragraph at lines 11865--11866


Underfull \hbox (badness 10000) in paragraph at lines 11875--11876
[]\OT1/cmtt/m/n/10.95 void gt[]warning[]default[]handler([]void *data, const ch
ar *format, va[]list

Underfull \hbox (badness 10000) in paragraph at lines 11875--11876


Underfull \hbox (badness 10000) in paragraph at lines 11886--11887


Underfull \hbox (badness 10000) in paragraph at lines 11895--11896


Underfull \hbox (badness 10000) in paragraph at lines 11907--11908


Underfull \hbox (badness 10000) in paragraph at lines 11916--11917


Underfull \hbox (badness 10000) in paragraph at lines 11925--11926


Underfull \hbox (badness 10000) in paragraph at lines 11934--11935


Underfull \hbox (badness 10000) in paragraph at lines 11943--11944


Underfull \hbox (badness 10000) in paragraph at lines 11952--11953


Underfull \hbox (badness 10000) in paragraph at lines 11961--11962


Underfull \hbox (badness 10000) in paragraph at lines 11970--11971


Underfull \hbox (badness 10000) in paragraph at lines 11979--11980


Underfull \hbox (badness 10000) in paragraph at lines 11988--11989


Underfull \hbox (badness 10000) in paragraph at lines 11997--11998


Underfull \hbox (badness 10000) in paragraph at lines 12007--12008


Underfull \hbox (badness 10000) in paragraph at lines 12016--12017


Underfull \hbox (badness 10000) in paragraph at lines 12025--12026


Underfull \hbox (badness 10000) in paragraph at lines 12034--12035


Underfull \hbox (badness 10000) in paragraph at lines 12044--12045


Underfull \hbox (badness 10000) in paragraph at lines 12053--12054


Underfull \hbox (badness 10000) in paragraph at lines 12062--12063


Underfull \hbox (badness 10000) in paragraph at lines 12071--12072


Underfull \hbox (badness 10000) in paragraph at lines 12080--12081


Underfull \hbox (badness 10000) in paragraph at lines 12089--12090

[145] [146]) [147] (./annotationsketch.aux)
kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+264/600 --dpi 864 cmttb10
mkdir: cannot create directory '././sbuild-nonexistent': Permission denied
mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+264/600; nonstopmode; input cmttb10
This is METAFONT, Version 2.7182818 (TeX Live 2015/Debian) (preloaded base=mf)

(/usr/share/texlive/texmf-dist/fonts/source/public/cm/cmttb10.mf
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/cmbase.mf)
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/roman.mf
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romanu.mf [65] [66]
[67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81]
[82] [83] [84] [85] [86] [87] [88] [89] [90])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romanl.mf [97] [98]
[99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111]
[112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/greeku.mf [0] [1]
[2] [3] [4] [5] [6] [7] [8] [9] [10])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romand.mf [48] [49]
[50] [51] [52] [53] [54] [55] [56] [57])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romanp.mf [36] [38]
[63] [15]) (/usr/share/texlive/texmf-dist/fonts/source/public/cm/romspl.mf
[16] [17] [25] [26] [27] [28])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romspu.mf [29] [30]
[31]) (/usr/share/texlive/texmf-dist/fonts/source/public/cm/punct.mf [33]
[14] [35] [37] [39] [40] [41] [42] [43] [44] [46] [47] [58] [59] [61] [64]
[91] [93] [96]) (/usr/share/texlive/texmf-dist/fonts/source/public/cm/accent.mf
[18] [19] [20] [21] [22] [23] [24] [94] [126] [127])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romsub.mf
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/sym.mf [45] [12] [11]
[60] [62] [95] [92] [124] [123] [125] [34]) [13] [32]) ) )
Font metrics written on cmttb10.tfm.
Output written on cmttb10.864gf (128 characters, 26792 bytes).
Transcript written on cmttb10.log.
mktexpk: /tmp/texfonts/pk/ljfour/public/cm/cmttb10.864pk: successfully generated.


Package rerunfilecheck Warning: File `annotationsketch.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.


LaTeX Font Warning: Some font shapes were not available, defaults substituted.


LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information) </tmp/texfonts/pk/ljfour/p
ublic/cm/cmttb10.864pk>
kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 0+480/600 --dpi 480 cmttb10
mkdir: cannot create directory '././sbuild-nonexistent': Permission denied
mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=0+480/600; nonstopmode; input cmttb10
This is METAFONT, Version 2.7182818 (TeX Live 2015/Debian) (preloaded base=mf)

(/usr/share/texlive/texmf-dist/fonts/source/public/cm/cmttb10.mf
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/cmbase.mf)
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/roman.mf
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romanu.mf [65] [66]
[67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81]
[82] [83] [84] [85] [86] [87] [88] [89] [90])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romanl.mf [97] [98]
[99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111]
[112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/greeku.mf [0] [1]
[2] [3] [4] [5] [6] [7] [8] [9] [10])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romand.mf [48] [49]
[50] [51] [52] [53] [54] [55] [56] [57])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romanp.mf [36] [38]
[63] [15]) (/usr/share/texlive/texmf-dist/fonts/source/public/cm/romspl.mf
[16] [17] [25] [26] [27] [28])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romspu.mf [29] [30]
[31]) (/usr/share/texlive/texmf-dist/fonts/source/public/cm/punct.mf [33]
[14] [35] [37] [39] [40] [41] [42] [43] [44] [46] [47] [58] [59] [61] [64]
[91] [93] [96]) (/usr/share/texlive/texmf-dist/fonts/source/public/cm/accent.mf
[18] [19] [20] [21] [22] [23] [24] [94] [126] [127])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romsub.mf
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/sym.mf [45] [12] [11]
[60] [62] [95] [92] [124] [123] [125] [34]) [13] [32]) ) )
Font metrics written on cmttb10.tfm.
Output written on cmttb10.480gf (128 characters, 15944 bytes).
Transcript written on cmttb10.log.
mktexpk: /tmp/texfonts/pk/ljfour/public/cm/cmttb10.480pk: successfully generated.
 </tmp/texfonts/pk/ljfour/public/cm/cmttb10.480pk>{/usr/
share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmssbx10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmtt8.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/ut
mb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on annotationsketch.pdf (147 pages, 1148583 bytes).
Transcript written on annotationsketch.log.
mv annotationsketch.aux annotationsketch-pdf.aux
test -e annotationsketch-pdf.aux && mv annotationsketch-pdf.aux annotationsketch.aux
bibtex annotationsketch
This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
The top-level auxiliary file: annotationsketch.aux
I found no \citation commands---while reading file annotationsketch.aux
I found no \bibdata command---while reading file annotationsketch.aux
I found no \bibstyle command---while reading file annotationsketch.aux
(There were 3 error messages)
Makefile:32: recipe for target 'annotationsketch-pdf.bbl' failed
make[3]: [annotationsketch-pdf.bbl] Error 2 (ignored)
test -e annotationsketch-pdf.bbl || touch annotationsketch-pdf.bbl
diff annotationsketch-pdf.bbl annotationsketch.bbl || mv annotationsketch.bbl annotationsketch-pdf.bbl && rm -f annotationsketch.bbl
mv annotationsketch.aux annotationsketch-pdf.aux
test -e annotationsketch-pdf.aux && mv annotationsketch-pdf.aux annotationsketch.aux
test -e annotationsketch-pdf.bbl && mv annotationsketch-pdf.bbl annotationsketch.bbl
pdflatex annotationsketch.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./annotationsketch.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrreprt.cls
Document Class: scrreprt 2015/10/03 v3.19a KOMA-Script document class (report)
(/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrkbase.sty
(/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrbase.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrlfile.sty
Package scrlfile, 2015/10/03 v3.19a KOMA-Script package (loading files)
                  Copyright (C) Markus Kohm

))) (/usr/share/texlive/texmf-dist/tex/latex/koma-script/tocbasic.sty)
(/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrsize11pt.clo)
(/usr/share/texlive/texmf-dist/tex/latex/koma-script/typearea.sty
Package typearea, 2015/10/03 v3.19a KOMA-Script package (type area)
                  Copyright (C) Frank Neukam, 1992-1994
                  Copyright (C) Markus Kohm, 1994-

)) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg)))
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/mathptmx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/bold-extra/bold-extra.sty)
(/usr/share/texlive/texmf-dist/tex/latex/caption/caption.sty
(/usr/share/texlive/texmf-dist/tex/latex/caption/caption3.sty))
(./annotationsketch.aux)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./annotationsketch.out) (./annotationsketch.out)

LaTeX Font Warning: Font shape `OT1/cmss/bx/it' undefined
(Font)              using `OT1/cmss/bx/n' instead on input line 56.

(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omlztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omxztmcm.fd) [1{/var/lib/texmf/
fonts/map/pdftex/updmap/pdftex.map}] (./annotationsketch.toc [2] [3] [4]
[5]) [6]
chapter 1.

Class scrreprt Warning: \float@addtolists detected!
(scrreprt)              Implementation of \float@addtolist became
(scrreprt)              deprecated in KOMA-Script v3.01 2008/11/14 and
(scrreprt)              has been replaced by several more flexible
(scrreprt)              features of package `tocbasic`.
(scrreprt)              Since Version 3.12 support for deprecated
(scrreprt)              \float@addtolist interface has been
(scrreprt)              restricted to only some of the KOMA-Script
(scrreprt)              features and been removed from others.
(scrreprt)              Loading of package `scrhack' may help to
(scrreprt)              avoid this warning, if you are using a
(scrreprt)              a package that still implements the
(scrreprt)              deprecated \float@addtolist interface .


<../../www/genometools.org/htdocs/images/dataflow.pdf, id=901, 680.33936pt x 86
1.9156pt> <use ../../www/genometools.org/htdocs/images/dataflow.pdf>
<../../www/genometools.org/htdocs/images/gfftree.pdf, id=903, 510.53029pt x 138
.67685pt> <use ../../www/genometools.org/htdocs/images/gfftree.pdf> [7]
<../../www/genometools.org/htdocs/images/diagram.pdf, id=912, 1363.36378pt x 59
3.45078pt> <use ../../www/genometools.org/htdocs/images/diagram.pdf> [8 <../../
www/genometools.org/htdocs/images/dataflow.pdf>] [9 <../../www/genometools.org/
htdocs/images/gfftree.pdf> <../../www/genometools.org/htdocs/images/diagram.pdf


pdfTeX warning: /usr/bin/pdflatex (file ../../www/genometools.org/htdocs/images
/diagram.pdf): PDF inclusion: multiple pdfs with page group included in a singl
e page
>]
<../../www/genometools.org/htdocs/images/collapse_types.pdf, id=944, 215.72322p
t x 285.93611pt>
<use ../../www/genometools.org/htdocs/images/collapse_types.pdf>
<../../www/genometools.org/htdocs/images/cnn_large.jpg, id=945, 1589.94pt x 654
.7662pt> <use ../../www/genometools.org/htdocs/images/cnn_large.jpg> [10 <../..
/www/genometools.org/htdocs/images/collapse_types.pdf>] [11 <../../www/genometo
ols.org/htdocs/images/cnn_large.jpg>]
<../../www/genometools.org/htdocs/images/callbacks.jpg, id=1020, 602.25pt x 379
.4175pt> <use ../../www/genometools.org/htdocs/images/callbacks.jpg> [12 <../..
/www/genometools.org/htdocs/images/callbacks.jpg>]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)
<../../www/genometools.org/htdocs/images/example_nocollapse_noselect.jpg, id=10
33, 602.25pt x 242.9075pt>
<use ../../www/genometools.org/htdocs/images/example_nocollapse_noselect.jpg>
[13] (/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
<../../www/genometools.org/htdocs/images/example_strandselect.jpg, id=1043, 602
.25pt x 319.1925pt>
<use ../../www/genometools.org/htdocs/images/example_strandselect.jpg> [14 <../
../www/genometools.org/htdocs/images/example_nocollapse_noselect.jpg>]
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang2.sty)
<../../www/genometools.org/htdocs/images/example_filterselect.jpg, id=1059, 602
.25pt x 319.1925pt>
<use ../../www/genometools.org/htdocs/images/example_filterselect.jpg> [15 <../
../www/genometools.org/htdocs/images/example_strandselect.jpg>]
<../../www/genometools.org/htdocs/images/example_ct.jpg, id=1086, 602.25pt x 55
4.07pt> <use ../../www/genometools.org/htdocs/images/example_ct.jpg> [16 <../..
/www/genometools.org/htdocs/images/example_filterselect.jpg>] [17 <../../www/ge
nometools.org/htdocs/images/example_ct.jpg>]
Overfull \hbox (4.75348pt too wide) in paragraph at lines 388--389
[][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] 

Overfull \hbox (4.75348pt too wide) in paragraph at lines 390--391
[][][][][][][][][][][][][][][][][][][][][][][][][][] 

Overfull \hbox (4.75348pt too wide) in paragraph at lines 391--392
[][][][][][][][][][][][][][] 

Overfull \hbox (4.75348pt too wide) in paragraph at lines 393--394
[][][][][][][][][][][][][][][][][][] 

Overfull \hbox (4.75348pt too wide) in paragraph at lines 394--395
[][][][][][][][][][][][][][][][][][][][][][] 

Overfull \hbox (4.75348pt too wide) in paragraph at lines 396--397
[][][][][][][][][][][][][][][][][][][][][][][][][][] 

Overfull \hbox (4.75348pt too wide) in paragraph at lines 397--398
[][][][][][][][][][][][][][][][][][][][][][] 

<../../www/genometools.org/htdocs/images/example_ct2.jpg, id=1098, 602.25pt x 2
98.11375pt> <use ../../www/genometools.org/htdocs/images/example_ct2.jpg>
[18]
<../../www/genometools.org/htdocs/images/parsed.jpg, id=1143, 602.25pt x 404.51
125pt> <use ../../www/genometools.org/htdocs/images/parsed.jpg>
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(../../src/examples/sketch_parsed.c [19 <../../www/genometools.org/htdocs/image
s/example_ct2.jpg>] [20 <../../www/genometools.org/htdocs/images/parsed.jpg>])
Overfull \hbox (37.5989pt too wide) in paragraph at lines 441--442
\OT1/ptm/m/n/10.95 the com-mand line \OT1/cmtt/m/n/10.95 gt gtscripts/sketch[]p
arsed.lua <style[]file> <PNG[]file> <GFF3[]file>\OT1/ptm/m/n/10.95 ) 
(../../gtscripts/sketch_parsed.lua [21]) (../../gtruby/sketch_parsed.rb
[22]) (../../gtpython/sketch_parsed.py [23])
<../../www/genometools.org/htdocs/images/constructed.jpg, id=1387, 602.25pt x 1
49.55875pt> <use ../../www/genometools.org/htdocs/images/constructed.jpg>
(../../src/examples/sketch_constructed.c [24 <../../www/genometools.org/htdocs/
images/constructed.jpg>] [25])
Overfull \hbox (28.675pt too wide) in paragraph at lines 464--465
\OT1/ptm/m/n/10.95 run by the com-mand line \OT1/cmtt/m/n/10.95 gt gtscripts/sk
etch[]constructed.lua <style[]file> <PNG[]file>\OT1/ptm/m/n/10.95 ) 
(../../gtscripts/sketch_constructed.lua [26])
(../../gtruby/sketch_constructed.rb [27]) (../../gtpython/sketch_constructed.py
[28]) (./api_reference.tex [29]
chapter 2.
[30] [31] [32] [33] [34]
Underfull \hbox (badness 10000) in paragraph at lines 321--322
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]gfflike[]get[]all[]features([]GtF
eatureIndex *gfi, GtArray

Underfull \hbox (badness 10000) in paragraph at lines 321--322


Underfull \hbox (badness 10000) in paragraph at lines 333--334
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]dup[]feature[]stream[]new([]GtNodeStrea
m*, const char

Underfull \hbox (badness 10000) in paragraph at lines 333--334


Underfull \hbox (badness 10000) in paragraph at lines 343--344


Underfull \hbox (badness 10000) in paragraph at lines 354--355

[35]
Underfull \hbox (badness 10000) in paragraph at lines 376--377


Underfull \hbox (badness 10000) in paragraph at lines 394--395


Underfull \hbox (badness 10000) in paragraph at lines 403--404


Underfull \hbox (badness 10000) in paragraph at lines 412--413


Underfull \hbox (badness 10000) in paragraph at lines 421--422


Underfull \hbox (badness 10000) in paragraph at lines 432--433
[]\OT1/cmtt/m/n/10.95 GtAlphabet* gt[]alphabet[]new[]from[]file[]no[]suffix([]c
onst char *filename,

Underfull \hbox (badness 10000) in paragraph at lines 432--433


Underfull \hbox (badness 10000) in paragraph at lines 443--444
[]\OT1/cmtt/m/n/10.95 GtAlphabet* gt[]alphabet[]new[]from[]string([]const char 
*alphadef, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 443--444


Underfull \hbox (badness 10000) in paragraph at lines 454--455
[]\OT1/cmtt/m/n/10.95 GtAlphabet* gt[]alphabet[]new[]from[]sequence([]const GtS
trArray *filenametab,

Underfull \hbox (badness 10000) in paragraph at lines 454--455


Underfull \hbox (badness 10000) in paragraph at lines 466--467


Underfull \hbox (badness 10000) in paragraph at lines 476--477


Underfull \hbox (badness 10000) in paragraph at lines 485--486


Underfull \hbox (badness 10000) in paragraph at lines 495--496


Underfull \hbox (badness 10000) in paragraph at lines 505--506
[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]add[]mapping([]GtAlphabet *alphabet, c
onst char

Underfull \hbox (badness 10000) in paragraph at lines 505--506


Underfull \hbox (badness 10000) in paragraph at lines 515--516


Underfull \hbox (badness 10000) in paragraph at lines 524--525


Underfull \hbox (badness 10000) in paragraph at lines 534--535


Underfull \hbox (badness 10000) in paragraph at lines 543--544


Underfull \hbox (badness 10000) in paragraph at lines 552--553


Underfull \hbox (badness 10000) in paragraph at lines 561--562


Underfull \hbox (badness 10000) in paragraph at lines 570--571


Underfull \hbox (badness 10000) in paragraph at lines 580--581


Underfull \hbox (badness 10000) in paragraph at lines 591--592
[]\OT1/cmtt/m/n/10.95 int gt[]alphabet[]to[]file([]const GtAlphabet *alphabet, 
const char

Underfull \hbox (badness 10000) in paragraph at lines 591--592


Underfull \hbox (badness 10000) in paragraph at lines 601--602


Underfull \hbox (badness 10000) in paragraph at lines 612--613
[]\OT1/cmtt/m/n/10.95 GtUchar gt[]alphabet[]pretty[]symbol([]const GtAlphabet *
alphabet, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 612--613


Underfull \hbox (badness 10000) in paragraph at lines 623--624
[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]echo[]pretty[]symbol([]const GtAlphabe
t *alphabet, FILE

Underfull \hbox (badness 10000) in paragraph at lines 623--624


Underfull \hbox (badness 10000) in paragraph at lines 633--634


Underfull \hbox (badness 10000) in paragraph at lines 645--646


Underfull \hbox (badness 10000) in paragraph at lines 656--657


Underfull \hbox (badness 10000) in paragraph at lines 665--666


Underfull \hbox (badness 10000) in paragraph at lines 675--676


Underfull \hbox (badness 10000) in paragraph at lines 685--686
[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]encode[]seq([]const GtAlphabet *alphab
et, GtUchar *out,

Underfull \hbox (badness 10000) in paragraph at lines 685--686


Underfull \hbox (badness 10000) in paragraph at lines 698--699
[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]decode[]seq[]to[]fp([]const GtAlphabet
 *alphabet, FILE *fpout,

Underfull \hbox (badness 10000) in paragraph at lines 698--699


Underfull \hbox (badness 10000) in paragraph at lines 713--714
[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]decode[]seq[]to[]cstr([]const GtAlphab
et *alphabet, char

Underfull \hbox (badness 10000) in paragraph at lines 713--714


Underfull \hbox (badness 10000) in paragraph at lines 728--729
[]\OT1/cmtt/m/n/10.95 GtStr* gt[]alphabet[]decode[]seq[]to[]str([]const GtAlpha
bet *alphabet, const

Underfull \hbox (badness 10000) in paragraph at lines 728--729


Underfull \hbox (badness 10000) in paragraph at lines 738--739

[36] [37] [38]
Underfull \hbox (badness 10000) in paragraph at lines 757--758


Underfull \hbox (badness 10000) in paragraph at lines 775--776
[]\OT1/cmtt/m/n/10.95 GtFeatureIndex* gt[]anno[]db[]schema[]get[]feature[]index
([]GtAnnoDBSchema

Underfull \hbox (badness 10000) in paragraph at lines 775--776


Underfull \hbox (badness 10000) in paragraph at lines 786--787

[39]
Underfull \hbox (badness 10000) in paragraph at lines 803--804


Underfull \hbox (badness 10000) in paragraph at lines 812--813


Underfull \hbox (badness 10000) in paragraph at lines 822--823


Underfull \hbox (badness 10000) in paragraph at lines 831--832


Underfull \hbox (badness 10000) in paragraph at lines 841--842


Underfull \hbox (badness 10000) in paragraph at lines 850--851


Underfull \hbox (badness 10000) in paragraph at lines 859--860


Underfull \hbox (badness 10000) in paragraph at lines 868--869


Underfull \hbox (badness 10000) in paragraph at lines 878--879


Underfull \hbox (badness 10000) in paragraph at lines 889--890


Underfull \hbox (badness 10000) in paragraph at lines 901--902


Underfull \hbox (badness 10000) in paragraph at lines 911--912


Underfull \hbox (badness 10000) in paragraph at lines 922--923


Underfull \hbox (badness 10000) in paragraph at lines 934--935


Underfull \hbox (badness 10000) in paragraph at lines 943--944


Underfull \hbox (badness 5563) in paragraph at lines 947--949
[]\OT1/ptm/m/n/10.95 Set the size of \OT1/cmtt/m/n/10.95 array \OT1/ptm/m/n/10.
95 to \OT1/cmtt/m/n/10.95 size\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 size \OT
1/ptm/m/n/10.95 must be smaller or equal than

Underfull \hbox (badness 10000) in paragraph at lines 953--954


Underfull \hbox (badness 10000) in paragraph at lines 962--963


Underfull \hbox (badness 10000) in paragraph at lines 971--972


Underfull \hbox (badness 10000) in paragraph at lines 981--982


Underfull \hbox (badness 10000) in paragraph at lines 990--991


Underfull \hbox (badness 10000) in paragraph at lines 1000--1001
[]\OT1/cmtt/m/n/10.95 void gt[]array[]sort[]with[]data([]GtArray *array, GtComp
areWithData compar,

Underfull \hbox (badness 10000) in paragraph at lines 1000--1001


Underfull \hbox (badness 10000) in paragraph at lines 1011--1012
[]\OT1/cmtt/m/n/10.95 void gt[]array[]sort[]stable[]with[]data([]GtArray *array
, GtCompareWithData

Underfull \hbox (badness 10000) in paragraph at lines 1011--1012


Underfull \hbox (badness 10000) in paragraph at lines 1021--1022


Underfull \hbox (badness 10000) in paragraph at lines 1032--1033

[40] [41]
Overfull \hbox (7.61789pt too wide) in paragraph at lines 1043--1046
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. \OT1/cmtt/m/n/10.95 GtArrayOutStream \OT1/ptm/m/n/10.95 tak
es an ar-ray of \OT1/cmtt/m/n/10.95 GtGenomeNodes

Underfull \hbox (badness 10000) in paragraph at lines 1052--1053
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]in[]stream[]new([]GtArray *nodes
, GtUword *progress,

Underfull \hbox (badness 10000) in paragraph at lines 1052--1053


Underfull \hbox (badness 10000) in paragraph at lines 1074--1075
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]out[]stream[]new([]GtNodeStream 
*in[]stream, GtArray

Underfull \hbox (badness 10000) in paragraph at lines 1074--1075


Underfull \hbox (badness 10000) in paragraph at lines 1086--1087
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]out[]stream[]all[]new([]GtNodeSt
ream *in[]stream, GtArray

Underfull \hbox (badness 10000) in paragraph at lines 1086--1087

[42]
Underfull \hbox (badness 10000) in paragraph at lines 1103--1104


Underfull \hbox (badness 10000) in paragraph at lines 1115--1116
[]\OT1/cmtt/m/n/10.95 void gt[]bed[]in[]stream[]set[]feature[]type([]GtBEDInStr
eam *bed[]in[]stream, const

Underfull \hbox (badness 10000) in paragraph at lines 1115--1116


Underfull \hbox (badness 10000) in paragraph at lines 1127--1128
[]\OT1/cmtt/m/n/10.95 void gt[]bed[]in[]stream[]set[]thick[]feature[]type([]GtB
EDInStream *bed[]in[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 1127--1128


Underfull \hbox (badness 10000) in paragraph at lines 1138--1139
[]\OT1/cmtt/m/n/10.95 void gt[]bed[]in[]stream[]set[]block[]type([]GtBEDInStrea
m *bed[]in[]stream, const

Underfull \hbox (badness 10000) in paragraph at lines 1138--1139


Underfull \hbox (badness 10000) in paragraph at lines 1155--1156


Underfull \hbox (badness 10000) in paragraph at lines 1165--1166


Underfull \hbox (badness 10000) in paragraph at lines 1174--1175


Underfull \hbox (badness 10000) in paragraph at lines 1183--1184


Underfull \hbox (badness 10000) in paragraph at lines 1192--1193


Underfull \hbox (badness 10000) in paragraph at lines 1202--1203
[]\OT1/cmtt/m/n/10.95 void gt[]bittab[]and([]GtBittab *bittab[]a, const GtBitta
b *bittab[]b, const

Underfull \hbox (badness 10000) in paragraph at lines 1202--1203


Underfull \hbox (badness 10000) in paragraph at lines 1212--1213
[]\OT1/cmtt/m/n/10.95 void gt[]bittab[]or([]GtBittab *bittab[]a, const GtBittab
 *bittab[]b, const

Underfull \hbox (badness 10000) in paragraph at lines 1212--1213


Underfull \hbox (badness 10000) in paragraph at lines 1222--1223
[]\OT1/cmtt/m/n/10.95 void gt[]bittab[]nand([]GtBittab *bittab[]a, const GtBitt
ab *bittab[]b, const

Underfull \hbox (badness 10000) in paragraph at lines 1222--1223


Underfull \hbox (badness 10000) in paragraph at lines 1231--1232


Underfull \hbox (badness 10000) in paragraph at lines 1240--1241


Underfull \hbox (badness 10000) in paragraph at lines 1249--1250


Underfull \hbox (badness 10000) in paragraph at lines 1258--1259


Underfull \hbox (badness 10000) in paragraph at lines 1267--1268


Underfull \hbox (badness 10000) in paragraph at lines 1276--1277


Underfull \hbox (badness 10000) in paragraph at lines 1285--1286


Underfull \hbox (badness 10000) in paragraph at lines 1294--1295


Underfull \hbox (badness 10000) in paragraph at lines 1303--1304


Underfull \hbox (badness 10000) in paragraph at lines 1312--1313


Underfull \hbox (badness 10000) in paragraph at lines 1321--1322


Underfull \hbox (badness 10000) in paragraph at lines 1330--1331


Underfull \hbox (badness 10000) in paragraph at lines 1340--1341


Underfull \hbox (badness 10000) in paragraph at lines 1349--1350


Underfull \hbox (badness 10000) in paragraph at lines 1358--1359

[43] [44]
Underfull \hbox (badness 10000) in paragraph at lines 1377--1378


Underfull \hbox (badness 10000) in paragraph at lines 1386--1387


Underfull \hbox (badness 10000) in paragraph at lines 1395--1396


Underfull \hbox (badness 10000) in paragraph at lines 1405--1406


Underfull \hbox (badness 10000) in paragraph at lines 1414--1415


Underfull \hbox (badness 10000) in paragraph at lines 1423--1424


Underfull \hbox (badness 10000) in paragraph at lines 1432--1433


Underfull \hbox (badness 10000) in paragraph at lines 1441--1442


Underfull \hbox (badness 10000) in paragraph at lines 1450--1451


Underfull \hbox (badness 10000) in paragraph at lines 1459--1460


Underfull \hbox (badness 10000) in paragraph at lines 1468--1469


Underfull \hbox (badness 10000) in paragraph at lines 1477--1478


Underfull \hbox (badness 10000) in paragraph at lines 1486--1487


Underfull \hbox (badness 10000) in paragraph at lines 1495--1496


Underfull \hbox (badness 10000) in paragraph at lines 1504--1505


Underfull \hbox (badness 10000) in paragraph at lines 1513--1514


Underfull \hbox (badness 10000) in paragraph at lines 1522--1523


Underfull \hbox (badness 10000) in paragraph at lines 1531--1532

[45]
Underfull \hbox (badness 10000) in paragraph at lines 1553--1554
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]cds[]stream[]new([]GtNodeStream *in[]st
ream, GtRegionMapping

Underfull \hbox (badness 10000) in paragraph at lines 1553--1554
\OT1/cmtt/m/n/10.95 *region[]mapping, unsigned int minorflen, const char *sourc
e, bool

Underfull \hbox (badness 10000) in paragraph at lines 1553--1554

[46]
Underfull \hbox (badness 10000) in paragraph at lines 1581--1582
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]csa[]stream[]new([]GtNodeStream *in[]st
ream, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 1581--1582


Underfull \hbox (badness 10000) in paragraph at lines 1601--1602


Underfull \hbox (badness 10000) in paragraph at lines 1610--1611


Underfull \hbox (badness 10000) in paragraph at lines 1633--1634
[]\OT1/cmtt/m/n/10.95 GtCanvas* gt[]canvas[]cairo[]context[]new([]GtStyle *styl
e, cairo[]t *context,

Underfull \hbox (badness 10000) in paragraph at lines 1633--1634
\OT1/cmtt/m/n/10.95 double offsetpos, GtUword width, GtUword height, GtImageInf
o *image[]info,

Underfull \hbox (badness 10000) in paragraph at lines 1633--1634

[47]
Underfull \hbox (badness 10000) in paragraph at lines 1658--1659
[]\OT1/cmtt/m/n/10.95 GtCanvas* gt[]canvas[]cairo[]file[]new([]GtStyle *style, 
GtGraphicsOutType

Underfull \hbox (badness 10000) in paragraph at lines 1658--1659
\OT1/cmtt/m/n/10.95 output[]type, GtUword width, GtUword height, GtImageInfo *i
mage[]info,

Underfull \hbox (badness 10000) in paragraph at lines 1658--1659


Underfull \hbox (badness 10000) in paragraph at lines 1673--1674
[]\OT1/cmtt/m/n/10.95 int gt[]canvas[]cairo[]file[]to[]file([]GtCanvasCairoFile
 *canvas, const char

Underfull \hbox (badness 10000) in paragraph at lines 1673--1674


Underfull \hbox (badness 10000) in paragraph at lines 1684--1685
[]\OT1/cmtt/m/n/10.95 int gt[]canvas[]cairo[]file[]to[]stream([]GtCanvasCairoFi
le *canvas, GtStr

Underfull \hbox (badness 10000) in paragraph at lines 1684--1685


Underfull \hbox (badness 10000) in paragraph at lines 1700--1701


Underfull \hbox (badness 10000) in paragraph at lines 1717--1718
[]\OT1/cmtt/m/n/10.95 GtUword gt[]codon[]iterator[]current[]position([]GtCodonI
terator

Underfull \hbox (badness 10000) in paragraph at lines 1717--1718


Underfull \hbox (badness 10000) in paragraph at lines 1728--1729


Underfull \hbox (badness 10000) in paragraph at lines 1738--1739


Underfull \hbox (badness 10000) in paragraph at lines 1751--1752
[]\OT1/cmtt/m/n/10.95 GtCodonIteratorStatus gt[]codon[]iterator[]next([]GtCodon
Iterator

Underfull \hbox (badness 10000) in paragraph at lines 1751--1752
\OT1/cmtt/m/n/10.95 *codon[]iterator, char *n1, char *n2, char *n3, unsigned in
t *frame,

Underfull \hbox (badness 10000) in paragraph at lines 1751--1752


Underfull \hbox (badness 10000) in paragraph at lines 1770--1771

[48]
Underfull \hbox (badness 10000) in paragraph at lines 1784--1785
[]\OT1/cmtt/m/n/10.95 GtCodonIterator* gt[]codon[]iterator[]encseq[]new([]GtEnc
seq *encseq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 1784--1785


Underfull \hbox (badness 10000) in paragraph at lines 1799--1800
[]\OT1/cmtt/m/n/10.95 GtCodonIterator* gt[]codon[]iterator[]encseq[]new[]with[]
readmode([]GtEncseq

Underfull \hbox (badness 10000) in paragraph at lines 1799--1800
\OT1/cmtt/m/n/10.95 *encseq, GtUword startpos, GtUword length, GtReadmode readm
ode, GtError

Underfull \hbox (badness 10000) in paragraph at lines 1799--1800


Underfull \hbox (badness 10000) in paragraph at lines 1815--1816
[]\OT1/cmtt/m/n/10.95 GtCodonIterator* gt[]codon[]iterator[]simple[]new([]const
 char *seq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 1815--1816

[49]
Underfull \hbox (badness 10000) in paragraph at lines 1832--1833
[]\OT1/cmtt/m/n/10.95 GtColor* gt[]color[]new([]double red, double green, doubl
e blue, double

Underfull \hbox (badness 10000) in paragraph at lines 1832--1833


Underfull \hbox (badness 10000) in paragraph at lines 1844--1845
[]\OT1/cmtt/m/n/10.95 void gt[]color[]set([]GtColor *color, double red, double 
green, double blue,

Underfull \hbox (badness 10000) in paragraph at lines 1844--1845


Underfull \hbox (badness 10000) in paragraph at lines 1855--1856


Underfull \hbox (badness 10000) in paragraph at lines 1864--1865


Underfull \hbox (badness 10000) in paragraph at lines 1881--1882


Underfull \hbox (badness 10000) in paragraph at lines 1893--1894


Underfull \hbox (badness 10000) in paragraph at lines 1902--1903


Underfull \hbox (badness 10000) in paragraph at lines 1914--1915

[50]
Underfull \hbox (badness 10000) in paragraph at lines 1931--1932


Underfull \hbox (badness 10000) in paragraph at lines 1940--1941


Underfull \hbox (badness 10000) in paragraph at lines 1949--1950


Underfull \hbox (badness 10000) in paragraph at lines 1959--1960


Underfull \hbox (badness 10000) in paragraph at lines 1969--1970


Underfull \hbox (badness 10000) in paragraph at lines 1978--1979


Underfull \hbox (badness 10000) in paragraph at lines 1987--1988


Underfull \hbox (badness 10000) in paragraph at lines 2006--2007


Underfull \hbox (badness 10000) in paragraph at lines 2015--2016

[51]
Underfull \hbox (badness 10000) in paragraph at lines 2038--2039
[]\OT1/cmtt/m/n/10.95 GtCustomTrack* gt[]custom[]track[]gc[]content[]new([]cons
t char *seq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 2038--2039


Underfull \hbox (badness 10000) in paragraph at lines 2068--2069
[]\OT1/cmtt/m/n/10.95 GtCustomTrack* gt[]custom[]track[]script[]wrapper[]new([]
GtCtScriptRenderFunc

Underfull \hbox (badness 10000) in paragraph at lines 2068--2069
\OT1/cmtt/m/n/10.95 render[]func, GtCtScriptGetHeightFunc get[]height[]func,

Underfull \hbox (badness 10000) in paragraph at lines 2068--2069


Underfull \hbox (badness 10000) in paragraph at lines 2090--2091
[]\OT1/cmtt/m/n/10.95 GtDiagram* gt[]diagram[]new([]GtFeatureIndex *feature[]in
dex, const char

Underfull \hbox (badness 10000) in paragraph at lines 2090--2091


Underfull \hbox (badness 10000) in paragraph at lines 2103--2104
[]\OT1/cmtt/m/n/10.95 GtDiagram* gt[]diagram[]new[]from[]array([]GtArray *featu
res, const GtRange

Underfull \hbox (badness 10000) in paragraph at lines 2103--2104


Underfull \hbox (badness 10000) in paragraph at lines 2115--2116


Underfull \hbox (badness 10000) in paragraph at lines 2125--2126
[]\OT1/cmtt/m/n/10.95 void gt[]diagram[]set[]track[]selector[]func([]GtDiagram*
, GtTrackSelectorFunc,

Underfull \hbox (badness 10000) in paragraph at lines 2125--2126


Underfull \hbox (badness 10000) in paragraph at lines 2136--2137


Underfull \hbox (badness 10000) in paragraph at lines 2146--2147


Underfull \hbox (badness 10000) in paragraph at lines 2155--2156

[52]
Underfull \hbox (badness 10000) in paragraph at lines 2174--2175


Underfull \hbox (badness 10000) in paragraph at lines 2184--2185


Underfull \hbox (badness 10000) in paragraph at lines 2193--2194


Underfull \hbox (badness 10000) in paragraph at lines 2203--2204
[]\OT1/cmtt/m/n/10.95 void gt[]disc[]distri[]add[]multi([]GtDiscDistri *d, GtUw
ord key, GtUint64

Underfull \hbox (badness 10000) in paragraph at lines 2203--2204


Underfull \hbox (badness 10000) in paragraph at lines 2212--2213


Underfull \hbox (badness 10000) in paragraph at lines 2221--2222


Underfull \hbox (badness 10000) in paragraph at lines 2233--2234
[]\OT1/cmtt/m/n/10.95 void gt[]disc[]distri[]foreach([]const GtDiscDistri *d, G
tDiscDistriIterFunc

Underfull \hbox (badness 10000) in paragraph at lines 2233--2234


Underfull \hbox (badness 10000) in paragraph at lines 2246--2247
[]\OT1/cmtt/m/n/10.95 void gt[]disc[]distri[]foreach[]in[]reverse[]order([]cons
t GtDiscDistri *d,

Underfull \hbox (badness 10000) in paragraph at lines 2246--2247

[53]
Underfull \hbox (badness 10000) in paragraph at lines 2263--2264


Underfull \hbox (badness 10000) in paragraph at lines 2273--2274


Underfull \hbox (badness 10000) in paragraph at lines 2284--2285


Underfull \hbox (badness 10000) in paragraph at lines 2293--2294


Underfull \hbox (badness 10000) in paragraph at lines 2302--2303


Underfull \hbox (badness 10000) in paragraph at lines 2312--2313


Underfull \hbox (badness 10000) in paragraph at lines 2321--2322


Underfull \hbox (badness 10000) in paragraph at lines 2331--2332


Underfull \hbox (badness 10000) in paragraph at lines 2340--2341


Underfull \hbox (badness 10000) in paragraph at lines 2349--2350

[54]
Underfull \hbox (badness 10000) in paragraph at lines 2360--2361


Underfull \hbox (badness 10000) in paragraph at lines 2370--2371


Underfull \hbox (badness 10000) in paragraph at lines 2380--2381


Underfull \hbox (badness 10000) in paragraph at lines 2397--2398


Underfull \hbox (badness 10000) in paragraph at lines 2406--2407

[55]
Underfull \hbox (badness 10000) in paragraph at lines 2442--2443


Underfull \hbox (badness 10000) in paragraph at lines 2452--2453


Underfull \hbox (badness 10000) in paragraph at lines 2462--2463


Underfull \hbox (badness 10000) in paragraph at lines 2473--2474
[]\OT1/cmtt/m/n/10.95 GtUchar gt[]encseq[]get[]encoded[]char([]const GtEncseq *
encseq, GtUword pos,

Underfull \hbox (badness 10000) in paragraph at lines 2473--2474


Underfull \hbox (badness 10000) in paragraph at lines 2485--2486
[]\OT1/cmtt/m/n/10.95 char gt[]encseq[]get[]decoded[]char([]const GtEncseq *enc
seq, GtUword pos,

Underfull \hbox (badness 10000) in paragraph at lines 2485--2486


Underfull \hbox (badness 10000) in paragraph at lines 2497--2498
[]\OT1/cmtt/m/n/10.95 bool gt[]encseq[]position[]is[]separator([]const GtEncseq
 *encseq, GtUword pos,

Underfull \hbox (badness 10000) in paragraph at lines 2497--2498


Underfull \hbox (badness 10000) in paragraph at lines 2509--2510
[]\OT1/cmtt/m/n/10.95 bool gt[]encseq[]position[]is[]wildcard([]const GtEncseq 
*encseq, GtUword pos,

Underfull \hbox (badness 10000) in paragraph at lines 2509--2510


Underfull \hbox (badness 10000) in paragraph at lines 2519--2520


Underfull \hbox (badness 10000) in paragraph at lines 2530--2531
[]\OT1/cmtt/m/n/10.95 GtEncseqReader* gt[]encseq[]create[]reader[]with[]readmod
e([]const GtEncseq

Underfull \hbox (badness 10000) in paragraph at lines 2530--2531


Underfull \hbox (badness 10000) in paragraph at lines 2546--2547
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]extract[]encoded([]const GtEncseq *encse
q, GtUchar *buffer,

Underfull \hbox (badness 10000) in paragraph at lines 2546--2547


Underfull \hbox (badness 10000) in paragraph at lines 2561--2562
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]extract[]decoded([]const GtEncseq *encse
q, char *buffer,

Underfull \hbox (badness 10000) in paragraph at lines 2561--2562


Underfull \hbox (badness 10000) in paragraph at lines 2576--2577


Underfull \hbox (badness 10000) in paragraph at lines 2586--2587


Underfull \hbox (badness 10000) in paragraph at lines 2595--2596


Underfull \hbox (badness 10000) in paragraph at lines 2604--2605


Underfull \hbox (badness 10000) in paragraph at lines 2613--2614


Underfull \hbox (badness 10000) in paragraph at lines 2622--2623


Underfull \hbox (badness 10000) in paragraph at lines 2632--2633


Underfull \hbox (badness 10000) in paragraph at lines 2643--2644


Underfull \hbox (badness 10000) in paragraph at lines 2655--2656
[]\OT1/cmtt/m/n/10.95 const char* gt[]encseq[]description([]const GtEncseq *enc
seq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 2655--2656


Underfull \hbox (badness 10000) in paragraph at lines 2668--2669


Underfull \hbox (badness 10000) in paragraph at lines 2678--2679


Underfull \hbox (badness 10000) in paragraph at lines 2688--2689
[]\OT1/cmtt/m/n/10.95 GtUint64 gt[]encseq[]effective[]filelength([]const GtEncs
eq *encseq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 2688--2689


Underfull \hbox (badness 10000) in paragraph at lines 2699--2700


Underfull \hbox (badness 10000) in paragraph at lines 2710--2711


Underfull \hbox (badness 10000) in paragraph at lines 2721--2722
[]\OT1/cmtt/m/n/10.95 GtUword gt[]encseq[]filenum[]first[]seqnum([]const GtEncs
eq *encseq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 2721--2722


Underfull \hbox (badness 10000) in paragraph at lines 2731--2732


Underfull \hbox (badness 10000) in paragraph at lines 2740--2741


Underfull \hbox (badness 10000) in paragraph at lines 2751--2752


Underfull \hbox (badness 10000) in paragraph at lines 2761--2762


Underfull \hbox (badness 10000) in paragraph at lines 2771--2772


Underfull \hbox (badness 10000) in paragraph at lines 2781--2782


Underfull \hbox (badness 10000) in paragraph at lines 2790--2791

[56] [57] [58]
Underfull \hbox (badness 10000) in paragraph at lines 2807--2808


Underfull \hbox (badness 10000) in paragraph at lines 2817--2818


Underfull \hbox (badness 10000) in paragraph at lines 2829--2830


Underfull \hbox (badness 10000) in paragraph at lines 2841--2842


Underfull \hbox (badness 10000) in paragraph at lines 2852--2853


Underfull \hbox (badness 10000) in paragraph at lines 2864--2865


Underfull \hbox (badness 10000) in paragraph at lines 2874--2875


Underfull \hbox (badness 10000) in paragraph at lines 2883--2884


Underfull \hbox (badness 10000) in paragraph at lines 2892--2893


Underfull \hbox (badness 10000) in paragraph at lines 2901--2902


Underfull \hbox (badness 10000) in paragraph at lines 2910--2911


Underfull \hbox (badness 10000) in paragraph at lines 2919--2920


Underfull \hbox (badness 10000) in paragraph at lines 2929--2930


Underfull \hbox (badness 10000) in paragraph at lines 2941--2942
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]cstr([]GtEncseqBuilder *eb
, const char *str,

Underfull \hbox (badness 10000) in paragraph at lines 2941--2942


Underfull \hbox (badness 10000) in paragraph at lines 2956--2957
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]str([]GtEncseqBuilder *eb,
 GtStr *str, const

Underfull \hbox (badness 10000) in paragraph at lines 2956--2957


Underfull \hbox (badness 10000) in paragraph at lines 2973--2974
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]encoded([]GtEncseqBuilder 
*eb, const GtUchar

Underfull \hbox (badness 10000) in paragraph at lines 2973--2974


Underfull \hbox (badness 10000) in paragraph at lines 2990--2991
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]encoded[]own([]GtEncseqBui
lder *eb, const GtUchar

Underfull \hbox (badness 10000) in paragraph at lines 2990--2991


Underfull \hbox (badness 10000) in paragraph at lines 3007--3008
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]multiple[]encoded([]GtEncs
eqBuilder *eb, const

Underfull \hbox (badness 10000) in paragraph at lines 3007--3008


Underfull \hbox (badness 10000) in paragraph at lines 3019--3020


Underfull \hbox (badness 10000) in paragraph at lines 3029--3030


Underfull \hbox (badness 10000) in paragraph at lines 3042--3043


Underfull \hbox (badness 10000) in paragraph at lines 3052--3053

[59] [60]
Underfull \hbox (badness 10000) in paragraph at lines 3070--3071


Underfull \hbox (badness 10000) in paragraph at lines 3079--3080


Underfull \hbox (badness 10000) in paragraph at lines 3089--3090


Underfull \hbox (badness 10000) in paragraph at lines 3100--3101
[]\OT1/cmtt/m/n/10.95 int gt[]encseq[]encoder[]use[]representation([]GtEncseqEn
coder *ee, const char

Underfull \hbox (badness 10000) in paragraph at lines 3100--3101


Underfull \hbox (badness 10000) in paragraph at lines 3111--3112


Underfull \hbox (badness 10000) in paragraph at lines 3122--3123
[]\OT1/cmtt/m/n/10.95 int gt[]encseq[]encoder[]use[]symbolmap[]file([]GtEncseqE
ncoder *ee, const char

Underfull \hbox (badness 10000) in paragraph at lines 3122--3123


Underfull \hbox (badness 10000) in paragraph at lines 3134--3135


Underfull \hbox (badness 10000) in paragraph at lines 3144--3145


Underfull \hbox (badness 10000) in paragraph at lines 3154--3155


Underfull \hbox (badness 10000) in paragraph at lines 3166--3167


Underfull \hbox (badness 10000) in paragraph at lines 3179--3180


Underfull \hbox (badness 10000) in paragraph at lines 3191--3192


Underfull \hbox (badness 10000) in paragraph at lines 3204--3205


Underfull \hbox (badness 10000) in paragraph at lines 3215--3216


Underfull \hbox (badness 3039) in paragraph at lines 3219--3224
[]\OT1/ptm/m/n/10.95 Enables sup-port for loss-less re-pro-duc-tion of the orig
-i-nal se-quence, re-gard-less

Underfull \hbox (badness 1655) in paragraph at lines 3219--3224
\OT1/ptm/m/n/10.95 of al-pha-bet trans-for-ma-tions that may ap-ply. En-coded s
e-quences cre-ated with-

Underfull \hbox (badness 2359) in paragraph at lines 3219--3224
\OT1/ptm/m/n/10.95 out this sup-port will not be able to be loaded via a \OT1/c
mtt/m/n/10.95 GtEncseqLoader \OT1/ptm/m/n/10.95 with

Underfull \hbox (badness 10000) in paragraph at lines 3228--3229


Underfull \hbox (badness 10000) in paragraph at lines 3238--3239


Underfull \hbox (badness 10000) in paragraph at lines 3249--3250


Underfull \hbox (badness 10000) in paragraph at lines 3259--3260


Underfull \hbox (badness 10000) in paragraph at lines 3268--3269


Underfull \hbox (badness 10000) in paragraph at lines 3278--3279


Underfull \hbox (badness 10000) in paragraph at lines 3288--3289


Underfull \hbox (badness 10000) in paragraph at lines 3297--3298


Underfull \hbox (badness 10000) in paragraph at lines 3307--3308


Underfull \hbox (badness 10000) in paragraph at lines 3317--3318


Underfull \hbox (badness 10000) in paragraph at lines 3326--3327


Underfull \hbox (badness 10000) in paragraph at lines 3336--3337


Underfull \hbox (badness 10000) in paragraph at lines 3346--3347


Underfull \hbox (badness 10000) in paragraph at lines 3355--3356


Underfull \hbox (badness 10000) in paragraph at lines 3365--3366


Underfull \hbox (badness 10000) in paragraph at lines 3374--3375


Underfull \hbox (badness 10000) in paragraph at lines 3383--3384


Underfull \hbox (badness 10000) in paragraph at lines 3392--3393


Underfull \hbox (badness 10000) in paragraph at lines 3401--3402


Underfull \hbox (badness 10000) in paragraph at lines 3411--3412


Underfull \hbox (badness 10000) in paragraph at lines 3423--3424
[]\OT1/cmtt/m/n/10.95 int gt[]encseq[]encoder[]encode([]GtEncseqEncoder *ee, Gt
StrArray *seqfiles,

Underfull \hbox (badness 10000) in paragraph at lines 3423--3424


Underfull \hbox (badness 10000) in paragraph at lines 3434--3435

[61] [62] [63]
Underfull \hbox (badness 10000) in paragraph at lines 3451--3452


Underfull \hbox (badness 10000) in paragraph at lines 3460--3461


Underfull \hbox (badness 10000) in paragraph at lines 3472--3473


Underfull \hbox (badness 10000) in paragraph at lines 3481--3482


Underfull \hbox (badness 10000) in paragraph at lines 3494--3495


Underfull \hbox (badness 10000) in paragraph at lines 3507--3508


Underfull \hbox (badness 10000) in paragraph at lines 3520--3521


Underfull \hbox (badness 10000) in paragraph at lines 3533--3534


Underfull \hbox (badness 10000) in paragraph at lines 3547--3548


Underfull \hbox (badness 10000) in paragraph at lines 3560--3561


Underfull \hbox (badness 10000) in paragraph at lines 3573--3574


Underfull \hbox (badness 10000) in paragraph at lines 3584--3585


Underfull \hbox (badness 10000) in paragraph at lines 3594--3595


Underfull \hbox (badness 10000) in paragraph at lines 3604--3605


Underfull \hbox (badness 10000) in paragraph at lines 3613--3614


Underfull \hbox (badness 10000) in paragraph at lines 3623--3624


Underfull \hbox (badness 10000) in paragraph at lines 3633--3634


Underfull \hbox (badness 10000) in paragraph at lines 3642--3643


Underfull \hbox (badness 10000) in paragraph at lines 3652--3653


Underfull \hbox (badness 10000) in paragraph at lines 3662--3663


Underfull \hbox (badness 10000) in paragraph at lines 3671--3672


Underfull \hbox (badness 10000) in paragraph at lines 3681--3682


Underfull \hbox (badness 10000) in paragraph at lines 3691--3692


Underfull \hbox (badness 10000) in paragraph at lines 3703--3704
[]\OT1/cmtt/m/n/10.95 GtEncseq* gt[]encseq[]loader[]load([]GtEncseqLoader *el, 
const char

Underfull \hbox (badness 10000) in paragraph at lines 3703--3704


Underfull \hbox (badness 10000) in paragraph at lines 3715--3716

[64] [65] [66]
Underfull \hbox (badness 10000) in paragraph at lines 3735--3736
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]reader[]reinit[]with[]readmode([]GtEncse
qReader *esr, const

Underfull \hbox (badness 10000) in paragraph at lines 3735--3736


Underfull \hbox (badness 10000) in paragraph at lines 3739--3741
[]\OT1/ptm/m/n/10.95 Reinitializes the given \OT1/cmtt/m/n/10.95 esr \OT1/ptm/m
/n/10.95 with the val-ues as de-scribed in

Underfull \hbox (badness 10000) in paragraph at lines 3745--3746


Underfull \hbox (badness 10000) in paragraph at lines 3755--3756


Underfull \hbox (badness 10000) in paragraph at lines 3765--3766

[67]
Underfull \hbox (badness 10000) in paragraph at lines 3791--3792


Underfull \hbox (badness 10000) in paragraph at lines 3800--3801


Underfull \hbox (badness 10000) in paragraph at lines 3812--3813


Underfull \hbox (badness 10000) in paragraph at lines 3822--3823


Underfull \hbox (badness 10000) in paragraph at lines 3832--3833


Underfull \hbox (badness 10000) in paragraph at lines 3841--3842


Underfull \hbox (badness 10000) in paragraph at lines 3850--3851


Underfull \hbox (badness 10000) in paragraph at lines 3859--3860


Underfull \hbox (badness 10000) in paragraph at lines 3868--3869


Underfull \hbox (badness 10000) in paragraph at lines 3890--3891
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]extract[]feature[]stream[]new([]GtNodeS
tream *in[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 3890--3891
\OT1/cmtt/m/n/10.95 GtRegionMapping *region[]Mapping, const char *type, bool jo
in, bool

Underfull \hbox (badness 10000) in paragraph at lines 3890--3891

[68]
Underfull \hbox (badness 10000) in paragraph at lines 3909--3910


Underfull \hbox (badness 10000) in paragraph at lines 3919--3920


Underfull \hbox (badness 10000) in paragraph at lines 3944--3945
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]add[]region[]node([]GtFeatureInde
x *feature[]index,

Underfull \hbox (badness 10000) in paragraph at lines 3944--3945


Underfull \hbox (badness 10000) in paragraph at lines 3955--3956
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]add[]feature[]node([]GtFeatureInd
ex *feature[]index,

Underfull \hbox (badness 10000) in paragraph at lines 3955--3956


Underfull \hbox (badness 10000) in paragraph at lines 3967--3968
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]remove[]node([]GtFeatureIndex *fe
ature[]index,

Underfull \hbox (badness 10000) in paragraph at lines 3967--3968


Underfull \hbox (badness 10000) in paragraph at lines 3977--3978
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]add[]gff3file([]GtFeatureIndex *f
eature[]index, const

Underfull \hbox (badness 10000) in paragraph at lines 3977--3978


Underfull \hbox (badness 10000) in paragraph at lines 3989--3990
[]\OT1/cmtt/m/n/10.95 GtArray* gt[]feature[]index[]get[]features[]for[]seqid([]
GtFeatureIndex*, const

Underfull \hbox (badness 10000) in paragraph at lines 3989--3990


Underfull \hbox (badness 10000) in paragraph at lines 4004--4005
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]get[]features[]for[]range([]GtFea
tureIndex *feature[]index,

Underfull \hbox (badness 10000) in paragraph at lines 4004--4005


Underfull \hbox (badness 10000) in paragraph at lines 4016--4017
[]\OT1/cmtt/m/n/10.95 char* gt[]feature[]index[]get[]first[]seqid([]const GtFea
tureIndex

Underfull \hbox (badness 10000) in paragraph at lines 4016--4017


Underfull \hbox (badness 10000) in paragraph at lines 4026--4027
[]\OT1/cmtt/m/n/10.95 GtStrArray* gt[]feature[]index[]get[]seqids([]const GtFea
tureIndex

Underfull \hbox (badness 10000) in paragraph at lines 4026--4027


Underfull \hbox (badness 10000) in paragraph at lines 4039--4040
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]get[]range[]for[]seqid([]GtFeatur
eIndex *feature[]index,

Underfull \hbox (badness 10000) in paragraph at lines 4039--4040


Underfull \hbox (badness 10000) in paragraph at lines 4053--4054
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]get[]orig[]range[]for[]seqid([]Gt
FeatureIndex

Underfull \hbox (badness 10000) in paragraph at lines 4053--4054


Underfull \hbox (badness 10000) in paragraph at lines 4067--4068
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]has[]seqid([]const GtFeatureIndex
 *feature[]index, bool

Underfull \hbox (badness 10000) in paragraph at lines 4067--4068


Underfull \hbox (badness 10000) in paragraph at lines 4077--4078


Underfull \hbox (badness 10000) in paragraph at lines 4088--4089

[69] [70]
Underfull \hbox (badness 10000) in paragraph at lines 4107--4108


Overfull \hbox (13.12596pt too wide) in paragraph at lines 4118--4119
[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]index[]memory[]get[]node[]by[
]ptr([]GtFeatureIndexMemory*,

Underfull \hbox (badness 10000) in paragraph at lines 4118--4119


Overfull \hbox (26.19778pt too wide) in paragraph at lines 4129--4148
\OT1/ptm/m/n/10.95 with the \OT1/cmtt/m/n/10.95 Parent \OT1/ptm/m/n/10.95 and \
OT1/cmtt/m/n/10.95 ID \OT1/ptm/m/n/10.95 at-tributes) are re-al-ized in the C A
PI with the \OT1/cmtt/m/n/10.95 gt[]feature[]node[]add[]child()

Underfull \hbox (badness 10000) in paragraph at lines 4155--4156
[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]feature[]node[]new([]GtStr *seqid, cons
t char *type, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 4155--4156


Underfull \hbox (badness 10000) in paragraph at lines 4170--4171
[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]feature[]node[]new[]pseudo([]GtStr *seq
id, GtUword start,

Underfull \hbox (badness 10000) in paragraph at lines 4170--4171


Underfull \hbox (badness 10000) in paragraph at lines 4184--4185
[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]feature[]node[]new[]pseudo[]template([]
GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4184--4185


Underfull \hbox (badness 10000) in paragraph at lines 4195--4196


Underfull \hbox (badness 10000) in paragraph at lines 4205--4206
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]add[]child([]GtFeatureNode *paren
t, GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4205--4206


Underfull \hbox (badness 10000) in paragraph at lines 4215--4216


Underfull \hbox (badness 10000) in paragraph at lines 4226--4227
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]source([]GtFeatureNode *feat
ure[]node, GtStr

Underfull \hbox (badness 10000) in paragraph at lines 4226--4227


Underfull \hbox (badness 10000) in paragraph at lines 4236--4237


Underfull \hbox (badness 10000) in paragraph at lines 4246--4247


Underfull \hbox (badness 10000) in paragraph at lines 4257--4258
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]type([]GtFeatureNode *featur
e[]node, const char

Underfull \hbox (badness 10000) in paragraph at lines 4257--4258


Underfull \hbox (badness 10000) in paragraph at lines 4267--4268
[]\OT1/cmtt/m/n/10.95 bool gt[]feature[]node[]has[]type([]GtFeatureNode *featur
e[]node, const char

Underfull \hbox (badness 10000) in paragraph at lines 4267--4268


Underfull \hbox (badness 10000) in paragraph at lines 4277--4278
[]\OT1/cmtt/m/n/10.95 GtUword gt[]feature[]node[]number[]of[]children([]const G
tFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4277--4278


Underfull \hbox (badness 10000) in paragraph at lines 4289--4290
[]\OT1/cmtt/m/n/10.95 GtUword gt[]feature[]node[]number[]of[]children[]of[]type
([]const GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4289--4290


Underfull \hbox (badness 10000) in paragraph at lines 4300--4301


Underfull \hbox (badness 10000) in paragraph at lines 4310--4311


Underfull \hbox (badness 10000) in paragraph at lines 4321--4322


Underfull \hbox (badness 10000) in paragraph at lines 4330--4331


Underfull \hbox (badness 10000) in paragraph at lines 4339--4340


Underfull \hbox (badness 10000) in paragraph at lines 4350--4351
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]strand([]GtFeatureNode *feat
ure[]node, GtStrand

Underfull \hbox (badness 10000) in paragraph at lines 4350--4351


Underfull \hbox (badness 10000) in paragraph at lines 4359--4360


Underfull \hbox (badness 10000) in paragraph at lines 4370--4371


Underfull \hbox (badness 10000) in paragraph at lines 4380--4381
[]\OT1/cmtt/m/n/10.95 const char* gt[]feature[]node[]get[]attribute([]const GtF
eatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4380--4381


Underfull \hbox (badness 10000) in paragraph at lines 4392--4393
[]\OT1/cmtt/m/n/10.95 GtStrArray* gt[]feature[]node[]get[]attribute[]list([]con
st GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4392--4393


Underfull \hbox (badness 10000) in paragraph at lines 4404--4405
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]add[]attribute([]GtFeatureNode *f
eature[]node, const char

Underfull \hbox (badness 10000) in paragraph at lines 4404--4405


Underfull \hbox (badness 10000) in paragraph at lines 4418--4419
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]attribute([]GtFeatureNode* f
eature[]node, const char

Underfull \hbox (badness 10000) in paragraph at lines 4418--4419


Underfull \hbox (badness 10000) in paragraph at lines 4432--4433
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]remove[]attribute([]GtFeatureNode
* feature[]node, const

Underfull \hbox (badness 10000) in paragraph at lines 4432--4433


Underfull \hbox (badness 10000) in paragraph at lines 4445--4446
[]\OT1/cmtt/m/n/10.95 void GtFeatureNodeAttributeIterFunc([]const char *attr[]n
ame, const char

Underfull \hbox (badness 10000) in paragraph at lines 4445--4446


Underfull \hbox (badness 10000) in paragraph at lines 4449--4452
[]\OT1/ptm/m/n/10.95 Delivers the key (in \OT1/cmtt/m/n/10.95 attr[]name\OT1/pt
m/m/n/10.95 )and value (in \OT1/cmtt/m/n/10.95 attr[]value\OT1/ptm/m/n/10.95 ) 
of an at-

Underfull \hbox (badness 8094) in paragraph at lines 4449--4452
\OT1/ptm/m/n/10.95 tribute. The \OT1/cmtt/m/n/10.95 data \OT1/ptm/m/n/10.95 pa-
ram-e-ter car-ries over ar-bi-trary user data from the

Underfull \hbox (badness 10000) in paragraph at lines 4458--4459
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]foreach[]attribute([]GtFeatureNod
e *feature[]node,

Underfull \hbox (badness 10000) in paragraph at lines 4458--4459


Underfull \hbox (badness 10000) in paragraph at lines 4468--4469


Underfull \hbox (badness 10000) in paragraph at lines 4477--4478


Underfull \hbox (badness 10000) in paragraph at lines 4487--4488
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]make[]multi[]representative([]GtF
eatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4487--4488


Underfull \hbox (badness 10000) in paragraph at lines 4500--4501
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]multi[]representative([]GtFe
atureNode *feature[]node,

Underfull \hbox (badness 10000) in paragraph at lines 4500--4501


Underfull \hbox (badness 10000) in paragraph at lines 4510--4511


Underfull \hbox (badness 10000) in paragraph at lines 4521--4522
[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]node[]get[]multi[]representat
ive([]GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4521--4522


Underfull \hbox (badness 10000) in paragraph at lines 4531--4532
[]\OT1/cmtt/m/n/10.95 bool gt[]feature[]node[]is[]similar([]const GtFeatureNode
 *feature[]node[]a, const

Underfull \hbox (badness 10000) in paragraph at lines 4531--4532


Underfull \hbox (badness 10000) in paragraph at lines 4542--4543


Underfull \hbox (badness 10000) in paragraph at lines 4551--4552


Underfull \hbox (badness 10000) in paragraph at lines 4560--4561


Underfull \hbox (badness 10000) in paragraph at lines 4569--4570


Underfull \hbox (badness 10000) in paragraph at lines 4579--4580
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]remove[]leaf([]GtFeatureNode *tre
e, GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4579--4580


Underfull \hbox (badness 10000) in paragraph at lines 4592--4593


Underfull \hbox (badness 10000) in paragraph at lines 4604--4605

[71] [72] [73] [74]
Underfull \hbox (badness 10000) in paragraph at lines 4617--4618
[]\OT1/cmtt/m/n/10.95 GtFeatureNodeIterator* gt[]feature[]node[]iterator[]new([
]const GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4617--4618


Underfull \hbox (badness 10000) in paragraph at lines 4629--4630
[]\OT1/cmtt/m/n/10.95 GtFeatureNodeIterator* gt[]feature[]node[]iterator[]new[]
direct([]const

Underfull \hbox (badness 10000) in paragraph at lines 4629--4630


Underfull \hbox (badness 10000) in paragraph at lines 4640--4641
[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]node[]iterator[]next([]GtFeat
ureNodeIterator

Underfull \hbox (badness 10000) in paragraph at lines 4640--4641


Underfull \hbox (badness 10000) in paragraph at lines 4651--4652
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]iterator[]delete([]GtFeatureNodeI
terator

Underfull \hbox (badness 10000) in paragraph at lines 4651--4652

[75]
Underfull \hbox (badness 10000) in paragraph at lines 4662--4663
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]feature[]out[]stream[]new([]GtNodeStrea
m*, GtFeatureIndex

Underfull \hbox (badness 10000) in paragraph at lines 4662--4663


Underfull \hbox (badness 10000) in paragraph at lines 4674--4675


Underfull \hbox (badness 1509) in paragraph at lines 4678--4681
\OT1/cmtt/m/n/10.95 fi\OT1/ptm/m/n/10.95 . Note: The \OT1/cmtt/m/n/10.95 GtFeat
ureStream \OT1/ptm/m/n/10.95 class is now dep-re-cated. Please use the

Underfull \hbox (badness 10000) in paragraph at lines 4694--4695


Underfull \hbox (badness 10000) in paragraph at lines 4707--4708


Underfull \hbox (badness 10000) in paragraph at lines 4716--4717


Underfull \hbox (badness 10000) in paragraph at lines 4725--4726


Underfull \hbox (badness 10000) in paragraph at lines 4734--4735


Underfull \hbox (badness 10000) in paragraph at lines 4744--4745


Underfull \hbox (badness 10000) in paragraph at lines 4754--4755


Underfull \hbox (badness 10000) in paragraph at lines 4763--4764


Underfull \hbox (badness 10000) in paragraph at lines 4773--4774


Underfull \hbox (badness 10000) in paragraph at lines 4782--4783


Underfull \hbox (badness 10000) in paragraph at lines 4791--4792


Underfull \hbox (badness 10000) in paragraph at lines 4800--4801

[76]
Underfull \hbox (badness 10000) in paragraph at lines 4818--4819
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]gff3[]in[]stream[]new[]unsorted([]int n
um[]of[]files, const char

Underfull \hbox (badness 10000) in paragraph at lines 4818--4819


Underfull \hbox (badness 10000) in paragraph at lines 4830--4831


Underfull \hbox (badness 10000) in paragraph at lines 4842--4843


Underfull \hbox (badness 10000) in paragraph at lines 4853--4854


Underfull \hbox (badness 10000) in paragraph at lines 4864--4865


Underfull \hbox (badness 10000) in paragraph at lines 4874--4875


Underfull \hbox (badness 10000) in paragraph at lines 4884--4885


Underfull \hbox (badness 10000) in paragraph at lines 4896--4897
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]in[]stream[]set[]type[]checker([]GtNodeStr
eam *gff3[]in[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 4896--4897

[77]
Underfull \hbox (badness 10000) in paragraph at lines 4915--4916
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]gff3[]out[]stream[]new([]GtNodeStream *
in[]stream, GtFile

Underfull \hbox (badness 10000) in paragraph at lines 4915--4916


Underfull \hbox (badness 10000) in paragraph at lines 4927--4928
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]out[]stream[]set[]fasta[]width([]GtGFF3Out
Stream *gff3[]out[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 4927--4928


Underfull \hbox (badness 10000) in paragraph at lines 4939--4940
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]out[]stream[]retain[]id[]attributes([]GtGF
F3OutStream

Underfull \hbox (badness 10000) in paragraph at lines 4939--4940

[78]
Underfull \hbox (badness 10000) in paragraph at lines 4963--4964


Underfull \hbox (badness 10000) in paragraph at lines 4974--4975


Underfull \hbox (badness 10000) in paragraph at lines 4985--4986


Underfull \hbox (badness 10000) in paragraph at lines 4997--4998
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]parser[]do[]not[]check[]region[]boundaries
([]GtGFF3Parser

Underfull \hbox (badness 10000) in paragraph at lines 4997--4998


Underfull \hbox (badness 10000) in paragraph at lines 5008--5009


Underfull \hbox (badness 10000) in paragraph at lines 5018--5019
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]parser[]set[]type[]checker([]GtGFF3Parser 
*gff3[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 5018--5019


Underfull \hbox (badness 10000) in paragraph at lines 5028--5029
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]parser[]set[]xrf[]checker([]GtGFF3Parser *
gff3[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 5028--5029


Underfull \hbox (badness 10000) in paragraph at lines 5037--5038


Underfull \hbox (badness 10000) in paragraph at lines 5054--5055
[]\OT1/cmtt/m/n/10.95 int gt[]gff3[]parser[]parse[]genome[]nodes([]GtGFF3Parser
 *gff3[]parser, int

Underfull \hbox (badness 10000) in paragraph at lines 5054--5055
\OT1/cmtt/m/n/10.95 *status[]code, GtQueue *genome[]nodes, GtCstrTable *used[]t
ypes, GtStr

Underfull \hbox (badness 10000) in paragraph at lines 5054--5055


Underfull \hbox (badness 10000) in paragraph at lines 5073--5074


Underfull \hbox (badness 10000) in paragraph at lines 5082--5083

[79]
Underfull \hbox (badness 10000) in paragraph at lines 5100--5101


Underfull \hbox (badness 10000) in paragraph at lines 5112--5113
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]visitor[]set[]fasta[]width([]GtGFF3Visitor
 *gff3[]visitor, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 5112--5113


Underfull \hbox (badness 10000) in paragraph at lines 5124--5125

[80]
Underfull \hbox (badness 10000) in paragraph at lines 5144--5145


Underfull \hbox (badness 10000) in paragraph at lines 5163--5164
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]gtf[]out[]stream[]new([]GtNodeStream *i
n[]stream, GtFile

Underfull \hbox (badness 10000) in paragraph at lines 5163--5164


Underfull \hbox (badness 10000) in paragraph at lines 5182--5183


Underfull \hbox (badness 10000) in paragraph at lines 5192--5193


Underfull \hbox (badness 10000) in paragraph at lines 5202--5203


Underfull \hbox (badness 10000) in paragraph at lines 5212--5213


Underfull \hbox (badness 10000) in paragraph at lines 5222--5223


Underfull \hbox (badness 10000) in paragraph at lines 5232--5233


Underfull \hbox (badness 10000) in paragraph at lines 5242--5243


Underfull \hbox (badness 10000) in paragraph at lines 5253--5254


Underfull \hbox (badness 10000) in paragraph at lines 5264--5265
[]\OT1/cmtt/m/n/10.95 void gt[]genome[]node[]set[]range([]GtGenomeNode *genome[
]node, const GtRange

Underfull \hbox (badness 10000) in paragraph at lines 5264--5265


Underfull \hbox (badness 10000) in paragraph at lines 5275--5276
[]\OT1/cmtt/m/n/10.95 void gt[]genome[]node[]add[]user[]data([]GtGenomeNode *ge
nome[]node, const char

Underfull \hbox (badness 10000) in paragraph at lines 5275--5276


Underfull \hbox (badness 10000) in paragraph at lines 5286--5287
[]\OT1/cmtt/m/n/10.95 void* gt[]genome[]node[]get[]user[]data([]const GtGenomeN
ode *genome[]node, const

Underfull \hbox (badness 10000) in paragraph at lines 5286--5287


Underfull \hbox (badness 10000) in paragraph at lines 5296--5297
[]\OT1/cmtt/m/n/10.95 void gt[]genome[]node[]release[]user[]data([]GtGenomeNode
 *genome[]node, const

Underfull \hbox (badness 10000) in paragraph at lines 5296--5297


Underfull \hbox (badness 10000) in paragraph at lines 5307--5308
[]\OT1/cmtt/m/n/10.95 int gt[]genome[]node[]cmp([]GtGenomeNode *genome[]node[]a
, GtGenomeNode

Underfull \hbox (badness 10000) in paragraph at lines 5307--5308


Underfull \hbox (badness 1424) in paragraph at lines 5311--5313
[]\OT1/ptm/m/n/10.95 Compare \OT1/cmtt/m/n/10.95 genome[]node[]a \OT1/ptm/m/n/1
0.95 with \OT1/cmtt/m/n/10.95 genome[]node[]b \OT1/ptm/m/n/10.95 and re-turn th
e re-sult (sim-i-lar to

Underfull \hbox (badness 10000) in paragraph at lines 5317--5318


Underfull \hbox (badness 10000) in paragraph at lines 5326--5327


Underfull \hbox (badness 10000) in paragraph at lines 5336--5337
[]\OT1/cmtt/m/n/10.95 int gt[]genome[]node[]accept([]GtGenomeNode *genome[]node
, GtNodeVisitor

Underfull \hbox (badness 10000) in paragraph at lines 5336--5337


Underfull \hbox (badness 10000) in paragraph at lines 5346--5347

[81] [82]
Underfull \hbox (badness 10000) in paragraph at lines 5366--5367


Underfull \hbox (badness 10000) in paragraph at lines 5376--5377
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]text[]clip([]GtGraphics*, double
 x, double y, const

Underfull \hbox (badness 10000) in paragraph at lines 5376--5377


Underfull \hbox (badness 10000) in paragraph at lines 5386--5387


Underfull \hbox (badness 10000) in paragraph at lines 5396--5397
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]text[]centered([]GtGraphics*, do
uble x, double y,

Underfull \hbox (badness 10000) in paragraph at lines 5396--5397


Underfull \hbox (badness 10000) in paragraph at lines 5407--5408
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]text[]right([]GtGraphics*, doubl
e x, double y, const

Underfull \hbox (badness 10000) in paragraph at lines 5407--5408


Underfull \hbox (badness 10000) in paragraph at lines 5418--5419
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]colored[]text([]GtGraphics*, dou
ble x, double y,

Underfull \hbox (badness 10000) in paragraph at lines 5418--5419


Underfull \hbox (badness 10000) in paragraph at lines 5428--5429


Underfull \hbox (badness 10000) in paragraph at lines 5437--5438


Underfull \hbox (badness 10000) in paragraph at lines 5447--5448


Underfull \hbox (badness 10000) in paragraph at lines 5457--5458
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]set[]font([]GtGraphics *g, const char 
*family, FontSlant

Underfull \hbox (badness 10000) in paragraph at lines 5457--5458


Underfull \hbox (badness 10000) in paragraph at lines 5470--5471


Underfull \hbox (badness 10000) in paragraph at lines 5479--5480


Underfull \hbox (badness 10000) in paragraph at lines 5489--5490
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]set[]margins([]GtGraphics*, double mar
gin[]x, double

Underfull \hbox (badness 10000) in paragraph at lines 5489--5490


Underfull \hbox (badness 10000) in paragraph at lines 5501--5502


Underfull \hbox (badness 10000) in paragraph at lines 5510--5511


Underfull \hbox (badness 10000) in paragraph at lines 5521--5522
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]horizontal[]line([]GtGraphics *g
, double x, double y,

Underfull \hbox (badness 10000) in paragraph at lines 5521--5522


Underfull \hbox (badness 10000) in paragraph at lines 5533--5534
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]vertical[]line([]GtGraphics *g, 
double x, double y,

Underfull \hbox (badness 10000) in paragraph at lines 5533--5534


Underfull \hbox (badness 10000) in paragraph at lines 5545--5546
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]line([]GtGraphics *g, double x, 
double y, double xto,

Underfull \hbox (badness 10000) in paragraph at lines 5545--5546


Underfull \hbox (badness 10000) in paragraph at lines 5559--5560
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]box([]GtGraphics*, double x, dou
ble y, double width,

Underfull \hbox (badness 10000) in paragraph at lines 5559--5560
\OT1/cmtt/m/n/10.95 double height, GtColor fill[]color, ArrowStatus arrow[]stat
us, double

Underfull \hbox (badness 10000) in paragraph at lines 5559--5560


Underfull \hbox (badness 10000) in paragraph at lines 5579--5580
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]dashes([]GtGraphics*, double x, 
double y, double

Underfull \hbox (badness 10000) in paragraph at lines 5579--5580
\OT1/cmtt/m/n/10.95 width, double height, ArrowStatus arrow[]status, double arr
ow[]width,

Underfull \hbox (badness 10000) in paragraph at lines 5579--5580


Underfull \hbox (badness 10000) in paragraph at lines 5597--5598
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]caret([]GtGraphics*, double x, d
ouble y, double

Underfull \hbox (badness 10000) in paragraph at lines 5597--5598
\OT1/cmtt/m/n/10.95 width, double height, ArrowStatus arrow[]status, double arr
ow[]width,

Underfull \hbox (badness 10000) in paragraph at lines 5597--5598


Underfull \hbox (badness 10000) in paragraph at lines 5616--5617
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]rectangle([]GtGraphics*, double 
x, double y, bool

Underfull \hbox (badness 10000) in paragraph at lines 5616--5617
\OT1/cmtt/m/n/10.95 filled, GtColor fill[]color, bool stroked, GtColor stroke[]
color, double

Underfull \hbox (badness 10000) in paragraph at lines 5616--5617


Underfull \hbox (badness 10000) in paragraph at lines 5630--5631
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]arrowhead([]GtGraphics*, double 
x, double y, GtColor,

Underfull \hbox (badness 10000) in paragraph at lines 5630--5631


Underfull \hbox (badness 10000) in paragraph at lines 5643--5644
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]curve[]data([]GtGraphics *g, dou
ble x, double y,

Underfull \hbox (badness 10000) in paragraph at lines 5643--5644
\OT1/cmtt/m/n/10.95 GtColor color, double data[], GtUword ndata, GtRange valran
ge, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 5643--5644


Underfull \hbox (badness 10000) in paragraph at lines 5657--5658
[]\OT1/cmtt/m/n/10.95 int gt[]graphics[]save[]to[]file([]const GtGraphics*, con
st char *filename,

Underfull \hbox (badness 10000) in paragraph at lines 5657--5658


Underfull \hbox (badness 10000) in paragraph at lines 5666--5667


Underfull \hbox (badness 10000) in paragraph at lines 5675--5676

[83] [84] [85]
Underfull \hbox (badness 10000) in paragraph at lines 5694--5695
[]\OT1/cmtt/m/n/10.95 GtGraphics* gt[]graphics[]cairo[]new([]GtGraphicsOutType 
type, unsigned int

Underfull \hbox (badness 10000) in paragraph at lines 5694--5695


Underfull \hbox (badness 10000) in paragraph at lines 5707--5708
[]\OT1/cmtt/m/n/10.95 GtGraphics* gt[]graphics[]cairo[]new[]from[]context([]cai
ro[]t *context, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 5707--5708


Underfull \hbox (badness 10000) in paragraph at lines 5722--5723
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]cairo[]draw[]curve[]data([]GtGraphics 
*gg, double x, double y,

Underfull \hbox (badness 10000) in paragraph at lines 5722--5723
\OT1/cmtt/m/n/10.95 GtColor color, double data[], GtUword ndata, GtRange valran
ge, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 5722--5723

[86]
Underfull \hbox (badness 10000) in paragraph at lines 5743--5744


Underfull \hbox (badness 10000) in paragraph at lines 5757--5758
[]\OT1/cmtt/m/n/10.95 GtHashmap* gt[]hashmap[]new([]GtHashType keyhashtype, GtF
ree keyfree, GtFree

Underfull \hbox (badness 10000) in paragraph at lines 5757--5758


Underfull \hbox (badness 10000) in paragraph at lines 5773--5774


Underfull \hbox (badness 10000) in paragraph at lines 5782--5783


Underfull \hbox (badness 10000) in paragraph at lines 5792--5793


Underfull \hbox (badness 10000) in paragraph at lines 5802--5803


Underfull \hbox (badness 10000) in paragraph at lines 5813--5814
[]\OT1/cmtt/m/n/10.95 int gt[]hashmap[]foreach[]ordered([]GtHashmap *hashmap, G
tHashmapVisitFunc

Underfull \hbox (badness 10000) in paragraph at lines 5813--5814


Underfull \hbox (badness 10000) in paragraph at lines 5824--5825
[]\OT1/cmtt/m/n/10.95 int gt[]hashmap[]foreach([]GtHashmap *hashmap, GtHashmapV
isitFunc func, void

Underfull \hbox (badness 10000) in paragraph at lines 5824--5825


Underfull \hbox (badness 10000) in paragraph at lines 5836--5837
[]\OT1/cmtt/m/n/10.95 int gt[]hashmap[]foreach[]in[]key[]order([]GtHashmap *has
hmap, GtHashmapVisitFunc

Underfull \hbox (badness 10000) in paragraph at lines 5836--5837


Underfull \hbox (badness 2875) in paragraph at lines 5840--5843
[]\OT1/ptm/m/n/10.95 Iterate over \OT1/cmtt/m/n/10.95 hashmap \OT1/ptm/m/n/10.9
5 in ei-ther al-pha-bet-i-cal or-der (if \OT1/cmtt/m/n/10.95 GtHashType \OT1/pt
m/m/n/10.95 was spec-i-

Underfull \hbox (badness 1762) in paragraph at lines 5840--5843
\OT1/ptm/m/n/10.95 fied as \OT1/cmtt/m/n/10.95 GT[]HASH[]STRING\OT1/ptm/m/n/10.
95 ) or nu-mer-i-cal or-der (if \OT1/cmtt/m/n/10.95 GtHashType \OT1/ptm/m/n/10.
95 was spec-i-fied as

Underfull \hbox (badness 10000) in paragraph at lines 5847--5848


Underfull \hbox (badness 10000) in paragraph at lines 5857--5858

[87]
Underfull \hbox (badness 10000) in paragraph at lines 5876--5877
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]id[]to[]md5[]stream[]new([]GtNodeStream
 *in[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 5876--5877

[88]
Underfull \hbox (badness 10000) in paragraph at lines 5902--5903


Underfull \hbox (badness 10000) in paragraph at lines 5911--5912


Underfull \hbox (badness 10000) in paragraph at lines 5920--5921


Underfull \hbox (badness 10000) in paragraph at lines 5930--5931
[]\OT1/cmtt/m/n/10.95 const GtRecMap* gt[]image[]info[]get[]rec[]map([]GtImageI
nfo *image[]info, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 5930--5931


Underfull \hbox (badness 10000) in paragraph at lines 5939--5940


Overfull \hbox (1.94502pt too wide) in paragraph at lines 5949--5951
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. A \OT1/cmtt/m/n/10.95 GtInterFeatureStream \OT1/ptm/m/n/10.
95 in-serts new fea-ture nodes

Underfull \hbox (badness 10000) in paragraph at lines 5958--5959
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]inter[]feature[]stream[]new([]GtNodeStr
eam *in[]stream, const

Underfull \hbox (badness 10000) in paragraph at lines 5958--5959


Underfull \hbox (badness 10000) in paragraph at lines 5978--5979


Underfull \hbox (badness 10000) in paragraph at lines 5989--5990


Overfull \hbox (10.59654pt too wide) in paragraph at lines 6000--6001
[]\OT1/cmtt/m/n/10.95 GtIntervalTreeNode* gt[]interval[]tree[]find[]first[]over
lapping([]GtIntervalTree*,

Underfull \hbox (badness 10000) in paragraph at lines 6000--6001


Underfull \hbox (badness 10000) in paragraph at lines 6011--6012
[]\OT1/cmtt/m/n/10.95 void gt[]interval[]tree[]insert([]GtIntervalTree *tree, G
tIntervalTreeNode

Underfull \hbox (badness 10000) in paragraph at lines 6011--6012


Underfull \hbox (badness 10000) in paragraph at lines 6023--6024
[]\OT1/cmtt/m/n/10.95 void gt[]interval[]tree[]find[]all[]overlapping([]GtInter
valTree*, GtUword start,

Underfull \hbox (badness 10000) in paragraph at lines 6023--6024


Underfull \hbox (badness 10000) in paragraph at lines 6037--6038
[]\OT1/cmtt/m/n/10.95 void gt[]interval[]tree[]iterate[]overlapping([]GtInterva
lTree *it,

Underfull \hbox (badness 10000) in paragraph at lines 6037--6038


Underfull \hbox (badness 10000) in paragraph at lines 6050--6051
[]\OT1/cmtt/m/n/10.95 int gt[]interval[]tree[]traverse([]GtIntervalTree*, GtInt
ervalTreeIteratorFunc

Underfull \hbox (badness 10000) in paragraph at lines 6050--6051


Underfull \hbox (badness 10000) in paragraph at lines 6062--6063


Underfull \hbox (badness 10000) in paragraph at lines 6076--6077

[89]
Underfull \hbox (badness 10000) in paragraph at lines 6091--6092
[]\OT1/cmtt/m/n/10.95 GtIntervalTreeNode* gt[]interval[]tree[]node[]new([]void 
*data, GtUword low,

Underfull \hbox (badness 10000) in paragraph at lines 6091--6092


Underfull \hbox (badness 10000) in paragraph at lines 6102--6103

[90]
Underfull \hbox (badness 10000) in paragraph at lines 6124--6125
[]\OT1/cmtt/m/n/10.95 GtLayout* gt[]layout[]new([]GtDiagram *diagram, unsigned 
int width, GtStyle*,

Underfull \hbox (badness 10000) in paragraph at lines 6124--6125


Underfull \hbox (badness 10000) in paragraph at lines 6139--6140
[]\OT1/cmtt/m/n/10.95 GtLayout* gt[]layout[]new[]with[]twc([]GtDiagram*, unsign
ed int width,

Underfull \hbox (badness 10000) in paragraph at lines 6139--6140


Underfull \hbox (badness 10000) in paragraph at lines 6151--6152
[]\OT1/cmtt/m/n/10.95 void gt[]layout[]set[]track[]ordering[]func([]GtLayout *l
ayout,

Underfull \hbox (badness 10000) in paragraph at lines 6151--6152


Underfull \hbox (badness 10000) in paragraph at lines 6166--6167


Underfull \hbox (badness 10000) in paragraph at lines 6179--6180


Underfull \hbox (badness 10000) in paragraph at lines 6188--6189

[91]
Underfull \hbox (badness 10000) in paragraph at lines 6199--6200


Underfull \hbox (badness 10000) in paragraph at lines 6211--6212


Underfull \hbox (badness 10000) in paragraph at lines 6220--6221


Underfull \hbox (badness 10000) in paragraph at lines 6229--6230


Underfull \hbox (badness 10000) in paragraph at lines 6238--6239


Underfull \hbox (badness 10000) in paragraph at lines 6247--6248


Underfull \hbox (badness 10000) in paragraph at lines 6256--6257


Underfull \hbox (badness 10000) in paragraph at lines 6265--6266


Underfull \hbox (badness 10000) in paragraph at lines 6274--6275


Underfull \hbox (badness 10000) in paragraph at lines 6283--6284


Underfull \hbox (badness 10000) in paragraph at lines 6292--6293


Underfull \hbox (badness 10000) in paragraph at lines 6309--6310


Underfull \hbox (badness 10000) in paragraph at lines 6319--6320
[]\OT1/cmtt/m/n/10.95 void gt[]md5[]encoder[]add[]block([]GtMD5Encoder *enc, co
nst char *message,

Underfull \hbox (badness 10000) in paragraph at lines 6319--6320


Underfull \hbox (badness 10000) in paragraph at lines 6330--6331
[]\OT1/cmtt/m/n/10.95 void gt[]md5[]encoder[]finish([]GtMD5Encoder *enc, unsign
ed char *output, char

Underfull \hbox (badness 10000) in paragraph at lines 6330--6331


Underfull \hbox (badness 10000) in paragraph at lines 6341--6342


Underfull \hbox (badness 10000) in paragraph at lines 6351--6352

[92]
Underfull \hbox (badness 10000) in paragraph at lines 6369--6370
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]md5[]to[]id[]stream[]new([]GtNodeStream
 *in[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 6369--6370


Underfull \hbox (badness 10000) in paragraph at lines 6391--6392


Underfull \hbox (badness 10000) in paragraph at lines 6402--6403
[]\OT1/cmtt/m/n/10.95 void gt[]match[]set[]seqid1[]nt([]GtMatch *match, const c
har *seqid, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 6402--6403


Underfull \hbox (badness 10000) in paragraph at lines 6413--6414


Underfull \hbox (badness 10000) in paragraph at lines 6424--6425
[]\OT1/cmtt/m/n/10.95 void gt[]match[]set[]seqid2[]nt([]GtMatch *match, const c
har *seqid, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 6424--6425


Underfull \hbox (badness 10000) in paragraph at lines 6435--6436


Underfull \hbox (badness 10000) in paragraph at lines 6445--6446


Underfull \hbox (badness 10000) in paragraph at lines 6456--6457


Underfull \hbox (badness 10000) in paragraph at lines 6467--6468


Underfull \hbox (badness 10000) in paragraph at lines 6477--6478


Underfull \hbox (badness 10000) in paragraph at lines 6490--6491


Underfull \hbox (badness 10000) in paragraph at lines 6503--6504


Underfull \hbox (badness 10000) in paragraph at lines 6512--6513

[93] [94]
Underfull \hbox (badness 10000) in paragraph at lines 6533--6534
[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]blast[]new([]char *seqid1, char *seqi
d2, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 6533--6534
\OT1/cmtt/m/n/10.95 start[]seq1, GtUword start[]seq2, GtUword end[]seq1, GtUwor
d end[]seq2,

Underfull \hbox (badness 10000) in paragraph at lines 6533--6534
\OT1/cmtt/m/n/10.95 double evalue, float bitscore, GtUword ali[]l, double simil
arity,

Underfull \hbox (badness 10000) in paragraph at lines 6533--6534


Underfull \hbox (badness 10000) in paragraph at lines 6546--6547


Underfull \hbox (badness 10000) in paragraph at lines 6555--6556


Underfull \hbox (badness 10000) in paragraph at lines 6564--6565


Underfull \hbox (badness 10000) in paragraph at lines 6573--6574


Underfull \hbox (badness 10000) in paragraph at lines 6582--6583


Underfull \hbox (badness 10000) in paragraph at lines 6591--6592


Underfull \hbox (badness 10000) in paragraph at lines 6600--6601


Underfull \hbox (badness 10000) in paragraph at lines 6609--6610


Underfull \hbox (badness 10000) in paragraph at lines 6621--6622
[]\OT1/cmtt/m/n/10.95 GtMatchIteratorStatus gt[]match[]iterator[]next([]GtMatch
Iterator *mp, GtMatch

Underfull \hbox (badness 10000) in paragraph at lines 6621--6622


Underfull \hbox (badness 10000) in paragraph at lines 6635--6636

[95]
Underfull \hbox (badness 10000) in paragraph at lines 6661--6662
[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]last[]new([]const char *seqid1, const
 char *seqid2,

Underfull \hbox (badness 10000) in paragraph at lines 6661--6662
\OT1/cmtt/m/n/10.95 GtUword score, GtUword seqno1, GtUword seqno2, GtUword star
t[]seq1,

Underfull \hbox (badness 10000) in paragraph at lines 6661--6662
\OT1/cmtt/m/n/10.95 GtUword start[]seq2, GtUword end[]seq1, GtUword end[]seq2, 
GtMatchDirection

Underfull \hbox (badness 10000) in paragraph at lines 6661--6662


Underfull \hbox (badness 10000) in paragraph at lines 6671--6672


Underfull \hbox (badness 10000) in paragraph at lines 6680--6681


Underfull \hbox (badness 10000) in paragraph at lines 6689--6690


Underfull \hbox (badness 10000) in paragraph at lines 6713--6714
[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]open[]new([]char *seqid1, char *seqid
2, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 6713--6714
\OT1/cmtt/m/n/10.95 start[]seq1, GtUword start[]seq2, GtUword end[]seq1, GtUwor
d end[]seq2,

Underfull \hbox (badness 10000) in paragraph at lines 6713--6714


Underfull \hbox (badness 10000) in paragraph at lines 6724--6725


Underfull \hbox (badness 10000) in paragraph at lines 6733--6734

[96]
Underfull \hbox (badness 10000) in paragraph at lines 6760--6761
[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]sw[]new([]const char *seqid1, const c
har *seqid2,

Underfull \hbox (badness 10000) in paragraph at lines 6760--6761
\OT1/cmtt/m/n/10.95 GtUword seqno1, GtUword seqno2, GtUword length, GtUword edi
st, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 6760--6761
\OT1/cmtt/m/n/10.95 start[]seq1, GtUword start[]seq2, GtUword end[]seq1, GtUwor
d end[]seq2,

Underfull \hbox (badness 10000) in paragraph at lines 6760--6761


Underfull \hbox (badness 10000) in paragraph at lines 6772--6773


Underfull \hbox (badness 10000) in paragraph at lines 6781--6782


Underfull \hbox (badness 10000) in paragraph at lines 6790--6791


Underfull \hbox (badness 10000) in paragraph at lines 6799--6800


Underfull \hbox (badness 10000) in paragraph at lines 6819--6820
[]\OT1/cmtt/m/n/10.95 int gt[]match[]visitor[]visit[]match[]blast([]GtMatchVisi
tor *match[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 6819--6820


Underfull \hbox (badness 10000) in paragraph at lines 6830--6831
[]\OT1/cmtt/m/n/10.95 int gt[]match[]visitor[]visit[]match[]open([]GtMatchVisit
or *match[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 6830--6831


Underfull \hbox (badness 10000) in paragraph at lines 6839--6840

[97]
Underfull \hbox (badness 10000) in paragraph at lines 6856--6857


Underfull \hbox (badness 10000) in paragraph at lines 6875--6876


Underfull \hbox (badness 10000) in paragraph at lines 6895--6896
[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]meta[]node[]new([]const char *meta[]dir
ective, const char

Underfull \hbox (badness 10000) in paragraph at lines 6895--6896


Underfull \hbox (badness 10000) in paragraph at lines 6909--6910


Underfull \hbox (badness 10000) in paragraph at lines 6918--6919


Underfull \hbox (badness 10000) in paragraph at lines 6927--6928


Underfull \hbox (badness 10000) in paragraph at lines 6939--6940

[98]
Underfull \hbox (badness 10000) in paragraph at lines 6956--6957


Underfull \hbox (badness 10000) in paragraph at lines 6965--6966


Underfull \hbox (badness 10000) in paragraph at lines 6974--6975


Underfull \hbox (badness 10000) in paragraph at lines 6983--6984


Underfull \hbox (badness 10000) in paragraph at lines 7000--7001


Underfull \hbox (badness 10000) in paragraph at lines 7011--7012
[]\OT1/cmtt/m/n/10.95 int gt[]node[]stream[]next([]GtNodeStream *node[]stream, 
GtGenomeNode

Underfull \hbox (badness 10000) in paragraph at lines 7011--7012


Underfull \hbox (badness 1655) in paragraph at lines 7015--7021
\OT1/ptm/m/n/10.95 (trans-fers own-er-ship to \OT1/cmtt/m/n/10.95 genome[]node\
OT1/ptm/m/n/10.95 ). If no er-ror oc-curs, 0 is re-turned and

Underfull \hbox (badness 10000) in paragraph at lines 7025--7026


Underfull \hbox (badness 3240) in paragraph at lines 7029--7036
\OT1/ptm/m/n/10.95 is ex-hausted (0 is re-turned) or an er-ror oc-curs (-1 is r
e-turned and \OT1/cmtt/m/n/10.95 err \OT1/ptm/m/n/10.95 is

Underfull \hbox (badness 4266) in paragraph at lines 7029--7036
\OT1/ptm/m/n/10.95 set). All re-trieved \OT1/cmtt/m/n/10.95 GtGenomeNode\OT1/pt
m/m/n/10.95 s are deleted au-to-mat-i-cally with calls to

Underfull \hbox (badness 2828) in paragraph at lines 7029--7036
\OT1/cmtt/m/n/10.95 gt[]genome[]node[]delete()\OT1/ptm/m/n/10.95 . This method 
is ba-si-cally a con-ve-nience method

Underfull \hbox (badness 10000) in paragraph at lines 7040--7041


Underfull \hbox (badness 10000) in paragraph at lines 7049--7050


Underfull \hbox (badness 10000) in paragraph at lines 7059--7060


Underfull \hbox (badness 10000) in paragraph at lines 7069--7070


Underfull \hbox (badness 10000) in paragraph at lines 7081--7082
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]node[]stream[]create([]const GtNodeStre
amClass

Underfull \hbox (badness 10000) in paragraph at lines 7081--7082


Underfull \hbox (badness 10000) in paragraph at lines 7097--7098
[]\OT1/cmtt/m/n/10.95 void* gt[]node[]stream[]cast([]const GtNodeStreamClass *n
ode[]stream[]class,

Underfull \hbox (badness 10000) in paragraph at lines 7097--7098

[99]
Underfull \hbox (badness 10000) in paragraph at lines 7113--7114
[]\OT1/cmtt/m/n/10.95 const GtNodeStreamClass* gt[]node[]stream[]class[]new([]s
ize[]t size,

Underfull \hbox (badness 10000) in paragraph at lines 7113--7114

[100]
Underfull \hbox (badness 10000) in paragraph at lines 7135--7136
[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]comment[]node([]GtNodeVisit
or *node[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 7135--7136


Underfull \hbox (badness 10000) in paragraph at lines 7146--7147
[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]feature[]node([]GtNodeVisit
or *node[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 7146--7147


Underfull \hbox (badness 10000) in paragraph at lines 7157--7158
[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]meta[]node([]GtNodeVisitor 
*node[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 7157--7158


Underfull \hbox (badness 10000) in paragraph at lines 7168--7169
[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]region[]node([]GtNodeVisito
r *node[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 7168--7169


Underfull \hbox (badness 10000) in paragraph at lines 7179--7180
[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]sequence[]node([]GtNodeVisi
tor *node[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 7179--7180


Underfull \hbox (badness 10000) in paragraph at lines 7188--7189


Underfull \hbox (badness 10000) in paragraph at lines 7207--7208
[]\OT1/cmtt/m/n/10.95 GtORFIterator* gt[]orf[]iterator[]new([]GtCodonIterator *
ci, GtTranslator

Underfull \hbox (badness 10000) in paragraph at lines 7207--7208


Underfull \hbox (badness 10000) in paragraph at lines 7220--7221
[]\OT1/cmtt/m/n/10.95 GtORFIteratorStatus gt[]orf[]iterator[]next([]GtORFIterat
or *orf[]iterator,

Underfull \hbox (badness 10000) in paragraph at lines 7220--7221


Underfull \hbox (badness 10000) in paragraph at lines 7237--7238

[101]
Underfull \hbox (badness 10000) in paragraph at lines 7259--7260
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]bool([]const char *option[]str
ing, const char

Underfull \hbox (badness 10000) in paragraph at lines 7259--7260


Underfull \hbox (badness 2856) in paragraph at lines 7263--7265
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7271--7272
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]double([]const char *option[]s
tring, const char

Underfull \hbox (badness 10000) in paragraph at lines 7271--7272


Underfull \hbox (badness 2856) in paragraph at lines 7275--7277
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7284--7285
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]double[]min([]const char *opti
on[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7284--7285


Underfull \hbox (badness 2856) in paragraph at lines 7288--7291
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7300--7301
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]double[]min[]max([]const char 
*option[]string,

Underfull \hbox (badness 10000) in paragraph at lines 7300--7301
\OT1/cmtt/m/n/10.95 const char *description, double *value, double default[]val
ue, double

Underfull \hbox (badness 10000) in paragraph at lines 7300--7301


Underfull \hbox (badness 2856) in paragraph at lines 7304--7308
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7315--7316
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]probability([]const char *opti
on[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7315--7316


Underfull \hbox (badness 2856) in paragraph at lines 7319--7323
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7329--7330
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int([]const char *option[]stri
ng, const char

Underfull \hbox (badness 10000) in paragraph at lines 7329--7330


Underfull \hbox (badness 2856) in paragraph at lines 7333--7335
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7341--7342
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int[]min([]const char *option[
]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7341--7342


Underfull \hbox (badness 2856) in paragraph at lines 7345--7348
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7354--7355
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int[]max([]const char *option[
]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7354--7355


Underfull \hbox (badness 2856) in paragraph at lines 7358--7361
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7368--7369
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int[]min[]max([]const char *op
tion[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7368--7369
\OT1/cmtt/m/n/10.95 *description, int *value, int default[]value, int minimum[]
value, int

Underfull \hbox (badness 10000) in paragraph at lines 7368--7369


Underfull \hbox (badness 2856) in paragraph at lines 7372--7376
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7383--7384
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint([]const char *option[]str
ing, const char

Underfull \hbox (badness 10000) in paragraph at lines 7383--7384


Underfull \hbox (badness 2856) in paragraph at lines 7387--7389
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7397--7398
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint[]min([]const char *option
[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7397--7398
\OT1/cmtt/m/n/10.95 *description, unsigned int *value, unsigned int default[]va
lue, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 7397--7398


Underfull \hbox (badness 2856) in paragraph at lines 7401--7404
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7412--7413
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint[]max([]const char *option
[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7412--7413
\OT1/cmtt/m/n/10.95 *description, unsigned int *value, unsigned int default[]va
lue, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 7412--7413


Underfull \hbox (badness 2856) in paragraph at lines 7416--7419
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7428--7429
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint[]min[]max([]const char *o
ption[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7428--7429
\OT1/cmtt/m/n/10.95 *description, unsigned int *value, unsigned int default[]va
lue, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 7428--7429


Underfull \hbox (badness 2856) in paragraph at lines 7432--7436
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7442--7443
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]word([]const char *option[]str
ing, const char

Underfull \hbox (badness 10000) in paragraph at lines 7442--7443


Underfull \hbox (badness 2856) in paragraph at lines 7446--7448
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7455--7456
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uword([]const char *option[]st
ring, const char

Underfull \hbox (badness 10000) in paragraph at lines 7455--7456


Underfull \hbox (badness 2856) in paragraph at lines 7459--7461
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7469--7470
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uword[]min([]const char *optio
n[]string, const

Underfull \hbox (badness 10000) in paragraph at lines 7469--7470
\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

Underfull \hbox (badness 10000) in paragraph at lines 7469--7470


Underfull \hbox (badness 2856) in paragraph at lines 7473--7476
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7485--7486
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uword[]min[]max([]const char *
option[]string, const

Underfull \hbox (badness 10000) in paragraph at lines 7485--7486
\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

Underfull \hbox (badness 10000) in paragraph at lines 7485--7486


Underfull \hbox (badness 2856) in paragraph at lines 7489--7493
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7499--7500
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]long([]const char *option[]str
ing, const char

Underfull \hbox (badness 10000) in paragraph at lines 7499--7500


Underfull \hbox (badness 10000) in paragraph at lines 7511--7512
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]ulong([]const char *option[]st
ring, const char

Underfull \hbox (badness 10000) in paragraph at lines 7511--7512


Underfull \hbox (badness 10000) in paragraph at lines 7524--7525
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]ulong[]min([]const char *optio
n[]string, const

Underfull \hbox (badness 10000) in paragraph at lines 7524--7525
\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

Underfull \hbox (badness 10000) in paragraph at lines 7524--7525


Underfull \hbox (badness 10000) in paragraph at lines 7538--7539
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]ulong[]min[]max([]const char *
option[]string, const

Underfull \hbox (badness 10000) in paragraph at lines 7538--7539
\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

Underfull \hbox (badness 10000) in paragraph at lines 7538--7539


Underfull \hbox (badness 10000) in paragraph at lines 7549--7550
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]range([]const char *option[]st
ring, const char

Underfull \hbox (badness 10000) in paragraph at lines 7549--7550


Underfull \hbox (badness 2856) in paragraph at lines 7553--7557
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7566--7567
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]range[]min[]max([]const char *
option[]string, const

Underfull \hbox (badness 10000) in paragraph at lines 7566--7567
\OT1/cmtt/m/n/10.95 char *description, GtRange *value, GtRange *default[]value,
 GtUword

Underfull \hbox (badness 10000) in paragraph at lines 7566--7567


Underfull \hbox (badness 2856) in paragraph at lines 7570--7575
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7581--7582
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]string([]const char *option[]s
tring, const char

Underfull \hbox (badness 10000) in paragraph at lines 7581--7582


Underfull \hbox (badness 2856) in paragraph at lines 7585--7587
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7593--7594
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]string[]array([]const char *op
tion[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7593--7594


Underfull \hbox (badness 2856) in paragraph at lines 7597--7599
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7606--7607
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]choice([]const char *option[]s
tring, const char

Underfull \hbox (badness 10000) in paragraph at lines 7606--7607
\OT1/cmtt/m/n/10.95 *description, GtStr *value, const char *default[]value, con
st char

Underfull \hbox (badness 10000) in paragraph at lines 7606--7607


Underfull \hbox (badness 10000) in paragraph at lines 7610--7613
[]\OT1/ptm/m/n/10.95 Return a \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.95 w
ith the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/cmtt/
m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7619--7620
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]filename([]const char *option[
]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7619--7620


Underfull \hbox (badness 10000) in paragraph at lines 7632--7633
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]filename[]array([]const char *
option[]string, const

Underfull \hbox (badness 10000) in paragraph at lines 7632--7633


Underfull \hbox (badness 2856) in paragraph at lines 7636--7638
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7642--7643


Underfull \hbox (badness 10000) in paragraph at lines 7652--7653


Underfull \hbox (badness 10000) in paragraph at lines 7662--7663


Underfull \hbox (badness 10000) in paragraph at lines 7673--7674


Underfull \hbox (badness 10000) in paragraph at lines 7682--7683


Underfull \hbox (badness 10000) in paragraph at lines 7691--7692


Underfull \hbox (badness 10000) in paragraph at lines 7701--7702
[]\OT1/cmtt/m/n/10.95 void gt[]option[]is[]mandatory[]either([]GtOption *option
[]a, const GtOption

Underfull \hbox (badness 10000) in paragraph at lines 7701--7702


Underfull \hbox (badness 10000) in paragraph at lines 7712--7713
[]\OT1/cmtt/m/n/10.95 void gt[]option[]is[]mandatory[]either[]3([]GtOption *opt
ion[]a, const GtOption

Underfull \hbox (badness 10000) in paragraph at lines 7712--7713


Underfull \hbox (badness 10000) in paragraph at lines 7725--7726
[]\OT1/cmtt/m/n/10.95 void gt[]option[]is[]mandatory[]either[]4([]GtOption *opt
ion[]a, const GtOption

Underfull \hbox (badness 10000) in paragraph at lines 7725--7726


Underfull \hbox (badness 10000) in paragraph at lines 7735--7736


Underfull \hbox (badness 10000) in paragraph at lines 7744--7745


Underfull \hbox (badness 10000) in paragraph at lines 7753--7754


Underfull \hbox (badness 10000) in paragraph at lines 7764--7765
[]\OT1/cmtt/m/n/10.95 void gt[]option[]imply[]either[]2([]GtOption *option[]a, 
const GtOption

Underfull \hbox (badness 10000) in paragraph at lines 7764--7765


Underfull \hbox (badness 10000) in paragraph at lines 7776--7777
[]\OT1/cmtt/m/n/10.95 void gt[]option[]imply[]either[]3([]GtOption *option[]a, 
const GtOption

Underfull \hbox (badness 10000) in paragraph at lines 7776--7777


Underfull \hbox (badness 10000) in paragraph at lines 7785--7786


Underfull \hbox (badness 10000) in paragraph at lines 7794--7795


Underfull \hbox (badness 10000) in paragraph at lines 7803--7804


Underfull \hbox (badness 10000) in paragraph at lines 7812--7813


Underfull \hbox (badness 10000) in paragraph at lines 7821--7822


Underfull \hbox (badness 10000) in paragraph at lines 7833--7834
[]\OT1/cmtt/m/n/10.95 int gt[]option[]parse[]spacespec([]GtUword *maximumspace,
 const char *optname,

Underfull \hbox (badness 10000) in paragraph at lines 7833--7834

[102] [103] [104] [105] [106]
Underfull \hbox (badness 10000) in paragraph at lines 7850--7851


Underfull \hbox (badness 10000) in paragraph at lines 7860--7861
[]\OT1/cmtt/m/n/10.95 GtOptionParser* gt[]option[]parser[]new([]const char *syn
opsis, const char

Underfull \hbox (badness 10000) in paragraph at lines 7860--7861


Underfull \hbox (badness 10000) in paragraph at lines 7874--7875
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]add[]option([]GtOptionParser *op
tion[]parser, GtOption

Underfull \hbox (badness 10000) in paragraph at lines 7874--7875


Underfull \hbox (badness 10000) in paragraph at lines 7884--7885
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]parser[]get[]option([]GtOptionParse
r *option[]parser, const

Underfull \hbox (badness 10000) in paragraph at lines 7884--7885


Underfull \hbox (badness 1496) in paragraph at lines 7888--7890
[]\OT1/ptm/m/n/10.95 Return the \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.95
 ob-ject if an op-tion named \OT1/cmtt/m/n/10.95 option[]string \OT1/ptm/m/n/10
.95 is present in

Underfull \hbox (badness 10000) in paragraph at lines 7894--7895


Underfull \hbox (badness 10000) in paragraph at lines 7906--7907
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]comment[]func([]GtOptionPar
ser *option[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 7906--7907


Underfull \hbox (badness 10000) in paragraph at lines 7917--7918
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]version[]func([]GtOptionPar
ser *option[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 7917--7918


Underfull \hbox (badness 10000) in paragraph at lines 7929--7930
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]mail[]address([]GtOptionPar
ser*, const char

Underfull \hbox (badness 10000) in paragraph at lines 7929--7930


Underfull \hbox (badness 10000) in paragraph at lines 7943--7944
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]register[]hook([]GtOptionParser 
*option[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 7943--7944


Underfull \hbox (badness 10000) in paragraph at lines 7957--7958
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]min[]args([]GtOptionParser 
*option[]parser, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 7957--7958


Underfull \hbox (badness 10000) in paragraph at lines 7968--7969
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]max[]args([]GtOptionParser 
*option[]parser, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 7968--7969


Underfull \hbox (badness 10000) in paragraph at lines 7980--7981
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]min[]max[]args([]GtOptionPa
rser *option[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 7980--7981


Underfull \hbox (badness 5446) in paragraph at lines 7984--7986
[]\OT1/ptm/m/n/10.95 The \OT1/cmtt/m/n/10.95 minimum \OT1/ptm/m/n/10.95 and \OT
1/cmtt/m/n/10.95 maximum \OT1/ptm/m/n/10.95 num-ber of ad-di-tional com-mand li
ne ar-gu-ments

Underfull \hbox (badness 10000) in paragraph at lines 7994--7995
[]\OT1/cmtt/m/n/10.95 GtOPrval gt[]option[]parser[]parse([]GtOptionParser *opti
on[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 7994--7995
\OT1/cmtt/m/n/10.95 int *parsed[]args, int argc, const char **argv, GtShowVersi
onFunc

Underfull \hbox (badness 10000) in paragraph at lines 7994--7995


Underfull \hbox (badness 10000) in paragraph at lines 8007--8008


Underfull \hbox (badness 10000) in paragraph at lines 8017--8018

[107] [108]
Underfull \hbox (badness 10000) in paragraph at lines 8033--8034


Underfull \hbox (badness 10000) in paragraph at lines 8044--8045
[]\OT1/cmtt/m/n/10.95 void gt[]output[]file[]info[]register[]options([]GtOutput
FileInfo

Underfull \hbox (badness 10000) in paragraph at lines 8044--8045


Underfull \hbox (badness 10000) in paragraph at lines 8057--8058

[109]
Underfull \hbox (badness 10000) in paragraph at lines 8075--8076


Underfull \hbox (badness 10000) in paragraph at lines 8084--8085


Underfull \hbox (badness 10000) in paragraph at lines 8102--8103


Underfull \hbox (badness 10000) in paragraph at lines 8111--8112


Underfull \hbox (badness 10000) in paragraph at lines 8120--8121


Underfull \hbox (badness 10000) in paragraph at lines 8130--8131


Underfull \hbox (badness 10000) in paragraph at lines 8139--8140


Underfull \hbox (badness 10000) in paragraph at lines 8150--8151


Underfull \hbox (badness 10000) in paragraph at lines 8159--8160

[110]
Underfull \hbox (badness 10000) in paragraph at lines 8179--8180
[]\OT1/cmtt/m/n/10.95 GtRDB* gt[]rdb[]mysql[]new([]const char *server, unsigned
 int port, const char

Underfull \hbox (badness 10000) in paragraph at lines 8179--8180


Underfull \hbox (badness 10000) in paragraph at lines 8200--8201


Underfull \hbox (badness 10000) in paragraph at lines 8218--8219
[]\OT1/cmtt/m/n/10.95 int gt[]rdb[]visitor[]visit[]sqlite([]GtRDBVisitor *rdbv,
 GtRDBSqlite *rdbs,

Underfull \hbox (badness 10000) in paragraph at lines 8218--8219


Underfull \hbox (badness 10000) in paragraph at lines 8229--8230
[]\OT1/cmtt/m/n/10.95 int gt[]rdb[]visitor[]visit[]mysql([]GtRDBVisitor *rdbv, 
GtRDBMySQL *rdbm,

Underfull \hbox (badness 10000) in paragraph at lines 8229--8230


Underfull \hbox (badness 10000) in paragraph at lines 8239--8240

[111]
Underfull \hbox (badness 10000) in paragraph at lines 8255--8256


Underfull \hbox (badness 10000) in paragraph at lines 8264--8265


Underfull \hbox (badness 10000) in paragraph at lines 8273--8274


Underfull \hbox (badness 10000) in paragraph at lines 8282--8283


Underfull \hbox (badness 10000) in paragraph at lines 8291--8292


Underfull \hbox (badness 10000) in paragraph at lines 8308--8309


Underfull \hbox (badness 10000) in paragraph at lines 8321--8322
[]\OT1/cmtt/m/n/10.95 int gt[]range[]compare[]with[]delta([]const GtRange *rang
e[]a, const GtRange

Underfull \hbox (badness 10000) in paragraph at lines 8321--8322


Underfull \hbox (badness 10000) in paragraph at lines 8334--8335


Underfull \hbox (badness 10000) in paragraph at lines 8345--8346
[]\OT1/cmtt/m/n/10.95 bool gt[]range[]overlap[]delta([]const GtRange *range[]a,
 const GtRange

Underfull \hbox (badness 10000) in paragraph at lines 8345--8346


Underfull \hbox (badness 10000) in paragraph at lines 8355--8356


Underfull \hbox (badness 10000) in paragraph at lines 8364--8365


Underfull \hbox (badness 10000) in paragraph at lines 8373--8374


Underfull \hbox (badness 10000) in paragraph at lines 8382--8383


Underfull \hbox (badness 10000) in paragraph at lines 8391--8392

[112]
Overfull \hbox (37.97119pt too wide) in paragraph at lines 8401--8403
\OT1/ptm/m/n/10.95 This enum type de-fines the pos-si-ble reamodes, namely \OT1
/cmtt/m/n/10.95 GT[]READMODE[]FORWARD\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/n/10.95 G
T[]READMODE[]REVERSE\OT1/ptm/m/n/10.95 ,

Underfull \hbox (badness 10000) in paragraph at lines 8408--8409


Underfull \hbox (badness 10000) in paragraph at lines 8417--8418


Underfull \hbox (badness 2626) in paragraph at lines 8421--8424
[]\OT1/ptm/m/n/10.95 Returns the \OT1/cmtt/m/n/10.95 GtReadmode \OT1/ptm/m/n/10
.95 for the de-scrip-tion \OT1/cmtt/m/n/10.95 string\OT1/ptm/m/n/10.95 , which 
must be one of

Underfull \hbox (badness 10000) in paragraph at lines 8428--8429


Underfull \hbox (badness 10000) in paragraph at lines 8450--8451
[]\OT1/cmtt/m/n/10.95 GtRecMap* gt[]rec[]map[]new([]double nw[]x, double nw[]y,
 double se[]x, double

Underfull \hbox (badness 10000) in paragraph at lines 8450--8451


Underfull \hbox (badness 10000) in paragraph at lines 8459--8460


Underfull \hbox (badness 10000) in paragraph at lines 8468--8469


Underfull \hbox (badness 10000) in paragraph at lines 8477--8478


Underfull \hbox (badness 10000) in paragraph at lines 8486--8487


Underfull \hbox (badness 10000) in paragraph at lines 8495--8496


Underfull \hbox (badness 10000) in paragraph at lines 8504--8505


Underfull \hbox (badness 10000) in paragraph at lines 8513--8514


Underfull \hbox (badness 10000) in paragraph at lines 8523--8524

[113]
Underfull \hbox (badness 10000) in paragraph at lines 8541--8542
[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]mapping([]GtSt
r *mapping[]filename,

Underfull \hbox (badness 10000) in paragraph at lines 8541--8542


Underfull \hbox (badness 2735) in paragraph at lines 8545--8548
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtRegionMapping \OT1/ptm/
m/n/10.95 ob-ject for the map-ping file with the given

Underfull \hbox (badness 10000) in paragraph at lines 8553--8554
[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]seqfiles([]GtS
trArray

Underfull \hbox (badness 10000) in paragraph at lines 8553--8554


Underfull \hbox (badness 10000) in paragraph at lines 8557--8563
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtRegionMapping \OT1/ptm/
m/n/10.95 ob-ject for the se-quence files given in

Underfull \hbox (badness 1189) in paragraph at lines 8557--8563
\OT1/cmtt/m/n/10.95 sequence[]filenames\OT1/ptm/m/n/10.95 . If \OT1/cmtt/m/n/10
.95 matchdesc \OT1/ptm/m/n/10.95 is \OT1/cmtt/m/n/10.95 true\OT1/ptm/m/n/10.95 
, the se-quence de-scrip-tions from

Underfull \hbox (badness 10000) in paragraph at lines 8568--8569
[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]encseq([]GtEnc
seq *encseq, bool

Underfull \hbox (badness 10000) in paragraph at lines 8568--8569


Underfull \hbox (badness 10000) in paragraph at lines 8579--8580
[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]rawseq([]const
 char *rawseq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 8579--8580


Underfull \hbox (badness 10000) in paragraph at lines 8589--8590


Underfull \hbox (badness 10000) in paragraph at lines 8602--8603
[]\OT1/cmtt/m/n/10.95 int gt[]region[]mapping[]get[]sequence([]GtRegionMapping 
*region[]mapping, char

Underfull \hbox (badness 10000) in paragraph at lines 8602--8603


Underfull \hbox (badness 10000) in paragraph at lines 8618--8619
[]\OT1/cmtt/m/n/10.95 int gt[]region[]mapping[]get[]sequence[]length([]GtRegion
Mapping *region[]mapping,

Underfull \hbox (badness 10000) in paragraph at lines 8618--8619


Underfull \hbox (badness 10000) in paragraph at lines 8633--8634
[]\OT1/cmtt/m/n/10.95 int gt[]region[]mapping[]get[]description([]GtRegionMappi
ng *region[]mapping,

Underfull \hbox (badness 10000) in paragraph at lines 8633--8634


Underfull \hbox (badness 10000) in paragraph at lines 8649--8650
[]\OT1/cmtt/m/n/10.95 const char* gt[]region[]mapping[]get[]md5[]fingerprint([]
GtRegionMapping

Underfull \hbox (badness 10000) in paragraph at lines 8649--8650
\OT1/cmtt/m/n/10.95 *region[]mapping, GtStr *seqid, const GtRange *range, GtUwo
rd *offset,

Underfull \hbox (badness 10000) in paragraph at lines 8649--8650


Underfull \hbox (badness 10000) in paragraph at lines 8661--8662

[114] [115]
Overfull \hbox (1.85855pt too wide) in paragraph at lines 8671--8673
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtGenomeNode \OT1/ptm/m/n
/10.95 in-ter-face. Re-gion nodes cor-re-spond to the \OT1/cmtt/m/n/10.95 ##seq
uence-region

Underfull \hbox (badness 10000) in paragraph at lines 8679--8680
[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]region[]node[]new([]GtStr *seqid, GtUwo
rd start, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 8679--8680


Underfull \hbox (badness 10000) in paragraph at lines 8692--8693


Underfull \hbox (badness 10000) in paragraph at lines 8704--8705


Underfull \hbox (badness 10000) in paragraph at lines 8725--8726
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]script[]wrapper[]stream[]new([]GtScript
WrapperStreamNextFunc,

Underfull \hbox (badness 10000) in paragraph at lines 8725--8726

[116]
Overfull \hbox (52.44699pt too wide) in paragraph at lines 8747--8748
[]\OT1/cmtt/m/n/10.95 GtNodeVisitor* gt[]script[]wrapper[]visitor[]new([]GtScri
ptWrapperVisitorCommentNodeFunc,

Overfull \hbox (18.64471pt too wide) in paragraph at lines 8747--8748
\OT1/cmtt/m/n/10.95 GtScriptWrapperVisitorFeatureNodeFunc, GtScriptWrapperVisit
orRegionNodeFunc,

Overfull \hbox (12.89603pt too wide) in paragraph at lines 8747--8748
\OT1/cmtt/m/n/10.95 GtScriptWrapperVisitorSequenceNodeFunc, GtScriptWrapperVisi
torMetaNodeFunc,

Underfull \hbox (badness 10000) in paragraph at lines 8747--8748


Underfull \hbox (badness 10000) in paragraph at lines 8780--8781
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]select[]stream[]new([]GtNodeStream *in[
]stream, GtStr

Underfull \hbox (badness 10000) in paragraph at lines 8780--8781
\OT1/cmtt/m/n/10.95 *seqid, GtStr *source, const GtRange *contain[]range, const
 GtRange

Underfull \hbox (badness 10000) in paragraph at lines 8780--8781
\OT1/cmtt/m/n/10.95 *overlap[]range, GtStrand strand, GtStrand targetstrand, bo
ol has[]CDS,

Underfull \hbox (badness 10000) in paragraph at lines 8780--8781
\OT1/cmtt/m/n/10.95 GtUword max[]gene[]length, GtUword max[]gene[]num, double m
in[]gene[]score,

Underfull \hbox (badness 10000) in paragraph at lines 8780--8781
\OT1/cmtt/m/n/10.95 double max[]gene[]score, double min[]average[]splice[]site[
]prob, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 8780--8781


Underfull \hbox (badness 10000) in paragraph at lines 8823--8824
[]\OT1/cmtt/m/n/10.95 void gt[]select[]stream[]set[]drophandler([]GtSelectStrea
m *sstr,

Underfull \hbox (badness 10000) in paragraph at lines 8823--8824

[117]
Underfull \hbox (badness 10000) in paragraph at lines 8837--8838
[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]set[]symbolmap([]GtSeqIterator*, 
const GtUchar

Underfull \hbox (badness 10000) in paragraph at lines 8837--8838


Underfull \hbox (badness 10000) in paragraph at lines 8848--8849


Underfull \hbox (badness 10000) in paragraph at lines 8862--8863
[]\OT1/cmtt/m/n/10.95 int gt[]seq[]iterator[]next([]GtSeqIterator *seqit, const
 GtUchar **sequence,

Underfull \hbox (badness 10000) in paragraph at lines 8862--8863


Underfull \hbox (badness 10000) in paragraph at lines 8876--8877
[]\OT1/cmtt/m/n/10.95 const GtUint64* gt[]seq[]iterator[]getcurrentcounter([]Gt
SeqIterator*,

Underfull \hbox (badness 10000) in paragraph at lines 8876--8877


Underfull \hbox (badness 10000) in paragraph at lines 8885--8886


Underfull \hbox (badness 10000) in paragraph at lines 8895--8896
[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]set[]quality[]buffer([]GtSeqItera
tor *seqit, const

Underfull \hbox (badness 10000) in paragraph at lines 8895--8896


Underfull \hbox (badness 10000) in paragraph at lines 8906--8907

[118]
Underfull \hbox (badness 10000) in paragraph at lines 8918--8919
[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]fastq[]new([]const GtSt
rArray *filenametab,

Underfull \hbox (badness 10000) in paragraph at lines 8918--8919


Underfull \hbox (badness 10000) in paragraph at lines 8929--8930
[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]fastq[]new[]colorspace(
[]const GtStrArray

Underfull \hbox (badness 10000) in paragraph at lines 8929--8930


Underfull \hbox (badness 10000) in paragraph at lines 8939--8940


Overfull \hbox (28.76239pt too wide) in paragraph at lines 8949--8950
[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]fastq[]relax[]check[]of[]quality[
]description([]GtSeqIteratorFastQ

Underfull \hbox (badness 10000) in paragraph at lines 8949--8950

[119]
Underfull \hbox (badness 10000) in paragraph at lines 8963--8964
[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]sequence[]buffer[]new([
]const GtStrArray

Underfull \hbox (badness 10000) in paragraph at lines 8963--8964


Underfull \hbox (badness 10000) in paragraph at lines 8984--8985
[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]sequence[]node[]new([]const char *descr
iption, GtStr

Underfull \hbox (badness 10000) in paragraph at lines 8984--8985


Underfull \hbox (badness 2698) in paragraph at lines 8988--8990
[]\OT1/ptm/m/n/10.95 Create a new \OT1/cmtt/m/n/10.95 GtSequenceNode* \OT1/ptm/
m/n/10.95 rep-re-sent-ing a FASTA en-try with the given

Underfull \hbox (badness 10000) in paragraph at lines 8996--8997
[]\OT1/cmtt/m/n/10.95 const char* gt[]sequence[]node[]get[]description([]const 
GtSequenceNode

Underfull \hbox (badness 10000) in paragraph at lines 8996--8997


Underfull \hbox (badness 10000) in paragraph at lines 9006--9007
[]\OT1/cmtt/m/n/10.95 const char* gt[]sequence[]node[]get[]sequence([]const GtS
equenceNode

Underfull \hbox (badness 10000) in paragraph at lines 9006--9007


Underfull \hbox (badness 10000) in paragraph at lines 9017--9018
[]\OT1/cmtt/m/n/10.95 GtUword gt[]sequence[]node[]get[]sequence[]length([]const
 GtSequenceNode

Underfull \hbox (badness 10000) in paragraph at lines 9017--9018


Underfull \hbox (badness 10000) in paragraph at lines 9026--9027


Underfull \hbox (badness 10000) in paragraph at lines 9038--9039

[120]
Overfull \hbox (58.46886pt too wide) in paragraph at lines 9049--9052
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeVisitor \OT1/ptm/m/
n/10.95 in-ter-face. Used with the \OT1/cmtt/m/n/10.95 GtVisitorStream \OT1/ptm
/m/n/10.95 class, a \OT1/cmtt/m/n/10.95 GtSetSourceVisitor

Underfull \hbox (badness 10000) in paragraph at lines 9057--9058


Underfull \hbox (badness 10000) in paragraph at lines 9075--9076


Underfull \hbox (badness 10000) in paragraph at lines 9094--9095


Underfull \hbox (badness 10000) in paragraph at lines 9104--9105
[]\OT1/cmtt/m/n/10.95 void gt[]splitter[]split([]GtSplitter *splitter, char *st
ring, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 9104--9105


Underfull \hbox (badness 10000) in paragraph at lines 9115--9116
[]\OT1/cmtt/m/n/10.95 void gt[]splitter[]split[]non[]empty([]GtSplitter *s, cha
r *string, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 9115--9116


Underfull \hbox (badness 10000) in paragraph at lines 9126--9127


Underfull \hbox (badness 10000) in paragraph at lines 9136--9137


Underfull \hbox (badness 10000) in paragraph at lines 9145--9146


Underfull \hbox (badness 10000) in paragraph at lines 9154--9155


Underfull \hbox (badness 10000) in paragraph at lines 9163--9164

[121]
Overfull \hbox (31.52028pt too wide) in paragraph at lines 9173--9176
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. A \OT1/cmtt/m/n/10.95 GtStatStream \OT1/ptm/m/n/10.95 gath-
ers statis-tics about the \OT1/cmtt/m/n/10.95 GtGenomeNode

Underfull \hbox (badness 10000) in paragraph at lines 9188--9189
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]stat[]stream[]new([]GtNodeStream *in[]s
tream, bool

Underfull \hbox (badness 10000) in paragraph at lines 9188--9189
\OT1/cmtt/m/n/10.95 gene[]length[]distribution, bool gene[]score[]distribution,
 bool

Underfull \hbox (badness 10000) in paragraph at lines 9188--9189
\OT1/cmtt/m/n/10.95 exon[]length[]distribution, bool exon[]number[]distribution
, bool

Underfull \hbox (badness 10000) in paragraph at lines 9188--9189
\OT1/cmtt/m/n/10.95 intron[]length[]distribution, bool cds[]length[]distributio
n, bool

Underfull \hbox (badness 10000) in paragraph at lines 9188--9189


Underfull \hbox (badness 3668) in paragraph at lines 9192--9200
\OT1/ptm/m/n/10.95 ment equals \OT1/cmtt/m/n/10.95 true\OT1/ptm/m/n/10.95 : \OT
1/cmtt/m/n/10.95 gene[]length[]distribution\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/n/1
0.95 gene[]score[]distribution\OT1/ptm/m/n/10.95 ,

Underfull \hbox (badness 10000) in paragraph at lines 9192--9200
\OT1/cmtt/m/n/10.95 exon[]length[]distribution\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/
n/10.95 exon[]number[]distribution\OT1/ptm/m/n/10.95 ,

Underfull \hbox (badness 10000) in paragraph at lines 9205--9206

[122]
Underfull \hbox (badness 10000) in paragraph at lines 9221--9222


Underfull \hbox (badness 10000) in paragraph at lines 9230--9231


Underfull \hbox (badness 10000) in paragraph at lines 9239--9240


Underfull \hbox (badness 10000) in paragraph at lines 9248--9249


Underfull \hbox (badness 10000) in paragraph at lines 9258--9259


Underfull \hbox (badness 10000) in paragraph at lines 9268--9269


Underfull \hbox (badness 10000) in paragraph at lines 9277--9278


Underfull \hbox (badness 10000) in paragraph at lines 9286--9287


Underfull \hbox (badness 10000) in paragraph at lines 9295--9296


Underfull \hbox (badness 10000) in paragraph at lines 9305--9306


Underfull \hbox (badness 10000) in paragraph at lines 9314--9315


Underfull \hbox (badness 10000) in paragraph at lines 9323--9324


Underfull \hbox (badness 10000) in paragraph at lines 9333--9334


Underfull \hbox (badness 10000) in paragraph at lines 9342--9343


Underfull \hbox (badness 10000) in paragraph at lines 9351--9352


Underfull \hbox (badness 10000) in paragraph at lines 9360--9361


Underfull \hbox (badness 5667) in paragraph at lines 9364--9366
[]\OT1/ptm/m/n/10.95 Set length of \OT1/cmtt/m/n/10.95 str \OT1/ptm/m/n/10.95 t
o \OT1/cmtt/m/n/10.95 length\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 length \OT
1/ptm/m/n/10.95 must be smaller or equal than

Underfull \hbox (badness 10000) in paragraph at lines 9370--9371


Underfull \hbox (badness 10000) in paragraph at lines 9379--9380


Underfull \hbox (badness 10000) in paragraph at lines 9388--9389


Underfull \hbox (badness 10000) in paragraph at lines 9397--9398

[123]
Underfull \hbox (badness 10000) in paragraph at lines 9414--9415


Underfull \hbox (badness 10000) in paragraph at lines 9423--9424


Underfull \hbox (badness 10000) in paragraph at lines 9432--9433


Underfull \hbox (badness 10000) in paragraph at lines 9442--9443
[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]add[]cstr[]nt([]GtStrArray *str[]arr
ay, const char *cstr,

Underfull \hbox (badness 10000) in paragraph at lines 9442--9443


Underfull \hbox (badness 10000) in paragraph at lines 9452--9453


Underfull \hbox (badness 10000) in paragraph at lines 9462--9463


Underfull \hbox (badness 10000) in paragraph at lines 9473--9474
[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]set[]cstr([]GtStrArray *str[]array, 
GtUword strnum, const

Underfull \hbox (badness 10000) in paragraph at lines 9473--9474


Underfull \hbox (badness 10000) in paragraph at lines 9483--9484
[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]set([]GtStrArray *str[]array, GtUwor
d strnum, const GtStr

Underfull \hbox (badness 10000) in paragraph at lines 9483--9484


Underfull \hbox (badness 10000) in paragraph at lines 9492--9493


Underfull \hbox (badness 2564) in paragraph at lines 9496--9498
[]\OT1/ptm/m/n/10.95 Set the size of \OT1/cmtt/m/n/10.95 str[]array \OT1/ptm/m/
n/10.95 to \OT1/cmtt/m/n/10.95 size\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 siz
e \OT1/ptm/m/n/10.95 must be smaller or equal than

Underfull \hbox (badness 10000) in paragraph at lines 9502--9503


Underfull \hbox (badness 10000) in paragraph at lines 9511--9512


Underfull \hbox (badness 10000) in paragraph at lines 9520--9521

[124]
Overfull \hbox (21.75429pt too wide) in paragraph at lines 9530--9533
\OT1/ptm/m/n/10.95 This enum type de-fines the pos-si-ble strands. The fol-low-
ing strands are de-fined: \OT1/cmtt/m/n/10.95 GT[]STRAND[]FORWARD\OT1/ptm/m/n/1
0.95 ,

Underfull \hbox (badness 10000) in paragraph at lines 9538--9539


Underfull \hbox (badness 10000) in paragraph at lines 9547--9548


Underfull \hbox (badness 10000) in paragraph at lines 9551--9553
[]\OT1/ptm/m/n/10.95 Map \OT1/cmtt/m/n/10.95 strand[]char \OT1/ptm/m/n/10.95 to
 the cor-re-spond-ing strand enum type. Re-turns

Underfull \hbox (badness 10000) in paragraph at lines 9568--9569


Underfull \hbox (badness 10000) in paragraph at lines 9577--9578


Underfull \hbox (badness 10000) in paragraph at lines 9586--9587


Underfull \hbox (badness 10000) in paragraph at lines 9595--9596


Underfull \hbox (badness 10000) in paragraph at lines 9604--9605


Underfull \hbox (badness 10000) in paragraph at lines 9613--9614


Underfull \hbox (badness 10000) in paragraph at lines 9622--9623


Underfull \hbox (badness 10000) in paragraph at lines 9632--9633


Underfull \hbox (badness 10000) in paragraph at lines 9642--9643


Underfull \hbox (badness 10000) in paragraph at lines 9652--9653


Underfull \hbox (badness 10000) in paragraph at lines 9662--9663
[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]color([]GtStyle*, const char *sectio
n, const char *key,

Underfull \hbox (badness 10000) in paragraph at lines 9662--9663


Underfull \hbox (badness 10000) in paragraph at lines 9674--9675
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]color([]const GtStyle 
*style, const char

Underfull \hbox (badness 10000) in paragraph at lines 9674--9675
\OT1/cmtt/m/n/10.95 *section, const char *key, GtColor *result, GtFeatureNode *
fn, GtError

Underfull \hbox (badness 10000) in paragraph at lines 9674--9675


Underfull \hbox (badness 10000) in paragraph at lines 9700--9701
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]color[]with[]track([]c
onst GtStyle *style,

Underfull \hbox (badness 10000) in paragraph at lines 9700--9701
\OT1/cmtt/m/n/10.95 const char *section, const char *key, GtColor *result, GtFe
atureNode

Underfull \hbox (badness 10000) in paragraph at lines 9700--9701


Underfull \hbox (badness 10000) in paragraph at lines 9711--9712
[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]str([]GtStyle*, const char *section,
 const char *key,

Underfull \hbox (badness 10000) in paragraph at lines 9711--9712


Underfull \hbox (badness 10000) in paragraph at lines 9722--9723
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]str([]const GtStyle *s
tyle, const char

Underfull \hbox (badness 10000) in paragraph at lines 9722--9723
\OT1/cmtt/m/n/10.95 *section, const char *key, GtStr *result, GtFeatureNode *fn
, GtError

Underfull \hbox (badness 10000) in paragraph at lines 9722--9723


Underfull \hbox (badness 10000) in paragraph at lines 9747--9748
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]str[]with[]track([]con
st GtStyle *style, const

Underfull \hbox (badness 10000) in paragraph at lines 9747--9748
\OT1/cmtt/m/n/10.95 char *section, const char *key, GtStr *result, GtFeatureNod
e *fn, const

Underfull \hbox (badness 10000) in paragraph at lines 9747--9748


Underfull \hbox (badness 10000) in paragraph at lines 9758--9759
[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]num([]GtStyle*, const char *section,
 const char *key,

Underfull \hbox (badness 10000) in paragraph at lines 9758--9759


Underfull \hbox (badness 10000) in paragraph at lines 9769--9770
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]num([]const GtStyle *s
tyle, const char

Underfull \hbox (badness 10000) in paragraph at lines 9769--9770
\OT1/cmtt/m/n/10.95 *section, const char *key, double *result, GtFeatureNode *f
n, GtError

Underfull \hbox (badness 10000) in paragraph at lines 9769--9770


Underfull \hbox (badness 10000) in paragraph at lines 9794--9795
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]num[]with[]track([]con
st GtStyle *style, const

Underfull \hbox (badness 10000) in paragraph at lines 9794--9795
\OT1/cmtt/m/n/10.95 char *section, const char *key, double *result, GtFeatureNo
de *fn, const

Underfull \hbox (badness 10000) in paragraph at lines 9794--9795


Underfull \hbox (badness 10000) in paragraph at lines 9805--9806
[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]bool([]GtStyle*, const char *section
, const char *key,

Underfull \hbox (badness 10000) in paragraph at lines 9805--9806


Underfull \hbox (badness 10000) in paragraph at lines 9816--9817
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]bool([]const GtStyle *
style, const char

Underfull \hbox (badness 10000) in paragraph at lines 9816--9817
\OT1/cmtt/m/n/10.95 *section, const char *key, bool *result, GtFeatureNode *fn,
 GtError

Underfull \hbox (badness 10000) in paragraph at lines 9816--9817


Underfull \hbox (badness 10000) in paragraph at lines 9841--9842
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]bool[]with[]track([]co
nst GtStyle *style,

Underfull \hbox (badness 10000) in paragraph at lines 9841--9842
\OT1/cmtt/m/n/10.95 const char *section, const char *key, bool *result, GtFeatu
reNode *fn,

Underfull \hbox (badness 10000) in paragraph at lines 9841--9842


Underfull \hbox (badness 10000) in paragraph at lines 9852--9853


Underfull \hbox (badness 10000) in paragraph at lines 9861--9862

[125] [126] [127] [128]
Underfull \hbox (badness 10000) in paragraph at lines 9885--9886
[]\OT1/cmtt/m/n/10.95 void GtTagValueMapIteratorFunc([]const char *tag, const c
har *value, void

Underfull \hbox (badness 10000) in paragraph at lines 9885--9886


Underfull \hbox (badness 10000) in paragraph at lines 9895--9896


Underfull \hbox (badness 10000) in paragraph at lines 9907--9908
[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]add([]GtTagValueMap *tag[]value
[]map, const char *tag,

Underfull \hbox (badness 10000) in paragraph at lines 9907--9908


Underfull \hbox (badness 10000) in paragraph at lines 9918--9919
[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]set([]GtTagValueMap *tag[]value
[]map, const char *tag,

Underfull \hbox (badness 10000) in paragraph at lines 9918--9919


Underfull \hbox (badness 10000) in paragraph at lines 9928--9929
[]\OT1/cmtt/m/n/10.95 const char* gt[]tag[]value[]map[]get([]const GtTagValueMa
p tag[]value[]map, const

Underfull \hbox (badness 10000) in paragraph at lines 9928--9929


Underfull \hbox (badness 10000) in paragraph at lines 9938--9939


Underfull \hbox (badness 10000) in paragraph at lines 9948--9949
[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]remove([]GtTagValueMap *tag[]va
lue[]map, const char

Underfull \hbox (badness 10000) in paragraph at lines 9948--9949


Underfull \hbox (badness 10000) in paragraph at lines 9961--9962
[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]foreach([]const GtTagValueMap t
ag[]value[]map,

Underfull \hbox (badness 10000) in paragraph at lines 9961--9962


Underfull \hbox (badness 10000) in paragraph at lines 9971--9972


Underfull \hbox (badness 10000) in paragraph at lines 9980--9981

[129]
Overfull \hbox (6.45749pt too wide) in paragraph at lines 9999--10000
[]\OT1/cmtt/m/n/10.95 GtTextWidthCalculator* gt[]text[]width[]calculator[]ref([
]GtTextWidthCalculator*[]) 

Underfull \hbox (badness 10000) in paragraph at lines 9999--10000


Underfull \hbox (badness 10000) in paragraph at lines 10010--10011
[]\OT1/cmtt/m/n/10.95 double gt[]text[]width[]calculator[]get[]text[]width([]Gt
TextWidthCalculator*,

Underfull \hbox (badness 10000) in paragraph at lines 10010--10011


Underfull \hbox (badness 10000) in paragraph at lines 10021--10022


Overfull \hbox (83.5338pt too wide) in paragraph at lines 10031--10037
\OT1/cmtt/m/n/10.95 cairo[]t \OT1/ptm/m/n/10.95 and which should be used later 
via a \OT1/cmtt/m/n/10.95 GtCanvasCairoContext\OT1/ptm/m/n/10.95 , cre-ate a \O
T1/cmtt/m/n/10.95 GtTextWidthCalculatorCairo

Underfull \hbox (badness 10000) in paragraph at lines 10043--10044
[]\OT1/cmtt/m/n/10.95 GtTextWidthCalculator* gt[]text[]width[]calculator[]cairo
[]new([]cairo[]t*,

Underfull \hbox (badness 10000) in paragraph at lines 10043--10044


Underfull \hbox (badness 10000) in paragraph at lines 10062--10063


Underfull \hbox (badness 10000) in paragraph at lines 10071--10072


Underfull \hbox (badness 10000) in paragraph at lines 10082--10083


Underfull \hbox (badness 10000) in paragraph at lines 10091--10092

[130]
Underfull \hbox (badness 10000) in paragraph at lines 10109--10110


Underfull \hbox (badness 10000) in paragraph at lines 10118--10119


Underfull \hbox (badness 10000) in paragraph at lines 10127--10128


Underfull \hbox (badness 10000) in paragraph at lines 10136--10137


Underfull \hbox (badness 10000) in paragraph at lines 10145--10146


Underfull \hbox (badness 3168) in paragraph at lines 10149--10153
[]\OT1/ptm/m/n/10.95 Output the cur-rent state of \OT1/cmtt/m/n/10.95 timer \OT
1/ptm/m/n/10.95 in the for-mat ""GT[]WD".pointer \OT1/cmtt/m/n/10.95 fp \OT1/pt
m/m/n/10.95 (see

Underfull \hbox (badness 10000) in paragraph at lines 10157--10158


Underfull \hbox (badness 10000) in paragraph at lines 10169--10170


Underfull \hbox (badness 10000) in paragraph at lines 10178--10179


Underfull \hbox (badness 10000) in paragraph at lines 10182--10186
[]\OT1/ptm/m/n/10.95 Output the cur-rent state of \OT1/cmtt/m/n/10.95 timer \OT
1/ptm/m/n/10.95 on \OT1/cmtt/m/n/10.95 fp \OT1/ptm/m/n/10.95 since the last cal
l of

Underfull \hbox (badness 1292) in paragraph at lines 10182--10186
\OT1/cmtt/m/n/10.95 gt[]timer[]show[]progress() \OT1/ptm/m/n/10.95 or the last 
start of \OT1/cmtt/m/n/10.95 timer\OT1/ptm/m/n/10.95 , along with the cur-rent

Underfull \hbox (badness 10000) in paragraph at lines 10191--10192
[]\OT1/cmtt/m/n/10.95 void gt[]timer[]show[]progress[]formatted([]GtTimer *time
r, FILE *fp, const

Underfull \hbox (badness 10000) in paragraph at lines 10191--10192


Underfull \hbox (badness 10000) in paragraph at lines 10202--10203
[]\OT1/cmtt/m/n/10.95 void gt[]timer[]show[]progress[]va([]GtTimer *timer, FILE
 *fp, const char

Underfull \hbox (badness 10000) in paragraph at lines 10202--10203


Underfull \hbox (badness 10000) in paragraph at lines 10212--10213


Underfull \hbox (badness 10000) in paragraph at lines 10221--10222


Underfull \hbox (badness 10000) in paragraph at lines 10231--10232


Underfull \hbox (badness 10000) in paragraph at lines 10240--10241

[131]
Underfull \hbox (badness 10000) in paragraph at lines 10257--10258


Underfull \hbox (badness 10000) in paragraph at lines 10267--10268


Underfull \hbox (badness 10000) in paragraph at lines 10277--10278


Underfull \hbox (badness 10000) in paragraph at lines 10289--10290
[]\OT1/cmtt/m/n/10.95 int GtToolArgumentsCheck([]int rest[]argc, void *tool[]ar
guments, GtError

Underfull \hbox (badness 10000) in paragraph at lines 10289--10290


Underfull \hbox (badness 10000) in paragraph at lines 10303--10304
[]\OT1/cmtt/m/n/10.95 int GtToolRunner([]int argc, const char **argv, int parse
d[]args, void

Underfull \hbox (badness 10000) in paragraph at lines 10303--10304


Underfull \hbox (badness 10000) in paragraph at lines 10319--10320


Underfull \hbox (badness 10000) in paragraph at lines 10332--10333
[]\OT1/cmtt/m/n/10.95 GtTool* gt[]tool[]new([]GtToolArgumentsNew tool[]argument
s[]new,

Underfull \hbox (badness 10000) in paragraph at lines 10332--10333
\OT1/cmtt/m/n/10.95 GtToolArgumentsDelete tool[]arguments[]delete, GtToolOption
ParserNew

Underfull \hbox (badness 10000) in paragraph at lines 10332--10333
\OT1/cmtt/m/n/10.95 tool[]option[]parser[]new, GtToolArgumentsCheck tool[]argum
ents[]check,

Underfull \hbox (badness 10000) in paragraph at lines 10332--10333


Underfull \hbox (badness 10000) in paragraph at lines 10348--10349


Underfull \hbox (badness 10000) in paragraph at lines 10367--10368

[132]
Underfull \hbox (badness 10000) in paragraph at lines 10384--10385


Underfull \hbox (badness 10000) in paragraph at lines 10394--10395
[]\OT1/cmtt/m/n/10.95 void gt[]toolbox[]add[]tool([]GtToolbox *toolbox, const c
har *toolname, GtTool

Underfull \hbox (badness 10000) in paragraph at lines 10394--10395


Underfull \hbox (badness 10000) in paragraph at lines 10404--10405
[]\OT1/cmtt/m/n/10.95 void gt[]toolbox[]add[]hidden[]tool([]GtToolbox *toolbox,
 const char *toolname,

Underfull \hbox (badness 10000) in paragraph at lines 10404--10405


Underfull \hbox (badness 10000) in paragraph at lines 10414--10415


Underfull \hbox (badness 10000) in paragraph at lines 10424--10425


Underfull \hbox (badness 10000) in paragraph at lines 10434--10435

[133]
Underfull \hbox (badness 10000) in paragraph at lines 10445--10446


Underfull \hbox (badness 2035) in paragraph at lines 10449--10453
[]\OT1/ptm/m/n/10.95 Returns a \OT1/cmtt/m/n/10.95 GtStrArray \OT1/ptm/m/n/10.9
5 of trans-la-tion scheme de-scrip-tions, each of the for-mat

Underfull \hbox (badness 10000) in paragraph at lines 10457--10458


Underfull \hbox (badness 10000) in paragraph at lines 10470--10471


Underfull \hbox (badness 10000) in paragraph at lines 10479--10480


Underfull \hbox (badness 10000) in paragraph at lines 10490--10491
[]\OT1/cmtt/m/n/10.95 int gt[]trans[]table[]translate[]codon([]const GtTransTab
le *tt, char c1, char

Underfull \hbox (badness 10000) in paragraph at lines 10490--10491


Underfull \hbox (badness 10000) in paragraph at lines 10502--10503

[134]
Underfull \hbox (badness 10000) in paragraph at lines 10520--10521
[]\OT1/cmtt/m/n/10.95 GtTranslator* gt[]translator[]new[]with[]table([]GtTransT
able *tt,

Underfull \hbox (badness 10000) in paragraph at lines 10520--10521


Underfull \hbox (badness 10000) in paragraph at lines 10531--10532


Underfull \hbox (badness 10000) in paragraph at lines 10543--10544
[]\OT1/cmtt/m/n/10.95 void gt[]translator[]set[]codon[]iterator([]GtTranslator 
*translator,

Underfull \hbox (badness 10000) in paragraph at lines 10543--10544


Underfull \hbox (badness 10000) in paragraph at lines 10554--10555
[]\OT1/cmtt/m/n/10.95 void gt[]translator[]set[]translation[]table([]GtTranslat
or *translator,

Underfull \hbox (badness 10000) in paragraph at lines 10554--10555


Underfull \hbox (badness 10000) in paragraph at lines 10567--10568
[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]next([]GtTranslator *t
ranslator, char

Underfull \hbox (badness 10000) in paragraph at lines 10567--10568


Underfull \hbox (badness 10000) in paragraph at lines 10584--10585
[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]find[]startcodon([]GtT
ranslator

Underfull \hbox (badness 10000) in paragraph at lines 10584--10585


Underfull \hbox (badness 10000) in paragraph at lines 10602--10603
[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]find[]stopcodon([]GtTr
anslator *translator,

Underfull \hbox (badness 10000) in paragraph at lines 10602--10603


Underfull \hbox (badness 10000) in paragraph at lines 10621--10622
[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]find[]codon([]GtTransl
ator *translator,

Underfull \hbox (badness 10000) in paragraph at lines 10621--10622


Underfull \hbox (badness 10000) in paragraph at lines 10636--10637

[135]
Underfull \hbox (badness 10000) in paragraph at lines 10653--10654


Underfull \hbox (badness 10000) in paragraph at lines 10662--10663


Underfull \hbox (badness 10000) in paragraph at lines 10672--10673
[]\OT1/cmtt/m/n/10.95 bool gt[]type[]checker[]is[]valid([]GtTypeChecker *type[]
checker, const char

Underfull \hbox (badness 10000) in paragraph at lines 10672--10673


Underfull \hbox (badness 10000) in paragraph at lines 10684--10685
[]\OT1/cmtt/m/n/10.95 bool gt[]type[]checker[]is[]partof([]GtTypeChecker *type[
]checker, const char

Underfull \hbox (badness 10000) in paragraph at lines 10684--10685


Underfull \hbox (badness 10000) in paragraph at lines 10695--10696
[]\OT1/cmtt/m/n/10.95 bool gt[]type[]checker[]is[]a([]GtTypeChecker *type[]chec
ker, const char

Underfull \hbox (badness 10000) in paragraph at lines 10695--10696


Underfull \hbox (badness 10000) in paragraph at lines 10704--10705

[136]
Underfull \hbox (badness 10000) in paragraph at lines 10721--10722
[]\OT1/cmtt/m/n/10.95 GtTypeChecker* gt[]type[]checker[]obo[]new([]const char *
obo[]file[]path, GtError

Underfull \hbox (badness 10000) in paragraph at lines 10721--10722


Underfull \hbox (badness 10000) in paragraph at lines 10740--10741


Underfull \hbox (badness 10000) in paragraph at lines 10764--10765
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]visitor[]stream[]new([]GtNodeStream *in
[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 10764--10765

[137]
Underfull \hbox (badness 10000) in paragraph at lines 10783--10784


Underfull \hbox (badness 10000) in paragraph at lines 10793--10794


Underfull \hbox (badness 10000) in paragraph at lines 10803--10804
[]\OT1/cmtt/m/n/10.95 bool gt[]xrf[]checker[]is[]valid([]GtXRFChecker *xrf[]che
cker, const char *value,

Underfull \hbox (badness 10000) in paragraph at lines 10803--10804


Underfull \hbox (badness 10000) in paragraph at lines 10814--10815


Underfull \hbox (badness 10000) in paragraph at lines 10825--10826


Underfull \hbox (badness 10000) in paragraph at lines 10837--10838


Underfull \hbox (badness 10000) in paragraph at lines 10850--10851


Underfull \hbox (badness 10000) in paragraph at lines 10859--10860


Underfull \hbox (badness 10000) in paragraph at lines 10871--10872

[138]
Underfull \hbox (badness 10000) in paragraph at lines 10886--10887
[]\OT1/cmtt/m/n/10.95 void* gt[]bsearch[]data([]const void *key, const void *ba
se, size[]t nmemb,

Underfull \hbox (badness 10000) in paragraph at lines 10886--10887


Underfull \hbox (badness 10000) in paragraph at lines 10897--10898
[]\OT1/cmtt/m/n/10.95 void gt[]bsearch[]all([]GtArray *members, const void *key
, const void *base,

Underfull \hbox (badness 10000) in paragraph at lines 10897--10898


Underfull \hbox (badness 10000) in paragraph at lines 10910--10911
[]\OT1/cmtt/m/n/10.95 void gt[]bsearch[]all[]mark([]GtArray *members, const voi
d *key, const

Underfull \hbox (badness 10000) in paragraph at lines 10910--10911
\OT1/cmtt/m/n/10.95 void *base, size[]t nmemb, size[]t size, GtCompareWithData,
 void *data,

Underfull \hbox (badness 10000) in paragraph at lines 10910--10911


Underfull \hbox (badness 10000) in paragraph at lines 10923--10924


Underfull \hbox (badness 10000) in paragraph at lines 10935--10936


Underfull \hbox (badness 10000) in paragraph at lines 10950--10951
[]\OT1/cmtt/m/n/10.95 void gt[]countingsort([]void *out, const void *in, size[]
t elem[]size, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 10950--10951


Underfull \hbox (badness 10000) in paragraph at lines 10966--10967
[]\OT1/cmtt/m/n/10.95 GtUword gt[]countingsort[]get[]max([]const void *in, size
[]t elem[]size, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 10966--10967

[139]
Underfull \hbox (badness 10000) in paragraph at lines 10977--10978


Underfull \hbox (badness 10000) in paragraph at lines 10987--10988


Underfull \hbox (badness 10000) in paragraph at lines 10999--11000


Underfull \hbox (badness 10000) in paragraph at lines 11010--11011


Underfull \hbox (badness 10000) in paragraph at lines 11019--11020


Underfull \hbox (badness 10000) in paragraph at lines 11029--11030


Underfull \hbox (badness 10000) in paragraph at lines 11039--11040


Underfull \hbox (badness 10000) in paragraph at lines 11050--11051

[140]
Underfull \hbox (badness 10000) in paragraph at lines 11063--11064


Underfull \hbox (badness 10000) in paragraph at lines 11075--11076
[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry([]const char *description, co
nst char *sequence,

Underfull \hbox (badness 10000) in paragraph at lines 11075--11076


Underfull \hbox (badness 10000) in paragraph at lines 11087--11088
[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry[]nt([]const char *description
, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 11087--11088
\OT1/cmtt/m/n/10.95 description[]length, const char *sequence, GtUword sequence
[]length,

Underfull \hbox (badness 10000) in paragraph at lines 11087--11088


Underfull \hbox (badness 3364) in paragraph at lines 11091--11096
[]\OT1/ptm/m/n/10.95 Print a fasta en-try with op-tional \OT1/cmtt/m/n/10.95 de
scription \OT1/ptm/m/n/10.95 and manda-tory \OT1/cmtt/m/n/10.95 sequence \OT1/p
tm/m/n/10.95 to

Underfull \hbox (badness 10000) in paragraph at lines 11102--11103
[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry[]str([]const char *descriptio
n, const char

Underfull \hbox (badness 10000) in paragraph at lines 11102--11103


Underfull \hbox (badness 10000) in paragraph at lines 11117--11118
[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry[]nt[]str([]const char *descri
ption, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 11117--11118
\OT1/cmtt/m/n/10.95 description[]length, const char *sequence, GtUword sequence
[]length,

Underfull \hbox (badness 10000) in paragraph at lines 11117--11118


Underfull \hbox (badness 3364) in paragraph at lines 11121--11126
[]\OT1/ptm/m/n/10.95 Print a fasta en-try with op-tional \OT1/cmtt/m/n/10.95 de
scription \OT1/ptm/m/n/10.95 and manda-tory \OT1/cmtt/m/n/10.95 sequence \OT1/p
tm/m/n/10.95 to

Underfull \hbox (badness 10000) in paragraph at lines 11132--11133


Underfull \hbox (badness 10000) in paragraph at lines 11144--11145


Underfull \hbox (badness 10000) in paragraph at lines 11153--11154


Underfull \hbox (badness 10000) in paragraph at lines 11163--11164


Underfull \hbox (badness 10000) in paragraph at lines 11173--11174


Underfull \hbox (badness 10000) in paragraph at lines 11182--11183


Underfull \hbox (badness 10000) in paragraph at lines 11191--11192


Overfull \hbox (183.05757pt too wide) in paragraph at lines 11195--11197
[]\OT1/ptm/m/n/10.95 Find \OT1/cmtt/m/n/10.95 file \OT1/ptm/m/n/10.95 in $\OML/
ztmcm/m/it/10.95 PATH; ifithasnodirname\OT1/ztmcm/m/n/10.95 ; \OML/ztmcm/m/it/1
0.95 set[]todirnameotherwise:Sets[]totheemptystringif[]couldnotbefoundin$\OT1/p
tm/m/n/10.95 PATH. 

Underfull \hbox (badness 10000) in paragraph at lines 11202--11203
[]\OT1/cmtt/m/n/10.95 int gt[]file[]find[]in[]env([]GtStr *path, const char *fi
le, const char *env,

Underfull \hbox (badness 10000) in paragraph at lines 11202--11203


Underfull \hbox (badness 10000) in paragraph at lines 11206--11210
[]\OT1/ptm/m/n/10.95 Find \OT1/cmtt/m/n/10.95 file \OT1/ptm/m/n/10.95 in the ':
'-separated di-rec-tory list (on Win-

Underfull \hbox (badness 10000) in paragraph at lines 11206--11210
\OT1/ptm/m/n/10.95 dows ';'-separated) spec-i-fied in en-vi-ron-ment vari-able

Overfull \hbox (105.20361pt too wide) in paragraph at lines 11206--11210
[]\OML/ztmcm/m/it/10.95 ; ifithasnodirname\OT1/ztmcm/m/n/10.95 ; \OML/ztmcm/m/i
t/10.95 set[]todirnameotherwise:Sets[]totheemptystringif[]couldnotbefoundin$\OT
1/cmtt/m/n/10.95 env\OT1/ptm/m/n/10.95 . 

Underfull \hbox (badness 10000) in paragraph at lines 11214--11215


Underfull \hbox (badness 10000) in paragraph at lines 11225--11226


Underfull \hbox (badness 5091) in paragraph at lines 11229--11231
[]\OT1/ptm/m/n/10.95 Return the (es-ti-mated) to-tal size of all files given in
 \OT1/cmtt/m/n/10.95 filenames\OT1/ptm/m/n/10.95 . Uses

Underfull \hbox (badness 10000) in paragraph at lines 11236--11237
[]\OT1/cmtt/m/n/10.95 int gt[]files[]guess[]if[]protein[]sequences([]const GtSt
rArray *filenames,

Underfull \hbox (badness 10000) in paragraph at lines 11236--11237


Underfull \hbox (badness 10000) in paragraph at lines 11250--11251


Overfull \hbox (344.88547pt too wide) in paragraph at lines 11254--11257
[]\OT1/ptm/m/n/10.95 Find reg-u-lar ex-e-cutable \OT1/cmtt/m/n/10.95 file \OT1/
ptm/m/n/10.95 in $\OML/ztmcm/m/it/10.95 PATH; ifithasnodirname\OT1/ztmcm/m/n/10
.95 ; \OML/ztmcm/m/it/10.95 set[]todirnameotherwise:Sets[]totheemptystringifreg
ularexecutable[]couldnotbefoundin$\OT1/ptm/m/n/10.95 PATH. 

Underfull \hbox (badness 10000) in paragraph at lines 11261--11262


Underfull \hbox (badness 10000) in paragraph at lines 11270--11271

[141] [142]
Underfull \hbox (badness 10000) in paragraph at lines 11282--11283


Underfull \hbox (badness 10000) in paragraph at lines 11295--11296


Underfull \hbox (badness 10000) in paragraph at lines 11304--11305


Underfull \hbox (badness 10000) in paragraph at lines 11315--11316


Underfull \hbox (badness 10000) in paragraph at lines 11325--11326
[]\OT1/cmtt/m/n/10.95 int gt[]grep[]nt([]bool *match, const char *pattern, cons
t char *line, size[]t

Underfull \hbox (badness 10000) in paragraph at lines 11325--11326


Underfull \hbox (badness 10000) in paragraph at lines 11337--11338


Underfull \hbox (badness 10000) in paragraph at lines 11347--11348


Underfull \hbox (badness 10000) in paragraph at lines 11356--11357

[143]
Underfull \hbox (badness 10000) in paragraph at lines 11369--11370


Underfull \hbox (badness 10000) in paragraph at lines 11378--11379


Underfull \hbox (badness 10000) in paragraph at lines 11387--11388


Underfull \hbox (badness 10000) in paragraph at lines 11398--11399


Underfull \hbox (badness 2065) in paragraph at lines 11402--11406
[]\OT1/ptm/m/n/10.95 Prints the log mes-sage ob-tained from for-mat and fol-low
-ing pa-ram-e-ter ac-cord-

Underfull \hbox (badness 4660) in paragraph at lines 11402--11406
\OT1/ptm/m/n/10.95 ing to if log-ging is en-abled ana-log to\OT1/cmtt/m/n/10.95
 gt[]log[]log()\OT1/ptm/m/n/10.95 . But in con-trast to

Underfull \hbox (badness 10000) in paragraph at lines 11410--11411


Underfull \hbox (badness 10000) in paragraph at lines 11419--11420


Underfull \hbox (badness 10000) in paragraph at lines 11430--11431


Underfull \hbox (badness 10000) in paragraph at lines 11443--11444


Underfull \hbox (badness 10000) in paragraph at lines 11454--11455


Underfull \hbox (badness 10000) in paragraph at lines 11465--11466


Underfull \hbox (badness 10000) in paragraph at lines 11476--11477


Underfull \hbox (badness 10000) in paragraph at lines 11486--11487

[144]
Underfull \hbox (badness 10000) in paragraph at lines 11497--11498


Underfull \hbox (badness 10000) in paragraph at lines 11509--11510
[]\OT1/cmtt/m/n/10.95 void gt[]msort[]r([]void *base, size[]t nmemb, size[]t si
ze, void *comparinfo,

Underfull \hbox (badness 10000) in paragraph at lines 11509--11510


Underfull \hbox (badness 10000) in paragraph at lines 11521--11522


Underfull \hbox (badness 10000) in paragraph at lines 11534--11535


Underfull \hbox (badness 2762) in paragraph at lines 11538--11548
[]\OT1/ptm/m/n/10.95 This mod-ule im-ple-ments the func-tion\OT1/cmtt/m/n/10.95
 gt[]basename() \OT1/ptm/m/n/10.95 ac-cord-ing to the spec-i-fi-

Underfull \hbox (badness 2951) in paragraph at lines 11538--11548
\OT1/ptm/m/n/10.95 ca-tions in http://www.unix-systems.org/onlinepubs/7908799/x
sh/basename.html and
[145]
Underfull \hbox (badness 10000) in paragraph at lines 11554--11555


Underfull \hbox (badness 10000) in paragraph at lines 11564--11565


Underfull \hbox (badness 10000) in paragraph at lines 11574--11575


Underfull \hbox (badness 10000) in paragraph at lines 11584--11585


Underfull \hbox (badness 10000) in paragraph at lines 11594--11595


Underfull \hbox (badness 10000) in paragraph at lines 11605--11606
[]\OT1/cmtt/m/n/10.95 int gt[]parse[]range([]GtRange *rng, const char *start, c
onst char *end,

Underfull \hbox (badness 10000) in paragraph at lines 11605--11606


Underfull \hbox (badness 10000) in paragraph at lines 11619--11620
[]\OT1/cmtt/m/n/10.95 int gt[]parse[]range[]tidy([]GtRange *rng, const char *st
art, const char *end,

Underfull \hbox (badness 10000) in paragraph at lines 11619--11620

[146]
Underfull \hbox (badness 10000) in paragraph at lines 11633--11634
[]\OT1/cmtt/m/n/10.95 void gt[]qsort[]r([]void *a, size[]t n, size[]t es, void 
*data,

Underfull \hbox (badness 10000) in paragraph at lines 11633--11634


Underfull \hbox (badness 10000) in paragraph at lines 11637--11639
[]\OT1/ptm/m/n/10.95 Like \OT1/cmtt/m/n/10.95 qsort(3)\OT1/ptm/m/n/10.95 , but 
al-lows an ad-di-tional \OT1/cmtt/m/n/10.95 data \OT1/ptm/m/n/10.95 pointer pas
sed to the

Underfull \hbox (badness 10000) in paragraph at lines 11645--11646


Underfull \hbox (badness 10000) in paragraph at lines 11656--11657


Underfull \hbox (badness 10000) in paragraph at lines 11669--11670


Underfull \hbox (badness 10000) in paragraph at lines 11686--11687


Underfull \hbox (badness 10000) in paragraph at lines 11697--11698


Underfull \hbox (badness 10000) in paragraph at lines 11706--11707


Underfull \hbox (badness 10000) in paragraph at lines 11715--11716


Underfull \hbox (badness 10000) in paragraph at lines 11724--11725


Underfull \hbox (badness 10000) in paragraph at lines 11733--11734


Underfull \hbox (badness 10000) in paragraph at lines 11742--11743


Underfull \hbox (badness 10000) in paragraph at lines 11751--11752


Underfull \hbox (badness 10000) in paragraph at lines 11760--11761


Underfull \hbox (badness 10000) in paragraph at lines 11769--11770


Underfull \hbox (badness 10000) in paragraph at lines 11778--11779


Underfull \hbox (badness 10000) in paragraph at lines 11787--11788

[147]
Underfull \hbox (badness 10000) in paragraph at lines 11798--11799


Underfull \hbox (badness 10000) in paragraph at lines 11812--11813
[]\OT1/cmtt/m/n/10.95 const char* gt[]version[]check([]unsigned int required[]m
ajor, unsigned int

Underfull \hbox (badness 10000) in paragraph at lines 11812--11813


Underfull \hbox (badness 10000) in paragraph at lines 11826--11827

[148]
Underfull \hbox (badness 10000) in paragraph at lines 11837--11838


Underfull \hbox (badness 10000) in paragraph at lines 11846--11847


Underfull \hbox (badness 10000) in paragraph at lines 11855--11856


Underfull \hbox (badness 10000) in paragraph at lines 11865--11866


Underfull \hbox (badness 10000) in paragraph at lines 11875--11876
[]\OT1/cmtt/m/n/10.95 void gt[]warning[]default[]handler([]void *data, const ch
ar *format, va[]list

Underfull \hbox (badness 10000) in paragraph at lines 11875--11876


Underfull \hbox (badness 10000) in paragraph at lines 11886--11887


Underfull \hbox (badness 10000) in paragraph at lines 11895--11896


Underfull \hbox (badness 10000) in paragraph at lines 11907--11908


Underfull \hbox (badness 10000) in paragraph at lines 11916--11917


Underfull \hbox (badness 10000) in paragraph at lines 11925--11926


Underfull \hbox (badness 10000) in paragraph at lines 11934--11935


Underfull \hbox (badness 10000) in paragraph at lines 11943--11944


Underfull \hbox (badness 10000) in paragraph at lines 11952--11953


Underfull \hbox (badness 10000) in paragraph at lines 11961--11962


Underfull \hbox (badness 10000) in paragraph at lines 11970--11971


Underfull \hbox (badness 10000) in paragraph at lines 11979--11980


Underfull \hbox (badness 10000) in paragraph at lines 11988--11989


Underfull \hbox (badness 10000) in paragraph at lines 11997--11998


Underfull \hbox (badness 10000) in paragraph at lines 12007--12008


Underfull \hbox (badness 10000) in paragraph at lines 12016--12017


Underfull \hbox (badness 10000) in paragraph at lines 12025--12026


Underfull \hbox (badness 10000) in paragraph at lines 12034--12035


Underfull \hbox (badness 10000) in paragraph at lines 12044--12045


Underfull \hbox (badness 10000) in paragraph at lines 12053--12054


Underfull \hbox (badness 10000) in paragraph at lines 12062--12063


Underfull \hbox (badness 10000) in paragraph at lines 12071--12072


Underfull \hbox (badness 10000) in paragraph at lines 12080--12081


Underfull \hbox (badness 10000) in paragraph at lines 12089--12090

[149] [150]) [151] (./annotationsketch.aux)

LaTeX Font Warning: Some font shapes were not available, defaults substituted.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information) </tmp/texfonts/pk/ljfour/p
ublic/cm/cmttb10.864pk> </tmp/texfonts/pk/ljfour/public/cm/cmttb10.480pk>{/usr/
share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmssbx10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmtt8.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/ut
mb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on annotationsketch.pdf (151 pages, 1171106 bytes).
Transcript written on annotationsketch.log.
pdflatex annotationsketch.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./annotationsketch.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrreprt.cls
Document Class: scrreprt 2015/10/03 v3.19a KOMA-Script document class (report)
(/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrkbase.sty
(/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrbase.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrlfile.sty
Package scrlfile, 2015/10/03 v3.19a KOMA-Script package (loading files)
                  Copyright (C) Markus Kohm

))) (/usr/share/texlive/texmf-dist/tex/latex/koma-script/tocbasic.sty)
(/usr/share/texlive/texmf-dist/tex/latex/koma-script/scrsize11pt.clo)
(/usr/share/texlive/texmf-dist/tex/latex/koma-script/typearea.sty
Package typearea, 2015/10/03 v3.19a KOMA-Script package (type area)
                  Copyright (C) Frank Neukam, 1992-1994
                  Copyright (C) Markus Kohm, 1994-

)) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg)))
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))

Package hyperref Message: Driver (autodetected): hpdftex.

(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/mathptmx.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/bold-extra/bold-extra.sty)
(/usr/share/texlive/texmf-dist/tex/latex/caption/caption.sty
(/usr/share/texlive/texmf-dist/tex/latex/caption/caption3.sty))
(./annotationsketch.aux)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))
(./annotationsketch.out) (./annotationsketch.out)

LaTeX Font Warning: Font shape `OT1/cmss/bx/it' undefined
(Font)              using `OT1/cmss/bx/n' instead on input line 56.

(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omlztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsztmcm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omxztmcm.fd) [1{/var/lib/texmf/
fonts/map/pdftex/updmap/pdftex.map}] (./annotationsketch.toc [2] [3] [4]
[5]) [6]
chapter 1.

Class scrreprt Warning: \float@addtolists detected!
(scrreprt)              Implementation of \float@addtolist became
(scrreprt)              deprecated in KOMA-Script v3.01 2008/11/14 and
(scrreprt)              has been replaced by several more flexible
(scrreprt)              features of package `tocbasic`.
(scrreprt)              Since Version 3.12 support for deprecated
(scrreprt)              \float@addtolist interface has been
(scrreprt)              restricted to only some of the KOMA-Script
(scrreprt)              features and been removed from others.
(scrreprt)              Loading of package `scrhack' may help to
(scrreprt)              avoid this warning, if you are using a
(scrreprt)              a package that still implements the
(scrreprt)              deprecated \float@addtolist interface .


<../../www/genometools.org/htdocs/images/dataflow.pdf, id=901, 680.33936pt x 86
1.9156pt> <use ../../www/genometools.org/htdocs/images/dataflow.pdf>
<../../www/genometools.org/htdocs/images/gfftree.pdf, id=903, 510.53029pt x 138
.67685pt> <use ../../www/genometools.org/htdocs/images/gfftree.pdf> [7]
<../../www/genometools.org/htdocs/images/diagram.pdf, id=912, 1363.36378pt x 59
3.45078pt> <use ../../www/genometools.org/htdocs/images/diagram.pdf> [8 <../../
www/genometools.org/htdocs/images/dataflow.pdf>] [9 <../../www/genometools.org/
htdocs/images/gfftree.pdf> <../../www/genometools.org/htdocs/images/diagram.pdf


pdfTeX warning: /usr/bin/pdflatex (file ../../www/genometools.org/htdocs/images
/diagram.pdf): PDF inclusion: multiple pdfs with page group included in a singl
e page
>]
<../../www/genometools.org/htdocs/images/collapse_types.pdf, id=944, 215.72322p
t x 285.93611pt>
<use ../../www/genometools.org/htdocs/images/collapse_types.pdf>
<../../www/genometools.org/htdocs/images/cnn_large.jpg, id=945, 1589.94pt x 654
.7662pt> <use ../../www/genometools.org/htdocs/images/cnn_large.jpg> [10 <../..
/www/genometools.org/htdocs/images/collapse_types.pdf>] [11 <../../www/genometo
ols.org/htdocs/images/cnn_large.jpg>]
<../../www/genometools.org/htdocs/images/callbacks.jpg, id=1020, 602.25pt x 379
.4175pt> <use ../../www/genometools.org/htdocs/images/callbacks.jpg> [12 <../..
/www/genometools.org/htdocs/images/callbacks.jpg>]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)
<../../www/genometools.org/htdocs/images/example_nocollapse_noselect.jpg, id=10
33, 602.25pt x 242.9075pt>
<use ../../www/genometools.org/htdocs/images/example_nocollapse_noselect.jpg>
[13] (/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
<../../www/genometools.org/htdocs/images/example_strandselect.jpg, id=1043, 602
.25pt x 319.1925pt>
<use ../../www/genometools.org/htdocs/images/example_strandselect.jpg> [14 <../
../www/genometools.org/htdocs/images/example_nocollapse_noselect.jpg>]
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang2.sty)
<../../www/genometools.org/htdocs/images/example_filterselect.jpg, id=1059, 602
.25pt x 319.1925pt>
<use ../../www/genometools.org/htdocs/images/example_filterselect.jpg> [15 <../
../www/genometools.org/htdocs/images/example_strandselect.jpg>]
<../../www/genometools.org/htdocs/images/example_ct.jpg, id=1086, 602.25pt x 55
4.07pt> <use ../../www/genometools.org/htdocs/images/example_ct.jpg> [16 <../..
/www/genometools.org/htdocs/images/example_filterselect.jpg>] [17 <../../www/ge
nometools.org/htdocs/images/example_ct.jpg>]
Overfull \hbox (4.75348pt too wide) in paragraph at lines 388--389
[][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] 

Overfull \hbox (4.75348pt too wide) in paragraph at lines 390--391
[][][][][][][][][][][][][][][][][][][][][][][][][][] 

Overfull \hbox (4.75348pt too wide) in paragraph at lines 391--392
[][][][][][][][][][][][][][] 

Overfull \hbox (4.75348pt too wide) in paragraph at lines 393--394
[][][][][][][][][][][][][][][][][][] 

Overfull \hbox (4.75348pt too wide) in paragraph at lines 394--395
[][][][][][][][][][][][][][][][][][][][][][] 

Overfull \hbox (4.75348pt too wide) in paragraph at lines 396--397
[][][][][][][][][][][][][][][][][][][][][][][][][][] 

Overfull \hbox (4.75348pt too wide) in paragraph at lines 397--398
[][][][][][][][][][][][][][][][][][][][][][] 

<../../www/genometools.org/htdocs/images/example_ct2.jpg, id=1098, 602.25pt x 2
98.11375pt> <use ../../www/genometools.org/htdocs/images/example_ct2.jpg>
[18]
<../../www/genometools.org/htdocs/images/parsed.jpg, id=1143, 602.25pt x 404.51
125pt> <use ../../www/genometools.org/htdocs/images/parsed.jpg>
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(../../src/examples/sketch_parsed.c [19 <../../www/genometools.org/htdocs/image
s/example_ct2.jpg>] [20 <../../www/genometools.org/htdocs/images/parsed.jpg>])
Overfull \hbox (37.5989pt too wide) in paragraph at lines 441--442
\OT1/ptm/m/n/10.95 the com-mand line \OT1/cmtt/m/n/10.95 gt gtscripts/sketch[]p
arsed.lua <style[]file> <PNG[]file> <GFF3[]file>\OT1/ptm/m/n/10.95 ) 
(../../gtscripts/sketch_parsed.lua [21]) (../../gtruby/sketch_parsed.rb
[22]) (../../gtpython/sketch_parsed.py [23])
<../../www/genometools.org/htdocs/images/constructed.jpg, id=1387, 602.25pt x 1
49.55875pt> <use ../../www/genometools.org/htdocs/images/constructed.jpg>
(../../src/examples/sketch_constructed.c [24 <../../www/genometools.org/htdocs/
images/constructed.jpg>] [25])
Overfull \hbox (28.675pt too wide) in paragraph at lines 464--465
\OT1/ptm/m/n/10.95 run by the com-mand line \OT1/cmtt/m/n/10.95 gt gtscripts/sk
etch[]constructed.lua <style[]file> <PNG[]file>\OT1/ptm/m/n/10.95 ) 
(../../gtscripts/sketch_constructed.lua [26])
(../../gtruby/sketch_constructed.rb [27]) (../../gtpython/sketch_constructed.py
[28]) (./api_reference.tex [29]
chapter 2.
[30] [31] [32] [33] [34]
Underfull \hbox (badness 10000) in paragraph at lines 321--322
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]gfflike[]get[]all[]features([]GtF
eatureIndex *gfi, GtArray

Underfull \hbox (badness 10000) in paragraph at lines 321--322


Underfull \hbox (badness 10000) in paragraph at lines 333--334
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]dup[]feature[]stream[]new([]GtNodeStrea
m*, const char

Underfull \hbox (badness 10000) in paragraph at lines 333--334


Underfull \hbox (badness 10000) in paragraph at lines 343--344


Underfull \hbox (badness 10000) in paragraph at lines 354--355

[35]
Underfull \hbox (badness 10000) in paragraph at lines 376--377


Underfull \hbox (badness 10000) in paragraph at lines 394--395


Underfull \hbox (badness 10000) in paragraph at lines 403--404


Underfull \hbox (badness 10000) in paragraph at lines 412--413


Underfull \hbox (badness 10000) in paragraph at lines 421--422


Underfull \hbox (badness 10000) in paragraph at lines 432--433
[]\OT1/cmtt/m/n/10.95 GtAlphabet* gt[]alphabet[]new[]from[]file[]no[]suffix([]c
onst char *filename,

Underfull \hbox (badness 10000) in paragraph at lines 432--433


Underfull \hbox (badness 10000) in paragraph at lines 443--444
[]\OT1/cmtt/m/n/10.95 GtAlphabet* gt[]alphabet[]new[]from[]string([]const char 
*alphadef, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 443--444


Underfull \hbox (badness 10000) in paragraph at lines 454--455
[]\OT1/cmtt/m/n/10.95 GtAlphabet* gt[]alphabet[]new[]from[]sequence([]const GtS
trArray *filenametab,

Underfull \hbox (badness 10000) in paragraph at lines 454--455


Underfull \hbox (badness 10000) in paragraph at lines 466--467


Underfull \hbox (badness 10000) in paragraph at lines 476--477


Underfull \hbox (badness 10000) in paragraph at lines 485--486


Underfull \hbox (badness 10000) in paragraph at lines 495--496


Underfull \hbox (badness 10000) in paragraph at lines 505--506
[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]add[]mapping([]GtAlphabet *alphabet, c
onst char

Underfull \hbox (badness 10000) in paragraph at lines 505--506


Underfull \hbox (badness 10000) in paragraph at lines 515--516


Underfull \hbox (badness 10000) in paragraph at lines 524--525


Underfull \hbox (badness 10000) in paragraph at lines 534--535


Underfull \hbox (badness 10000) in paragraph at lines 543--544


Underfull \hbox (badness 10000) in paragraph at lines 552--553


Underfull \hbox (badness 10000) in paragraph at lines 561--562


Underfull \hbox (badness 10000) in paragraph at lines 570--571


Underfull \hbox (badness 10000) in paragraph at lines 580--581


Underfull \hbox (badness 10000) in paragraph at lines 591--592
[]\OT1/cmtt/m/n/10.95 int gt[]alphabet[]to[]file([]const GtAlphabet *alphabet, 
const char

Underfull \hbox (badness 10000) in paragraph at lines 591--592


Underfull \hbox (badness 10000) in paragraph at lines 601--602


Underfull \hbox (badness 10000) in paragraph at lines 612--613
[]\OT1/cmtt/m/n/10.95 GtUchar gt[]alphabet[]pretty[]symbol([]const GtAlphabet *
alphabet, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 612--613


Underfull \hbox (badness 10000) in paragraph at lines 623--624
[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]echo[]pretty[]symbol([]const GtAlphabe
t *alphabet, FILE

Underfull \hbox (badness 10000) in paragraph at lines 623--624


Underfull \hbox (badness 10000) in paragraph at lines 633--634


Underfull \hbox (badness 10000) in paragraph at lines 645--646


Underfull \hbox (badness 10000) in paragraph at lines 656--657


Underfull \hbox (badness 10000) in paragraph at lines 665--666


Underfull \hbox (badness 10000) in paragraph at lines 675--676


Underfull \hbox (badness 10000) in paragraph at lines 685--686
[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]encode[]seq([]const GtAlphabet *alphab
et, GtUchar *out,

Underfull \hbox (badness 10000) in paragraph at lines 685--686


Underfull \hbox (badness 10000) in paragraph at lines 698--699
[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]decode[]seq[]to[]fp([]const GtAlphabet
 *alphabet, FILE *fpout,

Underfull \hbox (badness 10000) in paragraph at lines 698--699


Underfull \hbox (badness 10000) in paragraph at lines 713--714
[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]decode[]seq[]to[]cstr([]const GtAlphab
et *alphabet, char

Underfull \hbox (badness 10000) in paragraph at lines 713--714


Underfull \hbox (badness 10000) in paragraph at lines 728--729
[]\OT1/cmtt/m/n/10.95 GtStr* gt[]alphabet[]decode[]seq[]to[]str([]const GtAlpha
bet *alphabet, const

Underfull \hbox (badness 10000) in paragraph at lines 728--729


Underfull \hbox (badness 10000) in paragraph at lines 738--739

[36] [37] [38]
Underfull \hbox (badness 10000) in paragraph at lines 757--758


Underfull \hbox (badness 10000) in paragraph at lines 775--776
[]\OT1/cmtt/m/n/10.95 GtFeatureIndex* gt[]anno[]db[]schema[]get[]feature[]index
([]GtAnnoDBSchema

Underfull \hbox (badness 10000) in paragraph at lines 775--776


Underfull \hbox (badness 10000) in paragraph at lines 786--787

[39]
Underfull \hbox (badness 10000) in paragraph at lines 803--804


Underfull \hbox (badness 10000) in paragraph at lines 812--813


Underfull \hbox (badness 10000) in paragraph at lines 822--823


Underfull \hbox (badness 10000) in paragraph at lines 831--832


Underfull \hbox (badness 10000) in paragraph at lines 841--842


Underfull \hbox (badness 10000) in paragraph at lines 850--851


Underfull \hbox (badness 10000) in paragraph at lines 859--860


Underfull \hbox (badness 10000) in paragraph at lines 868--869


Underfull \hbox (badness 10000) in paragraph at lines 878--879


Underfull \hbox (badness 10000) in paragraph at lines 889--890


Underfull \hbox (badness 10000) in paragraph at lines 901--902


Underfull \hbox (badness 10000) in paragraph at lines 911--912


Underfull \hbox (badness 10000) in paragraph at lines 922--923


Underfull \hbox (badness 10000) in paragraph at lines 934--935


Underfull \hbox (badness 10000) in paragraph at lines 943--944


Underfull \hbox (badness 5563) in paragraph at lines 947--949
[]\OT1/ptm/m/n/10.95 Set the size of \OT1/cmtt/m/n/10.95 array \OT1/ptm/m/n/10.
95 to \OT1/cmtt/m/n/10.95 size\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 size \OT
1/ptm/m/n/10.95 must be smaller or equal than

Underfull \hbox (badness 10000) in paragraph at lines 953--954


Underfull \hbox (badness 10000) in paragraph at lines 962--963


Underfull \hbox (badness 10000) in paragraph at lines 971--972


Underfull \hbox (badness 10000) in paragraph at lines 981--982


Underfull \hbox (badness 10000) in paragraph at lines 990--991


Underfull \hbox (badness 10000) in paragraph at lines 1000--1001
[]\OT1/cmtt/m/n/10.95 void gt[]array[]sort[]with[]data([]GtArray *array, GtComp
areWithData compar,

Underfull \hbox (badness 10000) in paragraph at lines 1000--1001


Underfull \hbox (badness 10000) in paragraph at lines 1011--1012
[]\OT1/cmtt/m/n/10.95 void gt[]array[]sort[]stable[]with[]data([]GtArray *array
, GtCompareWithData

Underfull \hbox (badness 10000) in paragraph at lines 1011--1012


Underfull \hbox (badness 10000) in paragraph at lines 1021--1022


Underfull \hbox (badness 10000) in paragraph at lines 1032--1033

[40] [41]
Overfull \hbox (7.61789pt too wide) in paragraph at lines 1043--1046
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. \OT1/cmtt/m/n/10.95 GtArrayOutStream \OT1/ptm/m/n/10.95 tak
es an ar-ray of \OT1/cmtt/m/n/10.95 GtGenomeNodes

Underfull \hbox (badness 10000) in paragraph at lines 1052--1053
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]in[]stream[]new([]GtArray *nodes
, GtUword *progress,

Underfull \hbox (badness 10000) in paragraph at lines 1052--1053


Underfull \hbox (badness 10000) in paragraph at lines 1074--1075
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]out[]stream[]new([]GtNodeStream 
*in[]stream, GtArray

Underfull \hbox (badness 10000) in paragraph at lines 1074--1075


Underfull \hbox (badness 10000) in paragraph at lines 1086--1087
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]out[]stream[]all[]new([]GtNodeSt
ream *in[]stream, GtArray

Underfull \hbox (badness 10000) in paragraph at lines 1086--1087

[42]
Underfull \hbox (badness 10000) in paragraph at lines 1103--1104


Underfull \hbox (badness 10000) in paragraph at lines 1115--1116
[]\OT1/cmtt/m/n/10.95 void gt[]bed[]in[]stream[]set[]feature[]type([]GtBEDInStr
eam *bed[]in[]stream, const

Underfull \hbox (badness 10000) in paragraph at lines 1115--1116


Underfull \hbox (badness 10000) in paragraph at lines 1127--1128
[]\OT1/cmtt/m/n/10.95 void gt[]bed[]in[]stream[]set[]thick[]feature[]type([]GtB
EDInStream *bed[]in[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 1127--1128


Underfull \hbox (badness 10000) in paragraph at lines 1138--1139
[]\OT1/cmtt/m/n/10.95 void gt[]bed[]in[]stream[]set[]block[]type([]GtBEDInStrea
m *bed[]in[]stream, const

Underfull \hbox (badness 10000) in paragraph at lines 1138--1139


Underfull \hbox (badness 10000) in paragraph at lines 1155--1156


Underfull \hbox (badness 10000) in paragraph at lines 1165--1166


Underfull \hbox (badness 10000) in paragraph at lines 1174--1175


Underfull \hbox (badness 10000) in paragraph at lines 1183--1184


Underfull \hbox (badness 10000) in paragraph at lines 1192--1193


Underfull \hbox (badness 10000) in paragraph at lines 1202--1203
[]\OT1/cmtt/m/n/10.95 void gt[]bittab[]and([]GtBittab *bittab[]a, const GtBitta
b *bittab[]b, const

Underfull \hbox (badness 10000) in paragraph at lines 1202--1203


Underfull \hbox (badness 10000) in paragraph at lines 1212--1213
[]\OT1/cmtt/m/n/10.95 void gt[]bittab[]or([]GtBittab *bittab[]a, const GtBittab
 *bittab[]b, const

Underfull \hbox (badness 10000) in paragraph at lines 1212--1213


Underfull \hbox (badness 10000) in paragraph at lines 1222--1223
[]\OT1/cmtt/m/n/10.95 void gt[]bittab[]nand([]GtBittab *bittab[]a, const GtBitt
ab *bittab[]b, const

Underfull \hbox (badness 10000) in paragraph at lines 1222--1223


Underfull \hbox (badness 10000) in paragraph at lines 1231--1232


Underfull \hbox (badness 10000) in paragraph at lines 1240--1241


Underfull \hbox (badness 10000) in paragraph at lines 1249--1250


Underfull \hbox (badness 10000) in paragraph at lines 1258--1259


Underfull \hbox (badness 10000) in paragraph at lines 1267--1268


Underfull \hbox (badness 10000) in paragraph at lines 1276--1277


Underfull \hbox (badness 10000) in paragraph at lines 1285--1286


Underfull \hbox (badness 10000) in paragraph at lines 1294--1295


Underfull \hbox (badness 10000) in paragraph at lines 1303--1304


Underfull \hbox (badness 10000) in paragraph at lines 1312--1313


Underfull \hbox (badness 10000) in paragraph at lines 1321--1322


Underfull \hbox (badness 10000) in paragraph at lines 1330--1331


Underfull \hbox (badness 10000) in paragraph at lines 1340--1341


Underfull \hbox (badness 10000) in paragraph at lines 1349--1350


Underfull \hbox (badness 10000) in paragraph at lines 1358--1359

[43] [44]
Underfull \hbox (badness 10000) in paragraph at lines 1377--1378


Underfull \hbox (badness 10000) in paragraph at lines 1386--1387


Underfull \hbox (badness 10000) in paragraph at lines 1395--1396


Underfull \hbox (badness 10000) in paragraph at lines 1405--1406


Underfull \hbox (badness 10000) in paragraph at lines 1414--1415


Underfull \hbox (badness 10000) in paragraph at lines 1423--1424


Underfull \hbox (badness 10000) in paragraph at lines 1432--1433


Underfull \hbox (badness 10000) in paragraph at lines 1441--1442


Underfull \hbox (badness 10000) in paragraph at lines 1450--1451


Underfull \hbox (badness 10000) in paragraph at lines 1459--1460


Underfull \hbox (badness 10000) in paragraph at lines 1468--1469


Underfull \hbox (badness 10000) in paragraph at lines 1477--1478


Underfull \hbox (badness 10000) in paragraph at lines 1486--1487


Underfull \hbox (badness 10000) in paragraph at lines 1495--1496


Underfull \hbox (badness 10000) in paragraph at lines 1504--1505


Underfull \hbox (badness 10000) in paragraph at lines 1513--1514


Underfull \hbox (badness 10000) in paragraph at lines 1522--1523


Underfull \hbox (badness 10000) in paragraph at lines 1531--1532

[45]
Underfull \hbox (badness 10000) in paragraph at lines 1553--1554
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]cds[]stream[]new([]GtNodeStream *in[]st
ream, GtRegionMapping

Underfull \hbox (badness 10000) in paragraph at lines 1553--1554
\OT1/cmtt/m/n/10.95 *region[]mapping, unsigned int minorflen, const char *sourc
e, bool

Underfull \hbox (badness 10000) in paragraph at lines 1553--1554

[46]
Underfull \hbox (badness 10000) in paragraph at lines 1581--1582
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]csa[]stream[]new([]GtNodeStream *in[]st
ream, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 1581--1582


Underfull \hbox (badness 10000) in paragraph at lines 1601--1602


Underfull \hbox (badness 10000) in paragraph at lines 1610--1611


Underfull \hbox (badness 10000) in paragraph at lines 1633--1634
[]\OT1/cmtt/m/n/10.95 GtCanvas* gt[]canvas[]cairo[]context[]new([]GtStyle *styl
e, cairo[]t *context,

Underfull \hbox (badness 10000) in paragraph at lines 1633--1634
\OT1/cmtt/m/n/10.95 double offsetpos, GtUword width, GtUword height, GtImageInf
o *image[]info,

Underfull \hbox (badness 10000) in paragraph at lines 1633--1634

[47]
Underfull \hbox (badness 10000) in paragraph at lines 1658--1659
[]\OT1/cmtt/m/n/10.95 GtCanvas* gt[]canvas[]cairo[]file[]new([]GtStyle *style, 
GtGraphicsOutType

Underfull \hbox (badness 10000) in paragraph at lines 1658--1659
\OT1/cmtt/m/n/10.95 output[]type, GtUword width, GtUword height, GtImageInfo *i
mage[]info,

Underfull \hbox (badness 10000) in paragraph at lines 1658--1659


Underfull \hbox (badness 10000) in paragraph at lines 1673--1674
[]\OT1/cmtt/m/n/10.95 int gt[]canvas[]cairo[]file[]to[]file([]GtCanvasCairoFile
 *canvas, const char

Underfull \hbox (badness 10000) in paragraph at lines 1673--1674


Underfull \hbox (badness 10000) in paragraph at lines 1684--1685
[]\OT1/cmtt/m/n/10.95 int gt[]canvas[]cairo[]file[]to[]stream([]GtCanvasCairoFi
le *canvas, GtStr

Underfull \hbox (badness 10000) in paragraph at lines 1684--1685


Underfull \hbox (badness 10000) in paragraph at lines 1700--1701


Underfull \hbox (badness 10000) in paragraph at lines 1717--1718
[]\OT1/cmtt/m/n/10.95 GtUword gt[]codon[]iterator[]current[]position([]GtCodonI
terator

Underfull \hbox (badness 10000) in paragraph at lines 1717--1718


Underfull \hbox (badness 10000) in paragraph at lines 1728--1729


Underfull \hbox (badness 10000) in paragraph at lines 1738--1739


Underfull \hbox (badness 10000) in paragraph at lines 1751--1752
[]\OT1/cmtt/m/n/10.95 GtCodonIteratorStatus gt[]codon[]iterator[]next([]GtCodon
Iterator

Underfull \hbox (badness 10000) in paragraph at lines 1751--1752
\OT1/cmtt/m/n/10.95 *codon[]iterator, char *n1, char *n2, char *n3, unsigned in
t *frame,

Underfull \hbox (badness 10000) in paragraph at lines 1751--1752


Underfull \hbox (badness 10000) in paragraph at lines 1770--1771

[48]
Underfull \hbox (badness 10000) in paragraph at lines 1784--1785
[]\OT1/cmtt/m/n/10.95 GtCodonIterator* gt[]codon[]iterator[]encseq[]new([]GtEnc
seq *encseq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 1784--1785


Underfull \hbox (badness 10000) in paragraph at lines 1799--1800
[]\OT1/cmtt/m/n/10.95 GtCodonIterator* gt[]codon[]iterator[]encseq[]new[]with[]
readmode([]GtEncseq

Underfull \hbox (badness 10000) in paragraph at lines 1799--1800
\OT1/cmtt/m/n/10.95 *encseq, GtUword startpos, GtUword length, GtReadmode readm
ode, GtError

Underfull \hbox (badness 10000) in paragraph at lines 1799--1800


Underfull \hbox (badness 10000) in paragraph at lines 1815--1816
[]\OT1/cmtt/m/n/10.95 GtCodonIterator* gt[]codon[]iterator[]simple[]new([]const
 char *seq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 1815--1816

[49]
Underfull \hbox (badness 10000) in paragraph at lines 1832--1833
[]\OT1/cmtt/m/n/10.95 GtColor* gt[]color[]new([]double red, double green, doubl
e blue, double

Underfull \hbox (badness 10000) in paragraph at lines 1832--1833


Underfull \hbox (badness 10000) in paragraph at lines 1844--1845
[]\OT1/cmtt/m/n/10.95 void gt[]color[]set([]GtColor *color, double red, double 
green, double blue,

Underfull \hbox (badness 10000) in paragraph at lines 1844--1845


Underfull \hbox (badness 10000) in paragraph at lines 1855--1856


Underfull \hbox (badness 10000) in paragraph at lines 1864--1865


Underfull \hbox (badness 10000) in paragraph at lines 1881--1882


Underfull \hbox (badness 10000) in paragraph at lines 1893--1894


Underfull \hbox (badness 10000) in paragraph at lines 1902--1903


Underfull \hbox (badness 10000) in paragraph at lines 1914--1915

[50]
Underfull \hbox (badness 10000) in paragraph at lines 1931--1932


Underfull \hbox (badness 10000) in paragraph at lines 1940--1941


Underfull \hbox (badness 10000) in paragraph at lines 1949--1950


Underfull \hbox (badness 10000) in paragraph at lines 1959--1960


Underfull \hbox (badness 10000) in paragraph at lines 1969--1970


Underfull \hbox (badness 10000) in paragraph at lines 1978--1979


Underfull \hbox (badness 10000) in paragraph at lines 1987--1988


Underfull \hbox (badness 10000) in paragraph at lines 2006--2007


Underfull \hbox (badness 10000) in paragraph at lines 2015--2016

[51]
Underfull \hbox (badness 10000) in paragraph at lines 2038--2039
[]\OT1/cmtt/m/n/10.95 GtCustomTrack* gt[]custom[]track[]gc[]content[]new([]cons
t char *seq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 2038--2039


Underfull \hbox (badness 10000) in paragraph at lines 2068--2069
[]\OT1/cmtt/m/n/10.95 GtCustomTrack* gt[]custom[]track[]script[]wrapper[]new([]
GtCtScriptRenderFunc

Underfull \hbox (badness 10000) in paragraph at lines 2068--2069
\OT1/cmtt/m/n/10.95 render[]func, GtCtScriptGetHeightFunc get[]height[]func,

Underfull \hbox (badness 10000) in paragraph at lines 2068--2069


Underfull \hbox (badness 10000) in paragraph at lines 2090--2091
[]\OT1/cmtt/m/n/10.95 GtDiagram* gt[]diagram[]new([]GtFeatureIndex *feature[]in
dex, const char

Underfull \hbox (badness 10000) in paragraph at lines 2090--2091


Underfull \hbox (badness 10000) in paragraph at lines 2103--2104
[]\OT1/cmtt/m/n/10.95 GtDiagram* gt[]diagram[]new[]from[]array([]GtArray *featu
res, const GtRange

Underfull \hbox (badness 10000) in paragraph at lines 2103--2104


Underfull \hbox (badness 10000) in paragraph at lines 2115--2116


Underfull \hbox (badness 10000) in paragraph at lines 2125--2126
[]\OT1/cmtt/m/n/10.95 void gt[]diagram[]set[]track[]selector[]func([]GtDiagram*
, GtTrackSelectorFunc,

Underfull \hbox (badness 10000) in paragraph at lines 2125--2126


Underfull \hbox (badness 10000) in paragraph at lines 2136--2137


Underfull \hbox (badness 10000) in paragraph at lines 2146--2147


Underfull \hbox (badness 10000) in paragraph at lines 2155--2156

[52]
Underfull \hbox (badness 10000) in paragraph at lines 2174--2175


Underfull \hbox (badness 10000) in paragraph at lines 2184--2185


Underfull \hbox (badness 10000) in paragraph at lines 2193--2194


Underfull \hbox (badness 10000) in paragraph at lines 2203--2204
[]\OT1/cmtt/m/n/10.95 void gt[]disc[]distri[]add[]multi([]GtDiscDistri *d, GtUw
ord key, GtUint64

Underfull \hbox (badness 10000) in paragraph at lines 2203--2204


Underfull \hbox (badness 10000) in paragraph at lines 2212--2213


Underfull \hbox (badness 10000) in paragraph at lines 2221--2222


Underfull \hbox (badness 10000) in paragraph at lines 2233--2234
[]\OT1/cmtt/m/n/10.95 void gt[]disc[]distri[]foreach([]const GtDiscDistri *d, G
tDiscDistriIterFunc

Underfull \hbox (badness 10000) in paragraph at lines 2233--2234


Underfull \hbox (badness 10000) in paragraph at lines 2246--2247
[]\OT1/cmtt/m/n/10.95 void gt[]disc[]distri[]foreach[]in[]reverse[]order([]cons
t GtDiscDistri *d,

Underfull \hbox (badness 10000) in paragraph at lines 2246--2247

[53]
Underfull \hbox (badness 10000) in paragraph at lines 2263--2264


Underfull \hbox (badness 10000) in paragraph at lines 2273--2274


Underfull \hbox (badness 10000) in paragraph at lines 2284--2285


Underfull \hbox (badness 10000) in paragraph at lines 2293--2294


Underfull \hbox (badness 10000) in paragraph at lines 2302--2303


Underfull \hbox (badness 10000) in paragraph at lines 2312--2313


Underfull \hbox (badness 10000) in paragraph at lines 2321--2322


Underfull \hbox (badness 10000) in paragraph at lines 2331--2332


Underfull \hbox (badness 10000) in paragraph at lines 2340--2341


Underfull \hbox (badness 10000) in paragraph at lines 2349--2350

[54]
Underfull \hbox (badness 10000) in paragraph at lines 2360--2361


Underfull \hbox (badness 10000) in paragraph at lines 2370--2371


Underfull \hbox (badness 10000) in paragraph at lines 2380--2381


Underfull \hbox (badness 10000) in paragraph at lines 2397--2398


Underfull \hbox (badness 10000) in paragraph at lines 2406--2407

[55]
Underfull \hbox (badness 10000) in paragraph at lines 2442--2443


Underfull \hbox (badness 10000) in paragraph at lines 2452--2453


Underfull \hbox (badness 10000) in paragraph at lines 2462--2463


Underfull \hbox (badness 10000) in paragraph at lines 2473--2474
[]\OT1/cmtt/m/n/10.95 GtUchar gt[]encseq[]get[]encoded[]char([]const GtEncseq *
encseq, GtUword pos,

Underfull \hbox (badness 10000) in paragraph at lines 2473--2474


Underfull \hbox (badness 10000) in paragraph at lines 2485--2486
[]\OT1/cmtt/m/n/10.95 char gt[]encseq[]get[]decoded[]char([]const GtEncseq *enc
seq, GtUword pos,

Underfull \hbox (badness 10000) in paragraph at lines 2485--2486


Underfull \hbox (badness 10000) in paragraph at lines 2497--2498
[]\OT1/cmtt/m/n/10.95 bool gt[]encseq[]position[]is[]separator([]const GtEncseq
 *encseq, GtUword pos,

Underfull \hbox (badness 10000) in paragraph at lines 2497--2498


Underfull \hbox (badness 10000) in paragraph at lines 2509--2510
[]\OT1/cmtt/m/n/10.95 bool gt[]encseq[]position[]is[]wildcard([]const GtEncseq 
*encseq, GtUword pos,

Underfull \hbox (badness 10000) in paragraph at lines 2509--2510


Underfull \hbox (badness 10000) in paragraph at lines 2519--2520


Underfull \hbox (badness 10000) in paragraph at lines 2530--2531
[]\OT1/cmtt/m/n/10.95 GtEncseqReader* gt[]encseq[]create[]reader[]with[]readmod
e([]const GtEncseq

Underfull \hbox (badness 10000) in paragraph at lines 2530--2531


Underfull \hbox (badness 10000) in paragraph at lines 2546--2547
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]extract[]encoded([]const GtEncseq *encse
q, GtUchar *buffer,

Underfull \hbox (badness 10000) in paragraph at lines 2546--2547


Underfull \hbox (badness 10000) in paragraph at lines 2561--2562
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]extract[]decoded([]const GtEncseq *encse
q, char *buffer,

Underfull \hbox (badness 10000) in paragraph at lines 2561--2562


Underfull \hbox (badness 10000) in paragraph at lines 2576--2577


Underfull \hbox (badness 10000) in paragraph at lines 2586--2587


Underfull \hbox (badness 10000) in paragraph at lines 2595--2596


Underfull \hbox (badness 10000) in paragraph at lines 2604--2605


Underfull \hbox (badness 10000) in paragraph at lines 2613--2614


Underfull \hbox (badness 10000) in paragraph at lines 2622--2623


Underfull \hbox (badness 10000) in paragraph at lines 2632--2633


Underfull \hbox (badness 10000) in paragraph at lines 2643--2644


Underfull \hbox (badness 10000) in paragraph at lines 2655--2656
[]\OT1/cmtt/m/n/10.95 const char* gt[]encseq[]description([]const GtEncseq *enc
seq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 2655--2656


Underfull \hbox (badness 10000) in paragraph at lines 2668--2669


Underfull \hbox (badness 10000) in paragraph at lines 2678--2679


Underfull \hbox (badness 10000) in paragraph at lines 2688--2689
[]\OT1/cmtt/m/n/10.95 GtUint64 gt[]encseq[]effective[]filelength([]const GtEncs
eq *encseq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 2688--2689


Underfull \hbox (badness 10000) in paragraph at lines 2699--2700


Underfull \hbox (badness 10000) in paragraph at lines 2710--2711


Underfull \hbox (badness 10000) in paragraph at lines 2721--2722
[]\OT1/cmtt/m/n/10.95 GtUword gt[]encseq[]filenum[]first[]seqnum([]const GtEncs
eq *encseq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 2721--2722


Underfull \hbox (badness 10000) in paragraph at lines 2731--2732


Underfull \hbox (badness 10000) in paragraph at lines 2740--2741


Underfull \hbox (badness 10000) in paragraph at lines 2751--2752


Underfull \hbox (badness 10000) in paragraph at lines 2761--2762


Underfull \hbox (badness 10000) in paragraph at lines 2771--2772


Underfull \hbox (badness 10000) in paragraph at lines 2781--2782


Underfull \hbox (badness 10000) in paragraph at lines 2790--2791

[56] [57] [58]
Underfull \hbox (badness 10000) in paragraph at lines 2807--2808


Underfull \hbox (badness 10000) in paragraph at lines 2817--2818


Underfull \hbox (badness 10000) in paragraph at lines 2829--2830


Underfull \hbox (badness 10000) in paragraph at lines 2841--2842


Underfull \hbox (badness 10000) in paragraph at lines 2852--2853


Underfull \hbox (badness 10000) in paragraph at lines 2864--2865


Underfull \hbox (badness 10000) in paragraph at lines 2874--2875


Underfull \hbox (badness 10000) in paragraph at lines 2883--2884


Underfull \hbox (badness 10000) in paragraph at lines 2892--2893


Underfull \hbox (badness 10000) in paragraph at lines 2901--2902


Underfull \hbox (badness 10000) in paragraph at lines 2910--2911


Underfull \hbox (badness 10000) in paragraph at lines 2919--2920


Underfull \hbox (badness 10000) in paragraph at lines 2929--2930


Underfull \hbox (badness 10000) in paragraph at lines 2941--2942
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]cstr([]GtEncseqBuilder *eb
, const char *str,

Underfull \hbox (badness 10000) in paragraph at lines 2941--2942


Underfull \hbox (badness 10000) in paragraph at lines 2956--2957
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]str([]GtEncseqBuilder *eb,
 GtStr *str, const

Underfull \hbox (badness 10000) in paragraph at lines 2956--2957


Underfull \hbox (badness 10000) in paragraph at lines 2973--2974
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]encoded([]GtEncseqBuilder 
*eb, const GtUchar

Underfull \hbox (badness 10000) in paragraph at lines 2973--2974


Underfull \hbox (badness 10000) in paragraph at lines 2990--2991
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]encoded[]own([]GtEncseqBui
lder *eb, const GtUchar

Underfull \hbox (badness 10000) in paragraph at lines 2990--2991


Underfull \hbox (badness 10000) in paragraph at lines 3007--3008
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]multiple[]encoded([]GtEncs
eqBuilder *eb, const

Underfull \hbox (badness 10000) in paragraph at lines 3007--3008


Underfull \hbox (badness 10000) in paragraph at lines 3019--3020


Underfull \hbox (badness 10000) in paragraph at lines 3029--3030


Underfull \hbox (badness 10000) in paragraph at lines 3042--3043


Underfull \hbox (badness 10000) in paragraph at lines 3052--3053

[59] [60]
Underfull \hbox (badness 10000) in paragraph at lines 3070--3071


Underfull \hbox (badness 10000) in paragraph at lines 3079--3080


Underfull \hbox (badness 10000) in paragraph at lines 3089--3090


Underfull \hbox (badness 10000) in paragraph at lines 3100--3101
[]\OT1/cmtt/m/n/10.95 int gt[]encseq[]encoder[]use[]representation([]GtEncseqEn
coder *ee, const char

Underfull \hbox (badness 10000) in paragraph at lines 3100--3101


Underfull \hbox (badness 10000) in paragraph at lines 3111--3112


Underfull \hbox (badness 10000) in paragraph at lines 3122--3123
[]\OT1/cmtt/m/n/10.95 int gt[]encseq[]encoder[]use[]symbolmap[]file([]GtEncseqE
ncoder *ee, const char

Underfull \hbox (badness 10000) in paragraph at lines 3122--3123


Underfull \hbox (badness 10000) in paragraph at lines 3134--3135


Underfull \hbox (badness 10000) in paragraph at lines 3144--3145


Underfull \hbox (badness 10000) in paragraph at lines 3154--3155


Underfull \hbox (badness 10000) in paragraph at lines 3166--3167


Underfull \hbox (badness 10000) in paragraph at lines 3179--3180


Underfull \hbox (badness 10000) in paragraph at lines 3191--3192


Underfull \hbox (badness 10000) in paragraph at lines 3204--3205


Underfull \hbox (badness 10000) in paragraph at lines 3215--3216


Underfull \hbox (badness 3039) in paragraph at lines 3219--3224
[]\OT1/ptm/m/n/10.95 Enables sup-port for loss-less re-pro-duc-tion of the orig
-i-nal se-quence, re-gard-less

Underfull \hbox (badness 1655) in paragraph at lines 3219--3224
\OT1/ptm/m/n/10.95 of al-pha-bet trans-for-ma-tions that may ap-ply. En-coded s
e-quences cre-ated with-

Underfull \hbox (badness 2359) in paragraph at lines 3219--3224
\OT1/ptm/m/n/10.95 out this sup-port will not be able to be loaded via a \OT1/c
mtt/m/n/10.95 GtEncseqLoader \OT1/ptm/m/n/10.95 with

Underfull \hbox (badness 10000) in paragraph at lines 3228--3229


Underfull \hbox (badness 10000) in paragraph at lines 3238--3239


Underfull \hbox (badness 10000) in paragraph at lines 3249--3250


Underfull \hbox (badness 10000) in paragraph at lines 3259--3260


Underfull \hbox (badness 10000) in paragraph at lines 3268--3269


Underfull \hbox (badness 10000) in paragraph at lines 3278--3279


Underfull \hbox (badness 10000) in paragraph at lines 3288--3289


Underfull \hbox (badness 10000) in paragraph at lines 3297--3298


Underfull \hbox (badness 10000) in paragraph at lines 3307--3308


Underfull \hbox (badness 10000) in paragraph at lines 3317--3318


Underfull \hbox (badness 10000) in paragraph at lines 3326--3327


Underfull \hbox (badness 10000) in paragraph at lines 3336--3337


Underfull \hbox (badness 10000) in paragraph at lines 3346--3347


Underfull \hbox (badness 10000) in paragraph at lines 3355--3356


Underfull \hbox (badness 10000) in paragraph at lines 3365--3366


Underfull \hbox (badness 10000) in paragraph at lines 3374--3375


Underfull \hbox (badness 10000) in paragraph at lines 3383--3384


Underfull \hbox (badness 10000) in paragraph at lines 3392--3393


Underfull \hbox (badness 10000) in paragraph at lines 3401--3402


Underfull \hbox (badness 10000) in paragraph at lines 3411--3412


Underfull \hbox (badness 10000) in paragraph at lines 3423--3424
[]\OT1/cmtt/m/n/10.95 int gt[]encseq[]encoder[]encode([]GtEncseqEncoder *ee, Gt
StrArray *seqfiles,

Underfull \hbox (badness 10000) in paragraph at lines 3423--3424


Underfull \hbox (badness 10000) in paragraph at lines 3434--3435

[61] [62] [63]
Underfull \hbox (badness 10000) in paragraph at lines 3451--3452


Underfull \hbox (badness 10000) in paragraph at lines 3460--3461


Underfull \hbox (badness 10000) in paragraph at lines 3472--3473


Underfull \hbox (badness 10000) in paragraph at lines 3481--3482


Underfull \hbox (badness 10000) in paragraph at lines 3494--3495


Underfull \hbox (badness 10000) in paragraph at lines 3507--3508


Underfull \hbox (badness 10000) in paragraph at lines 3520--3521


Underfull \hbox (badness 10000) in paragraph at lines 3533--3534


Underfull \hbox (badness 10000) in paragraph at lines 3547--3548


Underfull \hbox (badness 10000) in paragraph at lines 3560--3561


Underfull \hbox (badness 10000) in paragraph at lines 3573--3574


Underfull \hbox (badness 10000) in paragraph at lines 3584--3585


Underfull \hbox (badness 10000) in paragraph at lines 3594--3595


Underfull \hbox (badness 10000) in paragraph at lines 3604--3605


Underfull \hbox (badness 10000) in paragraph at lines 3613--3614


Underfull \hbox (badness 10000) in paragraph at lines 3623--3624


Underfull \hbox (badness 10000) in paragraph at lines 3633--3634


Underfull \hbox (badness 10000) in paragraph at lines 3642--3643


Underfull \hbox (badness 10000) in paragraph at lines 3652--3653


Underfull \hbox (badness 10000) in paragraph at lines 3662--3663


Underfull \hbox (badness 10000) in paragraph at lines 3671--3672


Underfull \hbox (badness 10000) in paragraph at lines 3681--3682


Underfull \hbox (badness 10000) in paragraph at lines 3691--3692


Underfull \hbox (badness 10000) in paragraph at lines 3703--3704
[]\OT1/cmtt/m/n/10.95 GtEncseq* gt[]encseq[]loader[]load([]GtEncseqLoader *el, 
const char

Underfull \hbox (badness 10000) in paragraph at lines 3703--3704


Underfull \hbox (badness 10000) in paragraph at lines 3715--3716

[64] [65] [66]
Underfull \hbox (badness 10000) in paragraph at lines 3735--3736
[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]reader[]reinit[]with[]readmode([]GtEncse
qReader *esr, const

Underfull \hbox (badness 10000) in paragraph at lines 3735--3736


Underfull \hbox (badness 10000) in paragraph at lines 3739--3741
[]\OT1/ptm/m/n/10.95 Reinitializes the given \OT1/cmtt/m/n/10.95 esr \OT1/ptm/m
/n/10.95 with the val-ues as de-scribed in

Underfull \hbox (badness 10000) in paragraph at lines 3745--3746


Underfull \hbox (badness 10000) in paragraph at lines 3755--3756


Underfull \hbox (badness 10000) in paragraph at lines 3765--3766

[67]
Underfull \hbox (badness 10000) in paragraph at lines 3791--3792


Underfull \hbox (badness 10000) in paragraph at lines 3800--3801


Underfull \hbox (badness 10000) in paragraph at lines 3812--3813


Underfull \hbox (badness 10000) in paragraph at lines 3822--3823


Underfull \hbox (badness 10000) in paragraph at lines 3832--3833


Underfull \hbox (badness 10000) in paragraph at lines 3841--3842


Underfull \hbox (badness 10000) in paragraph at lines 3850--3851


Underfull \hbox (badness 10000) in paragraph at lines 3859--3860


Underfull \hbox (badness 10000) in paragraph at lines 3868--3869


Underfull \hbox (badness 10000) in paragraph at lines 3890--3891
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]extract[]feature[]stream[]new([]GtNodeS
tream *in[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 3890--3891
\OT1/cmtt/m/n/10.95 GtRegionMapping *region[]Mapping, const char *type, bool jo
in, bool

Underfull \hbox (badness 10000) in paragraph at lines 3890--3891

[68]
Underfull \hbox (badness 10000) in paragraph at lines 3909--3910


Underfull \hbox (badness 10000) in paragraph at lines 3919--3920


Underfull \hbox (badness 10000) in paragraph at lines 3944--3945
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]add[]region[]node([]GtFeatureInde
x *feature[]index,

Underfull \hbox (badness 10000) in paragraph at lines 3944--3945


Underfull \hbox (badness 10000) in paragraph at lines 3955--3956
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]add[]feature[]node([]GtFeatureInd
ex *feature[]index,

Underfull \hbox (badness 10000) in paragraph at lines 3955--3956


Underfull \hbox (badness 10000) in paragraph at lines 3967--3968
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]remove[]node([]GtFeatureIndex *fe
ature[]index,

Underfull \hbox (badness 10000) in paragraph at lines 3967--3968


Underfull \hbox (badness 10000) in paragraph at lines 3977--3978
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]add[]gff3file([]GtFeatureIndex *f
eature[]index, const

Underfull \hbox (badness 10000) in paragraph at lines 3977--3978


Underfull \hbox (badness 10000) in paragraph at lines 3989--3990
[]\OT1/cmtt/m/n/10.95 GtArray* gt[]feature[]index[]get[]features[]for[]seqid([]
GtFeatureIndex*, const

Underfull \hbox (badness 10000) in paragraph at lines 3989--3990


Underfull \hbox (badness 10000) in paragraph at lines 4004--4005
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]get[]features[]for[]range([]GtFea
tureIndex *feature[]index,

Underfull \hbox (badness 10000) in paragraph at lines 4004--4005


Underfull \hbox (badness 10000) in paragraph at lines 4016--4017
[]\OT1/cmtt/m/n/10.95 char* gt[]feature[]index[]get[]first[]seqid([]const GtFea
tureIndex

Underfull \hbox (badness 10000) in paragraph at lines 4016--4017


Underfull \hbox (badness 10000) in paragraph at lines 4026--4027
[]\OT1/cmtt/m/n/10.95 GtStrArray* gt[]feature[]index[]get[]seqids([]const GtFea
tureIndex

Underfull \hbox (badness 10000) in paragraph at lines 4026--4027


Underfull \hbox (badness 10000) in paragraph at lines 4039--4040
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]get[]range[]for[]seqid([]GtFeatur
eIndex *feature[]index,

Underfull \hbox (badness 10000) in paragraph at lines 4039--4040


Underfull \hbox (badness 10000) in paragraph at lines 4053--4054
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]get[]orig[]range[]for[]seqid([]Gt
FeatureIndex

Underfull \hbox (badness 10000) in paragraph at lines 4053--4054


Underfull \hbox (badness 10000) in paragraph at lines 4067--4068
[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]has[]seqid([]const GtFeatureIndex
 *feature[]index, bool

Underfull \hbox (badness 10000) in paragraph at lines 4067--4068


Underfull \hbox (badness 10000) in paragraph at lines 4077--4078


Underfull \hbox (badness 10000) in paragraph at lines 4088--4089

[69] [70]
Underfull \hbox (badness 10000) in paragraph at lines 4107--4108


Overfull \hbox (13.12596pt too wide) in paragraph at lines 4118--4119
[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]index[]memory[]get[]node[]by[
]ptr([]GtFeatureIndexMemory*,

Underfull \hbox (badness 10000) in paragraph at lines 4118--4119


Overfull \hbox (26.19778pt too wide) in paragraph at lines 4129--4148
\OT1/ptm/m/n/10.95 with the \OT1/cmtt/m/n/10.95 Parent \OT1/ptm/m/n/10.95 and \
OT1/cmtt/m/n/10.95 ID \OT1/ptm/m/n/10.95 at-tributes) are re-al-ized in the C A
PI with the \OT1/cmtt/m/n/10.95 gt[]feature[]node[]add[]child()

Underfull \hbox (badness 10000) in paragraph at lines 4155--4156
[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]feature[]node[]new([]GtStr *seqid, cons
t char *type, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 4155--4156


Underfull \hbox (badness 10000) in paragraph at lines 4170--4171
[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]feature[]node[]new[]pseudo([]GtStr *seq
id, GtUword start,

Underfull \hbox (badness 10000) in paragraph at lines 4170--4171


Underfull \hbox (badness 10000) in paragraph at lines 4184--4185
[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]feature[]node[]new[]pseudo[]template([]
GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4184--4185


Underfull \hbox (badness 10000) in paragraph at lines 4195--4196


Underfull \hbox (badness 10000) in paragraph at lines 4205--4206
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]add[]child([]GtFeatureNode *paren
t, GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4205--4206


Underfull \hbox (badness 10000) in paragraph at lines 4215--4216


Underfull \hbox (badness 10000) in paragraph at lines 4226--4227
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]source([]GtFeatureNode *feat
ure[]node, GtStr

Underfull \hbox (badness 10000) in paragraph at lines 4226--4227


Underfull \hbox (badness 10000) in paragraph at lines 4236--4237


Underfull \hbox (badness 10000) in paragraph at lines 4246--4247


Underfull \hbox (badness 10000) in paragraph at lines 4257--4258
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]type([]GtFeatureNode *featur
e[]node, const char

Underfull \hbox (badness 10000) in paragraph at lines 4257--4258


Underfull \hbox (badness 10000) in paragraph at lines 4267--4268
[]\OT1/cmtt/m/n/10.95 bool gt[]feature[]node[]has[]type([]GtFeatureNode *featur
e[]node, const char

Underfull \hbox (badness 10000) in paragraph at lines 4267--4268


Underfull \hbox (badness 10000) in paragraph at lines 4277--4278
[]\OT1/cmtt/m/n/10.95 GtUword gt[]feature[]node[]number[]of[]children([]const G
tFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4277--4278


Underfull \hbox (badness 10000) in paragraph at lines 4289--4290
[]\OT1/cmtt/m/n/10.95 GtUword gt[]feature[]node[]number[]of[]children[]of[]type
([]const GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4289--4290


Underfull \hbox (badness 10000) in paragraph at lines 4300--4301


Underfull \hbox (badness 10000) in paragraph at lines 4310--4311


Underfull \hbox (badness 10000) in paragraph at lines 4321--4322


Underfull \hbox (badness 10000) in paragraph at lines 4330--4331


Underfull \hbox (badness 10000) in paragraph at lines 4339--4340


Underfull \hbox (badness 10000) in paragraph at lines 4350--4351
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]strand([]GtFeatureNode *feat
ure[]node, GtStrand

Underfull \hbox (badness 10000) in paragraph at lines 4350--4351


Underfull \hbox (badness 10000) in paragraph at lines 4359--4360


Underfull \hbox (badness 10000) in paragraph at lines 4370--4371


Underfull \hbox (badness 10000) in paragraph at lines 4380--4381
[]\OT1/cmtt/m/n/10.95 const char* gt[]feature[]node[]get[]attribute([]const GtF
eatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4380--4381


Underfull \hbox (badness 10000) in paragraph at lines 4392--4393
[]\OT1/cmtt/m/n/10.95 GtStrArray* gt[]feature[]node[]get[]attribute[]list([]con
st GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4392--4393


Underfull \hbox (badness 10000) in paragraph at lines 4404--4405
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]add[]attribute([]GtFeatureNode *f
eature[]node, const char

Underfull \hbox (badness 10000) in paragraph at lines 4404--4405


Underfull \hbox (badness 10000) in paragraph at lines 4418--4419
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]attribute([]GtFeatureNode* f
eature[]node, const char

Underfull \hbox (badness 10000) in paragraph at lines 4418--4419


Underfull \hbox (badness 10000) in paragraph at lines 4432--4433
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]remove[]attribute([]GtFeatureNode
* feature[]node, const

Underfull \hbox (badness 10000) in paragraph at lines 4432--4433


Underfull \hbox (badness 10000) in paragraph at lines 4445--4446
[]\OT1/cmtt/m/n/10.95 void GtFeatureNodeAttributeIterFunc([]const char *attr[]n
ame, const char

Underfull \hbox (badness 10000) in paragraph at lines 4445--4446


Underfull \hbox (badness 10000) in paragraph at lines 4449--4452
[]\OT1/ptm/m/n/10.95 Delivers the key (in \OT1/cmtt/m/n/10.95 attr[]name\OT1/pt
m/m/n/10.95 )and value (in \OT1/cmtt/m/n/10.95 attr[]value\OT1/ptm/m/n/10.95 ) 
of an at-

Underfull \hbox (badness 8094) in paragraph at lines 4449--4452
\OT1/ptm/m/n/10.95 tribute. The \OT1/cmtt/m/n/10.95 data \OT1/ptm/m/n/10.95 pa-
ram-e-ter car-ries over ar-bi-trary user data from the

Underfull \hbox (badness 10000) in paragraph at lines 4458--4459
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]foreach[]attribute([]GtFeatureNod
e *feature[]node,

Underfull \hbox (badness 10000) in paragraph at lines 4458--4459


Underfull \hbox (badness 10000) in paragraph at lines 4468--4469


Underfull \hbox (badness 10000) in paragraph at lines 4477--4478


Underfull \hbox (badness 10000) in paragraph at lines 4487--4488
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]make[]multi[]representative([]GtF
eatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4487--4488


Underfull \hbox (badness 10000) in paragraph at lines 4500--4501
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]multi[]representative([]GtFe
atureNode *feature[]node,

Underfull \hbox (badness 10000) in paragraph at lines 4500--4501


Underfull \hbox (badness 10000) in paragraph at lines 4510--4511


Underfull \hbox (badness 10000) in paragraph at lines 4521--4522
[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]node[]get[]multi[]representat
ive([]GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4521--4522


Underfull \hbox (badness 10000) in paragraph at lines 4531--4532
[]\OT1/cmtt/m/n/10.95 bool gt[]feature[]node[]is[]similar([]const GtFeatureNode
 *feature[]node[]a, const

Underfull \hbox (badness 10000) in paragraph at lines 4531--4532


Underfull \hbox (badness 10000) in paragraph at lines 4542--4543


Underfull \hbox (badness 10000) in paragraph at lines 4551--4552


Underfull \hbox (badness 10000) in paragraph at lines 4560--4561


Underfull \hbox (badness 10000) in paragraph at lines 4569--4570


Underfull \hbox (badness 10000) in paragraph at lines 4579--4580
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]remove[]leaf([]GtFeatureNode *tre
e, GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4579--4580


Underfull \hbox (badness 10000) in paragraph at lines 4592--4593


Underfull \hbox (badness 10000) in paragraph at lines 4604--4605

[71] [72] [73] [74]
Underfull \hbox (badness 10000) in paragraph at lines 4617--4618
[]\OT1/cmtt/m/n/10.95 GtFeatureNodeIterator* gt[]feature[]node[]iterator[]new([
]const GtFeatureNode

Underfull \hbox (badness 10000) in paragraph at lines 4617--4618


Underfull \hbox (badness 10000) in paragraph at lines 4629--4630
[]\OT1/cmtt/m/n/10.95 GtFeatureNodeIterator* gt[]feature[]node[]iterator[]new[]
direct([]const

Underfull \hbox (badness 10000) in paragraph at lines 4629--4630


Underfull \hbox (badness 10000) in paragraph at lines 4640--4641
[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]node[]iterator[]next([]GtFeat
ureNodeIterator

Underfull \hbox (badness 10000) in paragraph at lines 4640--4641


Underfull \hbox (badness 10000) in paragraph at lines 4651--4652
[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]iterator[]delete([]GtFeatureNodeI
terator

Underfull \hbox (badness 10000) in paragraph at lines 4651--4652

[75]
Underfull \hbox (badness 10000) in paragraph at lines 4662--4663
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]feature[]out[]stream[]new([]GtNodeStrea
m*, GtFeatureIndex

Underfull \hbox (badness 10000) in paragraph at lines 4662--4663


Underfull \hbox (badness 10000) in paragraph at lines 4674--4675


Underfull \hbox (badness 1509) in paragraph at lines 4678--4681
\OT1/cmtt/m/n/10.95 fi\OT1/ptm/m/n/10.95 . Note: The \OT1/cmtt/m/n/10.95 GtFeat
ureStream \OT1/ptm/m/n/10.95 class is now dep-re-cated. Please use the

Underfull \hbox (badness 10000) in paragraph at lines 4694--4695


Underfull \hbox (badness 10000) in paragraph at lines 4707--4708


Underfull \hbox (badness 10000) in paragraph at lines 4716--4717


Underfull \hbox (badness 10000) in paragraph at lines 4725--4726


Underfull \hbox (badness 10000) in paragraph at lines 4734--4735


Underfull \hbox (badness 10000) in paragraph at lines 4744--4745


Underfull \hbox (badness 10000) in paragraph at lines 4754--4755


Underfull \hbox (badness 10000) in paragraph at lines 4763--4764


Underfull \hbox (badness 10000) in paragraph at lines 4773--4774


Underfull \hbox (badness 10000) in paragraph at lines 4782--4783


Underfull \hbox (badness 10000) in paragraph at lines 4791--4792


Underfull \hbox (badness 10000) in paragraph at lines 4800--4801

[76]
Underfull \hbox (badness 10000) in paragraph at lines 4818--4819
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]gff3[]in[]stream[]new[]unsorted([]int n
um[]of[]files, const char

Underfull \hbox (badness 10000) in paragraph at lines 4818--4819


Underfull \hbox (badness 10000) in paragraph at lines 4830--4831


Underfull \hbox (badness 10000) in paragraph at lines 4842--4843


Underfull \hbox (badness 10000) in paragraph at lines 4853--4854


Underfull \hbox (badness 10000) in paragraph at lines 4864--4865


Underfull \hbox (badness 10000) in paragraph at lines 4874--4875


Underfull \hbox (badness 10000) in paragraph at lines 4884--4885


Underfull \hbox (badness 10000) in paragraph at lines 4896--4897
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]in[]stream[]set[]type[]checker([]GtNodeStr
eam *gff3[]in[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 4896--4897

[77]
Underfull \hbox (badness 10000) in paragraph at lines 4915--4916
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]gff3[]out[]stream[]new([]GtNodeStream *
in[]stream, GtFile

Underfull \hbox (badness 10000) in paragraph at lines 4915--4916


Underfull \hbox (badness 10000) in paragraph at lines 4927--4928
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]out[]stream[]set[]fasta[]width([]GtGFF3Out
Stream *gff3[]out[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 4927--4928


Underfull \hbox (badness 10000) in paragraph at lines 4939--4940
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]out[]stream[]retain[]id[]attributes([]GtGF
F3OutStream

Underfull \hbox (badness 10000) in paragraph at lines 4939--4940

[78]
Underfull \hbox (badness 10000) in paragraph at lines 4963--4964


Underfull \hbox (badness 10000) in paragraph at lines 4974--4975


Underfull \hbox (badness 10000) in paragraph at lines 4985--4986


Underfull \hbox (badness 10000) in paragraph at lines 4997--4998
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]parser[]do[]not[]check[]region[]boundaries
([]GtGFF3Parser

Underfull \hbox (badness 10000) in paragraph at lines 4997--4998


Underfull \hbox (badness 10000) in paragraph at lines 5008--5009


Underfull \hbox (badness 10000) in paragraph at lines 5018--5019
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]parser[]set[]type[]checker([]GtGFF3Parser 
*gff3[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 5018--5019


Underfull \hbox (badness 10000) in paragraph at lines 5028--5029
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]parser[]set[]xrf[]checker([]GtGFF3Parser *
gff3[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 5028--5029


Underfull \hbox (badness 10000) in paragraph at lines 5037--5038


Underfull \hbox (badness 10000) in paragraph at lines 5054--5055
[]\OT1/cmtt/m/n/10.95 int gt[]gff3[]parser[]parse[]genome[]nodes([]GtGFF3Parser
 *gff3[]parser, int

Underfull \hbox (badness 10000) in paragraph at lines 5054--5055
\OT1/cmtt/m/n/10.95 *status[]code, GtQueue *genome[]nodes, GtCstrTable *used[]t
ypes, GtStr

Underfull \hbox (badness 10000) in paragraph at lines 5054--5055


Underfull \hbox (badness 10000) in paragraph at lines 5073--5074


Underfull \hbox (badness 10000) in paragraph at lines 5082--5083

[79]
Underfull \hbox (badness 10000) in paragraph at lines 5100--5101


Underfull \hbox (badness 10000) in paragraph at lines 5112--5113
[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]visitor[]set[]fasta[]width([]GtGFF3Visitor
 *gff3[]visitor, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 5112--5113


Underfull \hbox (badness 10000) in paragraph at lines 5124--5125

[80]
Underfull \hbox (badness 10000) in paragraph at lines 5144--5145


Underfull \hbox (badness 10000) in paragraph at lines 5163--5164
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]gtf[]out[]stream[]new([]GtNodeStream *i
n[]stream, GtFile

Underfull \hbox (badness 10000) in paragraph at lines 5163--5164


Underfull \hbox (badness 10000) in paragraph at lines 5182--5183


Underfull \hbox (badness 10000) in paragraph at lines 5192--5193


Underfull \hbox (badness 10000) in paragraph at lines 5202--5203


Underfull \hbox (badness 10000) in paragraph at lines 5212--5213


Underfull \hbox (badness 10000) in paragraph at lines 5222--5223


Underfull \hbox (badness 10000) in paragraph at lines 5232--5233


Underfull \hbox (badness 10000) in paragraph at lines 5242--5243


Underfull \hbox (badness 10000) in paragraph at lines 5253--5254


Underfull \hbox (badness 10000) in paragraph at lines 5264--5265
[]\OT1/cmtt/m/n/10.95 void gt[]genome[]node[]set[]range([]GtGenomeNode *genome[
]node, const GtRange

Underfull \hbox (badness 10000) in paragraph at lines 5264--5265


Underfull \hbox (badness 10000) in paragraph at lines 5275--5276
[]\OT1/cmtt/m/n/10.95 void gt[]genome[]node[]add[]user[]data([]GtGenomeNode *ge
nome[]node, const char

Underfull \hbox (badness 10000) in paragraph at lines 5275--5276


Underfull \hbox (badness 10000) in paragraph at lines 5286--5287
[]\OT1/cmtt/m/n/10.95 void* gt[]genome[]node[]get[]user[]data([]const GtGenomeN
ode *genome[]node, const

Underfull \hbox (badness 10000) in paragraph at lines 5286--5287


Underfull \hbox (badness 10000) in paragraph at lines 5296--5297
[]\OT1/cmtt/m/n/10.95 void gt[]genome[]node[]release[]user[]data([]GtGenomeNode
 *genome[]node, const

Underfull \hbox (badness 10000) in paragraph at lines 5296--5297


Underfull \hbox (badness 10000) in paragraph at lines 5307--5308
[]\OT1/cmtt/m/n/10.95 int gt[]genome[]node[]cmp([]GtGenomeNode *genome[]node[]a
, GtGenomeNode

Underfull \hbox (badness 10000) in paragraph at lines 5307--5308


Underfull \hbox (badness 1424) in paragraph at lines 5311--5313
[]\OT1/ptm/m/n/10.95 Compare \OT1/cmtt/m/n/10.95 genome[]node[]a \OT1/ptm/m/n/1
0.95 with \OT1/cmtt/m/n/10.95 genome[]node[]b \OT1/ptm/m/n/10.95 and re-turn th
e re-sult (sim-i-lar to

Underfull \hbox (badness 10000) in paragraph at lines 5317--5318


Underfull \hbox (badness 10000) in paragraph at lines 5326--5327


Underfull \hbox (badness 10000) in paragraph at lines 5336--5337
[]\OT1/cmtt/m/n/10.95 int gt[]genome[]node[]accept([]GtGenomeNode *genome[]node
, GtNodeVisitor

Underfull \hbox (badness 10000) in paragraph at lines 5336--5337


Underfull \hbox (badness 10000) in paragraph at lines 5346--5347

[81] [82]
Underfull \hbox (badness 10000) in paragraph at lines 5366--5367


Underfull \hbox (badness 10000) in paragraph at lines 5376--5377
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]text[]clip([]GtGraphics*, double
 x, double y, const

Underfull \hbox (badness 10000) in paragraph at lines 5376--5377


Underfull \hbox (badness 10000) in paragraph at lines 5386--5387


Underfull \hbox (badness 10000) in paragraph at lines 5396--5397
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]text[]centered([]GtGraphics*, do
uble x, double y,

Underfull \hbox (badness 10000) in paragraph at lines 5396--5397


Underfull \hbox (badness 10000) in paragraph at lines 5407--5408
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]text[]right([]GtGraphics*, doubl
e x, double y, const

Underfull \hbox (badness 10000) in paragraph at lines 5407--5408


Underfull \hbox (badness 10000) in paragraph at lines 5418--5419
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]colored[]text([]GtGraphics*, dou
ble x, double y,

Underfull \hbox (badness 10000) in paragraph at lines 5418--5419


Underfull \hbox (badness 10000) in paragraph at lines 5428--5429


Underfull \hbox (badness 10000) in paragraph at lines 5437--5438


Underfull \hbox (badness 10000) in paragraph at lines 5447--5448


Underfull \hbox (badness 10000) in paragraph at lines 5457--5458
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]set[]font([]GtGraphics *g, const char 
*family, FontSlant

Underfull \hbox (badness 10000) in paragraph at lines 5457--5458


Underfull \hbox (badness 10000) in paragraph at lines 5470--5471


Underfull \hbox (badness 10000) in paragraph at lines 5479--5480


Underfull \hbox (badness 10000) in paragraph at lines 5489--5490
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]set[]margins([]GtGraphics*, double mar
gin[]x, double

Underfull \hbox (badness 10000) in paragraph at lines 5489--5490


Underfull \hbox (badness 10000) in paragraph at lines 5501--5502


Underfull \hbox (badness 10000) in paragraph at lines 5510--5511


Underfull \hbox (badness 10000) in paragraph at lines 5521--5522
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]horizontal[]line([]GtGraphics *g
, double x, double y,

Underfull \hbox (badness 10000) in paragraph at lines 5521--5522


Underfull \hbox (badness 10000) in paragraph at lines 5533--5534
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]vertical[]line([]GtGraphics *g, 
double x, double y,

Underfull \hbox (badness 10000) in paragraph at lines 5533--5534


Underfull \hbox (badness 10000) in paragraph at lines 5545--5546
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]line([]GtGraphics *g, double x, 
double y, double xto,

Underfull \hbox (badness 10000) in paragraph at lines 5545--5546


Underfull \hbox (badness 10000) in paragraph at lines 5559--5560
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]box([]GtGraphics*, double x, dou
ble y, double width,

Underfull \hbox (badness 10000) in paragraph at lines 5559--5560
\OT1/cmtt/m/n/10.95 double height, GtColor fill[]color, ArrowStatus arrow[]stat
us, double

Underfull \hbox (badness 10000) in paragraph at lines 5559--5560


Underfull \hbox (badness 10000) in paragraph at lines 5579--5580
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]dashes([]GtGraphics*, double x, 
double y, double

Underfull \hbox (badness 10000) in paragraph at lines 5579--5580
\OT1/cmtt/m/n/10.95 width, double height, ArrowStatus arrow[]status, double arr
ow[]width,

Underfull \hbox (badness 10000) in paragraph at lines 5579--5580


Underfull \hbox (badness 10000) in paragraph at lines 5597--5598
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]caret([]GtGraphics*, double x, d
ouble y, double

Underfull \hbox (badness 10000) in paragraph at lines 5597--5598
\OT1/cmtt/m/n/10.95 width, double height, ArrowStatus arrow[]status, double arr
ow[]width,

Underfull \hbox (badness 10000) in paragraph at lines 5597--5598


Underfull \hbox (badness 10000) in paragraph at lines 5616--5617
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]rectangle([]GtGraphics*, double 
x, double y, bool

Underfull \hbox (badness 10000) in paragraph at lines 5616--5617
\OT1/cmtt/m/n/10.95 filled, GtColor fill[]color, bool stroked, GtColor stroke[]
color, double

Underfull \hbox (badness 10000) in paragraph at lines 5616--5617


Underfull \hbox (badness 10000) in paragraph at lines 5630--5631
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]arrowhead([]GtGraphics*, double 
x, double y, GtColor,

Underfull \hbox (badness 10000) in paragraph at lines 5630--5631


Underfull \hbox (badness 10000) in paragraph at lines 5643--5644
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]curve[]data([]GtGraphics *g, dou
ble x, double y,

Underfull \hbox (badness 10000) in paragraph at lines 5643--5644
\OT1/cmtt/m/n/10.95 GtColor color, double data[], GtUword ndata, GtRange valran
ge, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 5643--5644


Underfull \hbox (badness 10000) in paragraph at lines 5657--5658
[]\OT1/cmtt/m/n/10.95 int gt[]graphics[]save[]to[]file([]const GtGraphics*, con
st char *filename,

Underfull \hbox (badness 10000) in paragraph at lines 5657--5658


Underfull \hbox (badness 10000) in paragraph at lines 5666--5667


Underfull \hbox (badness 10000) in paragraph at lines 5675--5676

[83] [84] [85]
Underfull \hbox (badness 10000) in paragraph at lines 5694--5695
[]\OT1/cmtt/m/n/10.95 GtGraphics* gt[]graphics[]cairo[]new([]GtGraphicsOutType 
type, unsigned int

Underfull \hbox (badness 10000) in paragraph at lines 5694--5695


Underfull \hbox (badness 10000) in paragraph at lines 5707--5708
[]\OT1/cmtt/m/n/10.95 GtGraphics* gt[]graphics[]cairo[]new[]from[]context([]cai
ro[]t *context, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 5707--5708


Underfull \hbox (badness 10000) in paragraph at lines 5722--5723
[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]cairo[]draw[]curve[]data([]GtGraphics 
*gg, double x, double y,

Underfull \hbox (badness 10000) in paragraph at lines 5722--5723
\OT1/cmtt/m/n/10.95 GtColor color, double data[], GtUword ndata, GtRange valran
ge, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 5722--5723

[86]
Underfull \hbox (badness 10000) in paragraph at lines 5743--5744


Underfull \hbox (badness 10000) in paragraph at lines 5757--5758
[]\OT1/cmtt/m/n/10.95 GtHashmap* gt[]hashmap[]new([]GtHashType keyhashtype, GtF
ree keyfree, GtFree

Underfull \hbox (badness 10000) in paragraph at lines 5757--5758


Underfull \hbox (badness 10000) in paragraph at lines 5773--5774


Underfull \hbox (badness 10000) in paragraph at lines 5782--5783


Underfull \hbox (badness 10000) in paragraph at lines 5792--5793


Underfull \hbox (badness 10000) in paragraph at lines 5802--5803


Underfull \hbox (badness 10000) in paragraph at lines 5813--5814
[]\OT1/cmtt/m/n/10.95 int gt[]hashmap[]foreach[]ordered([]GtHashmap *hashmap, G
tHashmapVisitFunc

Underfull \hbox (badness 10000) in paragraph at lines 5813--5814


Underfull \hbox (badness 10000) in paragraph at lines 5824--5825
[]\OT1/cmtt/m/n/10.95 int gt[]hashmap[]foreach([]GtHashmap *hashmap, GtHashmapV
isitFunc func, void

Underfull \hbox (badness 10000) in paragraph at lines 5824--5825


Underfull \hbox (badness 10000) in paragraph at lines 5836--5837
[]\OT1/cmtt/m/n/10.95 int gt[]hashmap[]foreach[]in[]key[]order([]GtHashmap *has
hmap, GtHashmapVisitFunc

Underfull \hbox (badness 10000) in paragraph at lines 5836--5837


Underfull \hbox (badness 2875) in paragraph at lines 5840--5843
[]\OT1/ptm/m/n/10.95 Iterate over \OT1/cmtt/m/n/10.95 hashmap \OT1/ptm/m/n/10.9
5 in ei-ther al-pha-bet-i-cal or-der (if \OT1/cmtt/m/n/10.95 GtHashType \OT1/pt
m/m/n/10.95 was spec-i-

Underfull \hbox (badness 1762) in paragraph at lines 5840--5843
\OT1/ptm/m/n/10.95 fied as \OT1/cmtt/m/n/10.95 GT[]HASH[]STRING\OT1/ptm/m/n/10.
95 ) or nu-mer-i-cal or-der (if \OT1/cmtt/m/n/10.95 GtHashType \OT1/ptm/m/n/10.
95 was spec-i-fied as

Underfull \hbox (badness 10000) in paragraph at lines 5847--5848


Underfull \hbox (badness 10000) in paragraph at lines 5857--5858

[87]
Underfull \hbox (badness 10000) in paragraph at lines 5876--5877
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]id[]to[]md5[]stream[]new([]GtNodeStream
 *in[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 5876--5877

[88]
Underfull \hbox (badness 10000) in paragraph at lines 5902--5903


Underfull \hbox (badness 10000) in paragraph at lines 5911--5912


Underfull \hbox (badness 10000) in paragraph at lines 5920--5921


Underfull \hbox (badness 10000) in paragraph at lines 5930--5931
[]\OT1/cmtt/m/n/10.95 const GtRecMap* gt[]image[]info[]get[]rec[]map([]GtImageI
nfo *image[]info, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 5930--5931


Underfull \hbox (badness 10000) in paragraph at lines 5939--5940


Overfull \hbox (1.94502pt too wide) in paragraph at lines 5949--5951
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. A \OT1/cmtt/m/n/10.95 GtInterFeatureStream \OT1/ptm/m/n/10.
95 in-serts new fea-ture nodes

Underfull \hbox (badness 10000) in paragraph at lines 5958--5959
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]inter[]feature[]stream[]new([]GtNodeStr
eam *in[]stream, const

Underfull \hbox (badness 10000) in paragraph at lines 5958--5959


Underfull \hbox (badness 10000) in paragraph at lines 5978--5979


Underfull \hbox (badness 10000) in paragraph at lines 5989--5990


Overfull \hbox (10.59654pt too wide) in paragraph at lines 6000--6001
[]\OT1/cmtt/m/n/10.95 GtIntervalTreeNode* gt[]interval[]tree[]find[]first[]over
lapping([]GtIntervalTree*,

Underfull \hbox (badness 10000) in paragraph at lines 6000--6001


Underfull \hbox (badness 10000) in paragraph at lines 6011--6012
[]\OT1/cmtt/m/n/10.95 void gt[]interval[]tree[]insert([]GtIntervalTree *tree, G
tIntervalTreeNode

Underfull \hbox (badness 10000) in paragraph at lines 6011--6012


Underfull \hbox (badness 10000) in paragraph at lines 6023--6024
[]\OT1/cmtt/m/n/10.95 void gt[]interval[]tree[]find[]all[]overlapping([]GtInter
valTree*, GtUword start,

Underfull \hbox (badness 10000) in paragraph at lines 6023--6024


Underfull \hbox (badness 10000) in paragraph at lines 6037--6038
[]\OT1/cmtt/m/n/10.95 void gt[]interval[]tree[]iterate[]overlapping([]GtInterva
lTree *it,

Underfull \hbox (badness 10000) in paragraph at lines 6037--6038


Underfull \hbox (badness 10000) in paragraph at lines 6050--6051
[]\OT1/cmtt/m/n/10.95 int gt[]interval[]tree[]traverse([]GtIntervalTree*, GtInt
ervalTreeIteratorFunc

Underfull \hbox (badness 10000) in paragraph at lines 6050--6051


Underfull \hbox (badness 10000) in paragraph at lines 6062--6063


Underfull \hbox (badness 10000) in paragraph at lines 6076--6077

[89]
Underfull \hbox (badness 10000) in paragraph at lines 6091--6092
[]\OT1/cmtt/m/n/10.95 GtIntervalTreeNode* gt[]interval[]tree[]node[]new([]void 
*data, GtUword low,

Underfull \hbox (badness 10000) in paragraph at lines 6091--6092


Underfull \hbox (badness 10000) in paragraph at lines 6102--6103

[90]
Underfull \hbox (badness 10000) in paragraph at lines 6124--6125
[]\OT1/cmtt/m/n/10.95 GtLayout* gt[]layout[]new([]GtDiagram *diagram, unsigned 
int width, GtStyle*,

Underfull \hbox (badness 10000) in paragraph at lines 6124--6125


Underfull \hbox (badness 10000) in paragraph at lines 6139--6140
[]\OT1/cmtt/m/n/10.95 GtLayout* gt[]layout[]new[]with[]twc([]GtDiagram*, unsign
ed int width,

Underfull \hbox (badness 10000) in paragraph at lines 6139--6140


Underfull \hbox (badness 10000) in paragraph at lines 6151--6152
[]\OT1/cmtt/m/n/10.95 void gt[]layout[]set[]track[]ordering[]func([]GtLayout *l
ayout,

Underfull \hbox (badness 10000) in paragraph at lines 6151--6152


Underfull \hbox (badness 10000) in paragraph at lines 6166--6167


Underfull \hbox (badness 10000) in paragraph at lines 6179--6180


Underfull \hbox (badness 10000) in paragraph at lines 6188--6189

[91]
Underfull \hbox (badness 10000) in paragraph at lines 6199--6200


Underfull \hbox (badness 10000) in paragraph at lines 6211--6212


Underfull \hbox (badness 10000) in paragraph at lines 6220--6221


Underfull \hbox (badness 10000) in paragraph at lines 6229--6230


Underfull \hbox (badness 10000) in paragraph at lines 6238--6239


Underfull \hbox (badness 10000) in paragraph at lines 6247--6248


Underfull \hbox (badness 10000) in paragraph at lines 6256--6257


Underfull \hbox (badness 10000) in paragraph at lines 6265--6266


Underfull \hbox (badness 10000) in paragraph at lines 6274--6275


Underfull \hbox (badness 10000) in paragraph at lines 6283--6284


Underfull \hbox (badness 10000) in paragraph at lines 6292--6293


Underfull \hbox (badness 10000) in paragraph at lines 6309--6310


Underfull \hbox (badness 10000) in paragraph at lines 6319--6320
[]\OT1/cmtt/m/n/10.95 void gt[]md5[]encoder[]add[]block([]GtMD5Encoder *enc, co
nst char *message,

Underfull \hbox (badness 10000) in paragraph at lines 6319--6320


Underfull \hbox (badness 10000) in paragraph at lines 6330--6331
[]\OT1/cmtt/m/n/10.95 void gt[]md5[]encoder[]finish([]GtMD5Encoder *enc, unsign
ed char *output, char

Underfull \hbox (badness 10000) in paragraph at lines 6330--6331


Underfull \hbox (badness 10000) in paragraph at lines 6341--6342


Underfull \hbox (badness 10000) in paragraph at lines 6351--6352

[92]
Underfull \hbox (badness 10000) in paragraph at lines 6369--6370
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]md5[]to[]id[]stream[]new([]GtNodeStream
 *in[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 6369--6370


Underfull \hbox (badness 10000) in paragraph at lines 6391--6392


Underfull \hbox (badness 10000) in paragraph at lines 6402--6403
[]\OT1/cmtt/m/n/10.95 void gt[]match[]set[]seqid1[]nt([]GtMatch *match, const c
har *seqid, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 6402--6403


Underfull \hbox (badness 10000) in paragraph at lines 6413--6414


Underfull \hbox (badness 10000) in paragraph at lines 6424--6425
[]\OT1/cmtt/m/n/10.95 void gt[]match[]set[]seqid2[]nt([]GtMatch *match, const c
har *seqid, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 6424--6425


Underfull \hbox (badness 10000) in paragraph at lines 6435--6436


Underfull \hbox (badness 10000) in paragraph at lines 6445--6446


Underfull \hbox (badness 10000) in paragraph at lines 6456--6457


Underfull \hbox (badness 10000) in paragraph at lines 6467--6468


Underfull \hbox (badness 10000) in paragraph at lines 6477--6478


Underfull \hbox (badness 10000) in paragraph at lines 6490--6491


Underfull \hbox (badness 10000) in paragraph at lines 6503--6504


Underfull \hbox (badness 10000) in paragraph at lines 6512--6513

[93] [94]
Underfull \hbox (badness 10000) in paragraph at lines 6533--6534
[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]blast[]new([]char *seqid1, char *seqi
d2, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 6533--6534
\OT1/cmtt/m/n/10.95 start[]seq1, GtUword start[]seq2, GtUword end[]seq1, GtUwor
d end[]seq2,

Underfull \hbox (badness 10000) in paragraph at lines 6533--6534
\OT1/cmtt/m/n/10.95 double evalue, float bitscore, GtUword ali[]l, double simil
arity,

Underfull \hbox (badness 10000) in paragraph at lines 6533--6534


Underfull \hbox (badness 10000) in paragraph at lines 6546--6547


Underfull \hbox (badness 10000) in paragraph at lines 6555--6556


Underfull \hbox (badness 10000) in paragraph at lines 6564--6565


Underfull \hbox (badness 10000) in paragraph at lines 6573--6574


Underfull \hbox (badness 10000) in paragraph at lines 6582--6583


Underfull \hbox (badness 10000) in paragraph at lines 6591--6592


Underfull \hbox (badness 10000) in paragraph at lines 6600--6601


Underfull \hbox (badness 10000) in paragraph at lines 6609--6610


Underfull \hbox (badness 10000) in paragraph at lines 6621--6622
[]\OT1/cmtt/m/n/10.95 GtMatchIteratorStatus gt[]match[]iterator[]next([]GtMatch
Iterator *mp, GtMatch

Underfull \hbox (badness 10000) in paragraph at lines 6621--6622


Underfull \hbox (badness 10000) in paragraph at lines 6635--6636

[95]
Underfull \hbox (badness 10000) in paragraph at lines 6661--6662
[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]last[]new([]const char *seqid1, const
 char *seqid2,

Underfull \hbox (badness 10000) in paragraph at lines 6661--6662
\OT1/cmtt/m/n/10.95 GtUword score, GtUword seqno1, GtUword seqno2, GtUword star
t[]seq1,

Underfull \hbox (badness 10000) in paragraph at lines 6661--6662
\OT1/cmtt/m/n/10.95 GtUword start[]seq2, GtUword end[]seq1, GtUword end[]seq2, 
GtMatchDirection

Underfull \hbox (badness 10000) in paragraph at lines 6661--6662


Underfull \hbox (badness 10000) in paragraph at lines 6671--6672


Underfull \hbox (badness 10000) in paragraph at lines 6680--6681


Underfull \hbox (badness 10000) in paragraph at lines 6689--6690


Underfull \hbox (badness 10000) in paragraph at lines 6713--6714
[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]open[]new([]char *seqid1, char *seqid
2, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 6713--6714
\OT1/cmtt/m/n/10.95 start[]seq1, GtUword start[]seq2, GtUword end[]seq1, GtUwor
d end[]seq2,

Underfull \hbox (badness 10000) in paragraph at lines 6713--6714


Underfull \hbox (badness 10000) in paragraph at lines 6724--6725


Underfull \hbox (badness 10000) in paragraph at lines 6733--6734

[96]
Underfull \hbox (badness 10000) in paragraph at lines 6760--6761
[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]sw[]new([]const char *seqid1, const c
har *seqid2,

Underfull \hbox (badness 10000) in paragraph at lines 6760--6761
\OT1/cmtt/m/n/10.95 GtUword seqno1, GtUword seqno2, GtUword length, GtUword edi
st, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 6760--6761
\OT1/cmtt/m/n/10.95 start[]seq1, GtUword start[]seq2, GtUword end[]seq1, GtUwor
d end[]seq2,

Underfull \hbox (badness 10000) in paragraph at lines 6760--6761


Underfull \hbox (badness 10000) in paragraph at lines 6772--6773


Underfull \hbox (badness 10000) in paragraph at lines 6781--6782


Underfull \hbox (badness 10000) in paragraph at lines 6790--6791


Underfull \hbox (badness 10000) in paragraph at lines 6799--6800


Underfull \hbox (badness 10000) in paragraph at lines 6819--6820
[]\OT1/cmtt/m/n/10.95 int gt[]match[]visitor[]visit[]match[]blast([]GtMatchVisi
tor *match[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 6819--6820


Underfull \hbox (badness 10000) in paragraph at lines 6830--6831
[]\OT1/cmtt/m/n/10.95 int gt[]match[]visitor[]visit[]match[]open([]GtMatchVisit
or *match[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 6830--6831


Underfull \hbox (badness 10000) in paragraph at lines 6839--6840

[97]
Underfull \hbox (badness 10000) in paragraph at lines 6856--6857


Underfull \hbox (badness 10000) in paragraph at lines 6875--6876


Underfull \hbox (badness 10000) in paragraph at lines 6895--6896
[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]meta[]node[]new([]const char *meta[]dir
ective, const char

Underfull \hbox (badness 10000) in paragraph at lines 6895--6896


Underfull \hbox (badness 10000) in paragraph at lines 6909--6910


Underfull \hbox (badness 10000) in paragraph at lines 6918--6919


Underfull \hbox (badness 10000) in paragraph at lines 6927--6928


Underfull \hbox (badness 10000) in paragraph at lines 6939--6940

[98]
Underfull \hbox (badness 10000) in paragraph at lines 6956--6957


Underfull \hbox (badness 10000) in paragraph at lines 6965--6966


Underfull \hbox (badness 10000) in paragraph at lines 6974--6975


Underfull \hbox (badness 10000) in paragraph at lines 6983--6984


Underfull \hbox (badness 10000) in paragraph at lines 7000--7001


Underfull \hbox (badness 10000) in paragraph at lines 7011--7012
[]\OT1/cmtt/m/n/10.95 int gt[]node[]stream[]next([]GtNodeStream *node[]stream, 
GtGenomeNode

Underfull \hbox (badness 10000) in paragraph at lines 7011--7012


Underfull \hbox (badness 1655) in paragraph at lines 7015--7021
\OT1/ptm/m/n/10.95 (trans-fers own-er-ship to \OT1/cmtt/m/n/10.95 genome[]node\
OT1/ptm/m/n/10.95 ). If no er-ror oc-curs, 0 is re-turned and

Underfull \hbox (badness 10000) in paragraph at lines 7025--7026


Underfull \hbox (badness 3240) in paragraph at lines 7029--7036
\OT1/ptm/m/n/10.95 is ex-hausted (0 is re-turned) or an er-ror oc-curs (-1 is r
e-turned and \OT1/cmtt/m/n/10.95 err \OT1/ptm/m/n/10.95 is

Underfull \hbox (badness 4266) in paragraph at lines 7029--7036
\OT1/ptm/m/n/10.95 set). All re-trieved \OT1/cmtt/m/n/10.95 GtGenomeNode\OT1/pt
m/m/n/10.95 s are deleted au-to-mat-i-cally with calls to

Underfull \hbox (badness 2828) in paragraph at lines 7029--7036
\OT1/cmtt/m/n/10.95 gt[]genome[]node[]delete()\OT1/ptm/m/n/10.95 . This method 
is ba-si-cally a con-ve-nience method

Underfull \hbox (badness 10000) in paragraph at lines 7040--7041


Underfull \hbox (badness 10000) in paragraph at lines 7049--7050


Underfull \hbox (badness 10000) in paragraph at lines 7059--7060


Underfull \hbox (badness 10000) in paragraph at lines 7069--7070


Underfull \hbox (badness 10000) in paragraph at lines 7081--7082
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]node[]stream[]create([]const GtNodeStre
amClass

Underfull \hbox (badness 10000) in paragraph at lines 7081--7082


Underfull \hbox (badness 10000) in paragraph at lines 7097--7098
[]\OT1/cmtt/m/n/10.95 void* gt[]node[]stream[]cast([]const GtNodeStreamClass *n
ode[]stream[]class,

Underfull \hbox (badness 10000) in paragraph at lines 7097--7098

[99]
Underfull \hbox (badness 10000) in paragraph at lines 7113--7114
[]\OT1/cmtt/m/n/10.95 const GtNodeStreamClass* gt[]node[]stream[]class[]new([]s
ize[]t size,

Underfull \hbox (badness 10000) in paragraph at lines 7113--7114

[100]
Underfull \hbox (badness 10000) in paragraph at lines 7135--7136
[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]comment[]node([]GtNodeVisit
or *node[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 7135--7136


Underfull \hbox (badness 10000) in paragraph at lines 7146--7147
[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]feature[]node([]GtNodeVisit
or *node[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 7146--7147


Underfull \hbox (badness 10000) in paragraph at lines 7157--7158
[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]meta[]node([]GtNodeVisitor 
*node[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 7157--7158


Underfull \hbox (badness 10000) in paragraph at lines 7168--7169
[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]region[]node([]GtNodeVisito
r *node[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 7168--7169


Underfull \hbox (badness 10000) in paragraph at lines 7179--7180
[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]sequence[]node([]GtNodeVisi
tor *node[]visitor,

Underfull \hbox (badness 10000) in paragraph at lines 7179--7180


Underfull \hbox (badness 10000) in paragraph at lines 7188--7189


Underfull \hbox (badness 10000) in paragraph at lines 7207--7208
[]\OT1/cmtt/m/n/10.95 GtORFIterator* gt[]orf[]iterator[]new([]GtCodonIterator *
ci, GtTranslator

Underfull \hbox (badness 10000) in paragraph at lines 7207--7208


Underfull \hbox (badness 10000) in paragraph at lines 7220--7221
[]\OT1/cmtt/m/n/10.95 GtORFIteratorStatus gt[]orf[]iterator[]next([]GtORFIterat
or *orf[]iterator,

Underfull \hbox (badness 10000) in paragraph at lines 7220--7221


Underfull \hbox (badness 10000) in paragraph at lines 7237--7238

[101]
Underfull \hbox (badness 10000) in paragraph at lines 7259--7260
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]bool([]const char *option[]str
ing, const char

Underfull \hbox (badness 10000) in paragraph at lines 7259--7260


Underfull \hbox (badness 2856) in paragraph at lines 7263--7265
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7271--7272
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]double([]const char *option[]s
tring, const char

Underfull \hbox (badness 10000) in paragraph at lines 7271--7272


Underfull \hbox (badness 2856) in paragraph at lines 7275--7277
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7284--7285
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]double[]min([]const char *opti
on[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7284--7285


Underfull \hbox (badness 2856) in paragraph at lines 7288--7291
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7300--7301
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]double[]min[]max([]const char 
*option[]string,

Underfull \hbox (badness 10000) in paragraph at lines 7300--7301
\OT1/cmtt/m/n/10.95 const char *description, double *value, double default[]val
ue, double

Underfull \hbox (badness 10000) in paragraph at lines 7300--7301


Underfull \hbox (badness 2856) in paragraph at lines 7304--7308
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7315--7316
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]probability([]const char *opti
on[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7315--7316


Underfull \hbox (badness 2856) in paragraph at lines 7319--7323
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7329--7330
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int([]const char *option[]stri
ng, const char

Underfull \hbox (badness 10000) in paragraph at lines 7329--7330


Underfull \hbox (badness 2856) in paragraph at lines 7333--7335
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7341--7342
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int[]min([]const char *option[
]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7341--7342


Underfull \hbox (badness 2856) in paragraph at lines 7345--7348
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7354--7355
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int[]max([]const char *option[
]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7354--7355


Underfull \hbox (badness 2856) in paragraph at lines 7358--7361
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7368--7369
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int[]min[]max([]const char *op
tion[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7368--7369
\OT1/cmtt/m/n/10.95 *description, int *value, int default[]value, int minimum[]
value, int

Underfull \hbox (badness 10000) in paragraph at lines 7368--7369


Underfull \hbox (badness 2856) in paragraph at lines 7372--7376
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7383--7384
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint([]const char *option[]str
ing, const char

Underfull \hbox (badness 10000) in paragraph at lines 7383--7384


Underfull \hbox (badness 2856) in paragraph at lines 7387--7389
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7397--7398
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint[]min([]const char *option
[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7397--7398
\OT1/cmtt/m/n/10.95 *description, unsigned int *value, unsigned int default[]va
lue, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 7397--7398


Underfull \hbox (badness 2856) in paragraph at lines 7401--7404
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7412--7413
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint[]max([]const char *option
[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7412--7413
\OT1/cmtt/m/n/10.95 *description, unsigned int *value, unsigned int default[]va
lue, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 7412--7413


Underfull \hbox (badness 2856) in paragraph at lines 7416--7419
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7428--7429
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint[]min[]max([]const char *o
ption[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7428--7429
\OT1/cmtt/m/n/10.95 *description, unsigned int *value, unsigned int default[]va
lue, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 7428--7429


Underfull \hbox (badness 2856) in paragraph at lines 7432--7436
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7442--7443
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]word([]const char *option[]str
ing, const char

Underfull \hbox (badness 10000) in paragraph at lines 7442--7443


Underfull \hbox (badness 2856) in paragraph at lines 7446--7448
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7455--7456
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uword([]const char *option[]st
ring, const char

Underfull \hbox (badness 10000) in paragraph at lines 7455--7456


Underfull \hbox (badness 2856) in paragraph at lines 7459--7461
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7469--7470
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uword[]min([]const char *optio
n[]string, const

Underfull \hbox (badness 10000) in paragraph at lines 7469--7470
\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

Underfull \hbox (badness 10000) in paragraph at lines 7469--7470


Underfull \hbox (badness 2856) in paragraph at lines 7473--7476
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7485--7486
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uword[]min[]max([]const char *
option[]string, const

Underfull \hbox (badness 10000) in paragraph at lines 7485--7486
\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

Underfull \hbox (badness 10000) in paragraph at lines 7485--7486


Underfull \hbox (badness 2856) in paragraph at lines 7489--7493
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7499--7500
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]long([]const char *option[]str
ing, const char

Underfull \hbox (badness 10000) in paragraph at lines 7499--7500


Underfull \hbox (badness 10000) in paragraph at lines 7511--7512
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]ulong([]const char *option[]st
ring, const char

Underfull \hbox (badness 10000) in paragraph at lines 7511--7512


Underfull \hbox (badness 10000) in paragraph at lines 7524--7525
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]ulong[]min([]const char *optio
n[]string, const

Underfull \hbox (badness 10000) in paragraph at lines 7524--7525
\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

Underfull \hbox (badness 10000) in paragraph at lines 7524--7525


Underfull \hbox (badness 10000) in paragraph at lines 7538--7539
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]ulong[]min[]max([]const char *
option[]string, const

Underfull \hbox (badness 10000) in paragraph at lines 7538--7539
\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

Underfull \hbox (badness 10000) in paragraph at lines 7538--7539


Underfull \hbox (badness 10000) in paragraph at lines 7549--7550
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]range([]const char *option[]st
ring, const char

Underfull \hbox (badness 10000) in paragraph at lines 7549--7550


Underfull \hbox (badness 2856) in paragraph at lines 7553--7557
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7566--7567
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]range[]min[]max([]const char *
option[]string, const

Underfull \hbox (badness 10000) in paragraph at lines 7566--7567
\OT1/cmtt/m/n/10.95 char *description, GtRange *value, GtRange *default[]value,
 GtUword

Underfull \hbox (badness 10000) in paragraph at lines 7566--7567


Underfull \hbox (badness 2856) in paragraph at lines 7570--7575
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7581--7582
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]string([]const char *option[]s
tring, const char

Underfull \hbox (badness 10000) in paragraph at lines 7581--7582


Underfull \hbox (badness 2856) in paragraph at lines 7585--7587
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7593--7594
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]string[]array([]const char *op
tion[]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7593--7594


Underfull \hbox (badness 2856) in paragraph at lines 7597--7599
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7606--7607
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]choice([]const char *option[]s
tring, const char

Underfull \hbox (badness 10000) in paragraph at lines 7606--7607
\OT1/cmtt/m/n/10.95 *description, GtStr *value, const char *default[]value, con
st char

Underfull \hbox (badness 10000) in paragraph at lines 7606--7607


Underfull \hbox (badness 10000) in paragraph at lines 7610--7613
[]\OT1/ptm/m/n/10.95 Return a \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.95 w
ith the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/cmtt/
m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7619--7620
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]filename([]const char *option[
]string, const char

Underfull \hbox (badness 10000) in paragraph at lines 7619--7620


Underfull \hbox (badness 10000) in paragraph at lines 7632--7633
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]filename[]array([]const char *
option[]string, const

Underfull \hbox (badness 10000) in paragraph at lines 7632--7633


Underfull \hbox (badness 2856) in paragraph at lines 7636--7638
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 option[]string\OT1/ptm/m/n/10.95 , \OT1/c
mtt/m/n/10.95 description\OT1/ptm/m/n/10.95 , and

Underfull \hbox (badness 10000) in paragraph at lines 7642--7643


Underfull \hbox (badness 10000) in paragraph at lines 7652--7653


Underfull \hbox (badness 10000) in paragraph at lines 7662--7663


Underfull \hbox (badness 10000) in paragraph at lines 7673--7674


Underfull \hbox (badness 10000) in paragraph at lines 7682--7683


Underfull \hbox (badness 10000) in paragraph at lines 7691--7692


Underfull \hbox (badness 10000) in paragraph at lines 7701--7702
[]\OT1/cmtt/m/n/10.95 void gt[]option[]is[]mandatory[]either([]GtOption *option
[]a, const GtOption

Underfull \hbox (badness 10000) in paragraph at lines 7701--7702


Underfull \hbox (badness 10000) in paragraph at lines 7712--7713
[]\OT1/cmtt/m/n/10.95 void gt[]option[]is[]mandatory[]either[]3([]GtOption *opt
ion[]a, const GtOption

Underfull \hbox (badness 10000) in paragraph at lines 7712--7713


Underfull \hbox (badness 10000) in paragraph at lines 7725--7726
[]\OT1/cmtt/m/n/10.95 void gt[]option[]is[]mandatory[]either[]4([]GtOption *opt
ion[]a, const GtOption

Underfull \hbox (badness 10000) in paragraph at lines 7725--7726


Underfull \hbox (badness 10000) in paragraph at lines 7735--7736


Underfull \hbox (badness 10000) in paragraph at lines 7744--7745


Underfull \hbox (badness 10000) in paragraph at lines 7753--7754


Underfull \hbox (badness 10000) in paragraph at lines 7764--7765
[]\OT1/cmtt/m/n/10.95 void gt[]option[]imply[]either[]2([]GtOption *option[]a, 
const GtOption

Underfull \hbox (badness 10000) in paragraph at lines 7764--7765


Underfull \hbox (badness 10000) in paragraph at lines 7776--7777
[]\OT1/cmtt/m/n/10.95 void gt[]option[]imply[]either[]3([]GtOption *option[]a, 
const GtOption

Underfull \hbox (badness 10000) in paragraph at lines 7776--7777


Underfull \hbox (badness 10000) in paragraph at lines 7785--7786


Underfull \hbox (badness 10000) in paragraph at lines 7794--7795


Underfull \hbox (badness 10000) in paragraph at lines 7803--7804


Underfull \hbox (badness 10000) in paragraph at lines 7812--7813


Underfull \hbox (badness 10000) in paragraph at lines 7821--7822


Underfull \hbox (badness 10000) in paragraph at lines 7833--7834
[]\OT1/cmtt/m/n/10.95 int gt[]option[]parse[]spacespec([]GtUword *maximumspace,
 const char *optname,

Underfull \hbox (badness 10000) in paragraph at lines 7833--7834

[102] [103] [104] [105] [106]
Underfull \hbox (badness 10000) in paragraph at lines 7850--7851


Underfull \hbox (badness 10000) in paragraph at lines 7860--7861
[]\OT1/cmtt/m/n/10.95 GtOptionParser* gt[]option[]parser[]new([]const char *syn
opsis, const char

Underfull \hbox (badness 10000) in paragraph at lines 7860--7861


Underfull \hbox (badness 10000) in paragraph at lines 7874--7875
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]add[]option([]GtOptionParser *op
tion[]parser, GtOption

Underfull \hbox (badness 10000) in paragraph at lines 7874--7875


Underfull \hbox (badness 10000) in paragraph at lines 7884--7885
[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]parser[]get[]option([]GtOptionParse
r *option[]parser, const

Underfull \hbox (badness 10000) in paragraph at lines 7884--7885


Underfull \hbox (badness 1496) in paragraph at lines 7888--7890
[]\OT1/ptm/m/n/10.95 Return the \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.95
 ob-ject if an op-tion named \OT1/cmtt/m/n/10.95 option[]string \OT1/ptm/m/n/10
.95 is present in

Underfull \hbox (badness 10000) in paragraph at lines 7894--7895


Underfull \hbox (badness 10000) in paragraph at lines 7906--7907
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]comment[]func([]GtOptionPar
ser *option[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 7906--7907


Underfull \hbox (badness 10000) in paragraph at lines 7917--7918
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]version[]func([]GtOptionPar
ser *option[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 7917--7918


Underfull \hbox (badness 10000) in paragraph at lines 7929--7930
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]mail[]address([]GtOptionPar
ser*, const char

Underfull \hbox (badness 10000) in paragraph at lines 7929--7930


Underfull \hbox (badness 10000) in paragraph at lines 7943--7944
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]register[]hook([]GtOptionParser 
*option[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 7943--7944


Underfull \hbox (badness 10000) in paragraph at lines 7957--7958
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]min[]args([]GtOptionParser 
*option[]parser, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 7957--7958


Underfull \hbox (badness 10000) in paragraph at lines 7968--7969
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]max[]args([]GtOptionParser 
*option[]parser, unsigned

Underfull \hbox (badness 10000) in paragraph at lines 7968--7969


Underfull \hbox (badness 10000) in paragraph at lines 7980--7981
[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]min[]max[]args([]GtOptionPa
rser *option[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 7980--7981


Underfull \hbox (badness 5446) in paragraph at lines 7984--7986
[]\OT1/ptm/m/n/10.95 The \OT1/cmtt/m/n/10.95 minimum \OT1/ptm/m/n/10.95 and \OT
1/cmtt/m/n/10.95 maximum \OT1/ptm/m/n/10.95 num-ber of ad-di-tional com-mand li
ne ar-gu-ments

Underfull \hbox (badness 10000) in paragraph at lines 7994--7995
[]\OT1/cmtt/m/n/10.95 GtOPrval gt[]option[]parser[]parse([]GtOptionParser *opti
on[]parser,

Underfull \hbox (badness 10000) in paragraph at lines 7994--7995
\OT1/cmtt/m/n/10.95 int *parsed[]args, int argc, const char **argv, GtShowVersi
onFunc

Underfull \hbox (badness 10000) in paragraph at lines 7994--7995


Underfull \hbox (badness 10000) in paragraph at lines 8007--8008


Underfull \hbox (badness 10000) in paragraph at lines 8017--8018

[107] [108]
Underfull \hbox (badness 10000) in paragraph at lines 8033--8034


Underfull \hbox (badness 10000) in paragraph at lines 8044--8045
[]\OT1/cmtt/m/n/10.95 void gt[]output[]file[]info[]register[]options([]GtOutput
FileInfo

Underfull \hbox (badness 10000) in paragraph at lines 8044--8045


Underfull \hbox (badness 10000) in paragraph at lines 8057--8058

[109]
Underfull \hbox (badness 10000) in paragraph at lines 8075--8076


Underfull \hbox (badness 10000) in paragraph at lines 8084--8085


Underfull \hbox (badness 10000) in paragraph at lines 8102--8103


Underfull \hbox (badness 10000) in paragraph at lines 8111--8112


Underfull \hbox (badness 10000) in paragraph at lines 8120--8121


Underfull \hbox (badness 10000) in paragraph at lines 8130--8131


Underfull \hbox (badness 10000) in paragraph at lines 8139--8140


Underfull \hbox (badness 10000) in paragraph at lines 8150--8151


Underfull \hbox (badness 10000) in paragraph at lines 8159--8160

[110]
Underfull \hbox (badness 10000) in paragraph at lines 8179--8180
[]\OT1/cmtt/m/n/10.95 GtRDB* gt[]rdb[]mysql[]new([]const char *server, unsigned
 int port, const char

Underfull \hbox (badness 10000) in paragraph at lines 8179--8180


Underfull \hbox (badness 10000) in paragraph at lines 8200--8201


Underfull \hbox (badness 10000) in paragraph at lines 8218--8219
[]\OT1/cmtt/m/n/10.95 int gt[]rdb[]visitor[]visit[]sqlite([]GtRDBVisitor *rdbv,
 GtRDBSqlite *rdbs,

Underfull \hbox (badness 10000) in paragraph at lines 8218--8219


Underfull \hbox (badness 10000) in paragraph at lines 8229--8230
[]\OT1/cmtt/m/n/10.95 int gt[]rdb[]visitor[]visit[]mysql([]GtRDBVisitor *rdbv, 
GtRDBMySQL *rdbm,

Underfull \hbox (badness 10000) in paragraph at lines 8229--8230


Underfull \hbox (badness 10000) in paragraph at lines 8239--8240

[111]
Underfull \hbox (badness 10000) in paragraph at lines 8255--8256


Underfull \hbox (badness 10000) in paragraph at lines 8264--8265


Underfull \hbox (badness 10000) in paragraph at lines 8273--8274


Underfull \hbox (badness 10000) in paragraph at lines 8282--8283


Underfull \hbox (badness 10000) in paragraph at lines 8291--8292


Underfull \hbox (badness 10000) in paragraph at lines 8308--8309


Underfull \hbox (badness 10000) in paragraph at lines 8321--8322
[]\OT1/cmtt/m/n/10.95 int gt[]range[]compare[]with[]delta([]const GtRange *rang
e[]a, const GtRange

Underfull \hbox (badness 10000) in paragraph at lines 8321--8322


Underfull \hbox (badness 10000) in paragraph at lines 8334--8335


Underfull \hbox (badness 10000) in paragraph at lines 8345--8346
[]\OT1/cmtt/m/n/10.95 bool gt[]range[]overlap[]delta([]const GtRange *range[]a,
 const GtRange

Underfull \hbox (badness 10000) in paragraph at lines 8345--8346


Underfull \hbox (badness 10000) in paragraph at lines 8355--8356


Underfull \hbox (badness 10000) in paragraph at lines 8364--8365


Underfull \hbox (badness 10000) in paragraph at lines 8373--8374


Underfull \hbox (badness 10000) in paragraph at lines 8382--8383


Underfull \hbox (badness 10000) in paragraph at lines 8391--8392

[112]
Overfull \hbox (37.97119pt too wide) in paragraph at lines 8401--8403
\OT1/ptm/m/n/10.95 This enum type de-fines the pos-si-ble reamodes, namely \OT1
/cmtt/m/n/10.95 GT[]READMODE[]FORWARD\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/n/10.95 G
T[]READMODE[]REVERSE\OT1/ptm/m/n/10.95 ,

Underfull \hbox (badness 10000) in paragraph at lines 8408--8409


Underfull \hbox (badness 10000) in paragraph at lines 8417--8418


Underfull \hbox (badness 2626) in paragraph at lines 8421--8424
[]\OT1/ptm/m/n/10.95 Returns the \OT1/cmtt/m/n/10.95 GtReadmode \OT1/ptm/m/n/10
.95 for the de-scrip-tion \OT1/cmtt/m/n/10.95 string\OT1/ptm/m/n/10.95 , which 
must be one of

Underfull \hbox (badness 10000) in paragraph at lines 8428--8429


Underfull \hbox (badness 10000) in paragraph at lines 8450--8451
[]\OT1/cmtt/m/n/10.95 GtRecMap* gt[]rec[]map[]new([]double nw[]x, double nw[]y,
 double se[]x, double

Underfull \hbox (badness 10000) in paragraph at lines 8450--8451


Underfull \hbox (badness 10000) in paragraph at lines 8459--8460


Underfull \hbox (badness 10000) in paragraph at lines 8468--8469


Underfull \hbox (badness 10000) in paragraph at lines 8477--8478


Underfull \hbox (badness 10000) in paragraph at lines 8486--8487


Underfull \hbox (badness 10000) in paragraph at lines 8495--8496


Underfull \hbox (badness 10000) in paragraph at lines 8504--8505


Underfull \hbox (badness 10000) in paragraph at lines 8513--8514


Underfull \hbox (badness 10000) in paragraph at lines 8523--8524

[113]
Underfull \hbox (badness 10000) in paragraph at lines 8541--8542
[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]mapping([]GtSt
r *mapping[]filename,

Underfull \hbox (badness 10000) in paragraph at lines 8541--8542


Underfull \hbox (badness 2735) in paragraph at lines 8545--8548
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtRegionMapping \OT1/ptm/
m/n/10.95 ob-ject for the map-ping file with the given

Underfull \hbox (badness 10000) in paragraph at lines 8553--8554
[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]seqfiles([]GtS
trArray

Underfull \hbox (badness 10000) in paragraph at lines 8553--8554


Underfull \hbox (badness 10000) in paragraph at lines 8557--8563
[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtRegionMapping \OT1/ptm/
m/n/10.95 ob-ject for the se-quence files given in

Underfull \hbox (badness 1189) in paragraph at lines 8557--8563
\OT1/cmtt/m/n/10.95 sequence[]filenames\OT1/ptm/m/n/10.95 . If \OT1/cmtt/m/n/10
.95 matchdesc \OT1/ptm/m/n/10.95 is \OT1/cmtt/m/n/10.95 true\OT1/ptm/m/n/10.95 
, the se-quence de-scrip-tions from

Underfull \hbox (badness 10000) in paragraph at lines 8568--8569
[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]encseq([]GtEnc
seq *encseq, bool

Underfull \hbox (badness 10000) in paragraph at lines 8568--8569


Underfull \hbox (badness 10000) in paragraph at lines 8579--8580
[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]rawseq([]const
 char *rawseq, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 8579--8580


Underfull \hbox (badness 10000) in paragraph at lines 8589--8590


Underfull \hbox (badness 10000) in paragraph at lines 8602--8603
[]\OT1/cmtt/m/n/10.95 int gt[]region[]mapping[]get[]sequence([]GtRegionMapping 
*region[]mapping, char

Underfull \hbox (badness 10000) in paragraph at lines 8602--8603


Underfull \hbox (badness 10000) in paragraph at lines 8618--8619
[]\OT1/cmtt/m/n/10.95 int gt[]region[]mapping[]get[]sequence[]length([]GtRegion
Mapping *region[]mapping,

Underfull \hbox (badness 10000) in paragraph at lines 8618--8619


Underfull \hbox (badness 10000) in paragraph at lines 8633--8634
[]\OT1/cmtt/m/n/10.95 int gt[]region[]mapping[]get[]description([]GtRegionMappi
ng *region[]mapping,

Underfull \hbox (badness 10000) in paragraph at lines 8633--8634


Underfull \hbox (badness 10000) in paragraph at lines 8649--8650
[]\OT1/cmtt/m/n/10.95 const char* gt[]region[]mapping[]get[]md5[]fingerprint([]
GtRegionMapping

Underfull \hbox (badness 10000) in paragraph at lines 8649--8650
\OT1/cmtt/m/n/10.95 *region[]mapping, GtStr *seqid, const GtRange *range, GtUwo
rd *offset,

Underfull \hbox (badness 10000) in paragraph at lines 8649--8650


Underfull \hbox (badness 10000) in paragraph at lines 8661--8662

[114] [115]
Overfull \hbox (1.85855pt too wide) in paragraph at lines 8671--8673
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtGenomeNode \OT1/ptm/m/n
/10.95 in-ter-face. Re-gion nodes cor-re-spond to the \OT1/cmtt/m/n/10.95 ##seq
uence-region

Underfull \hbox (badness 10000) in paragraph at lines 8679--8680
[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]region[]node[]new([]GtStr *seqid, GtUwo
rd start, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 8679--8680


Underfull \hbox (badness 10000) in paragraph at lines 8692--8693


Underfull \hbox (badness 10000) in paragraph at lines 8704--8705


Underfull \hbox (badness 10000) in paragraph at lines 8725--8726
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]script[]wrapper[]stream[]new([]GtScript
WrapperStreamNextFunc,

Underfull \hbox (badness 10000) in paragraph at lines 8725--8726

[116]
Overfull \hbox (52.44699pt too wide) in paragraph at lines 8747--8748
[]\OT1/cmtt/m/n/10.95 GtNodeVisitor* gt[]script[]wrapper[]visitor[]new([]GtScri
ptWrapperVisitorCommentNodeFunc,

Overfull \hbox (18.64471pt too wide) in paragraph at lines 8747--8748
\OT1/cmtt/m/n/10.95 GtScriptWrapperVisitorFeatureNodeFunc, GtScriptWrapperVisit
orRegionNodeFunc,

Overfull \hbox (12.89603pt too wide) in paragraph at lines 8747--8748
\OT1/cmtt/m/n/10.95 GtScriptWrapperVisitorSequenceNodeFunc, GtScriptWrapperVisi
torMetaNodeFunc,

Underfull \hbox (badness 10000) in paragraph at lines 8747--8748


Underfull \hbox (badness 10000) in paragraph at lines 8780--8781
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]select[]stream[]new([]GtNodeStream *in[
]stream, GtStr

Underfull \hbox (badness 10000) in paragraph at lines 8780--8781
\OT1/cmtt/m/n/10.95 *seqid, GtStr *source, const GtRange *contain[]range, const
 GtRange

Underfull \hbox (badness 10000) in paragraph at lines 8780--8781
\OT1/cmtt/m/n/10.95 *overlap[]range, GtStrand strand, GtStrand targetstrand, bo
ol has[]CDS,

Underfull \hbox (badness 10000) in paragraph at lines 8780--8781
\OT1/cmtt/m/n/10.95 GtUword max[]gene[]length, GtUword max[]gene[]num, double m
in[]gene[]score,

Underfull \hbox (badness 10000) in paragraph at lines 8780--8781
\OT1/cmtt/m/n/10.95 double max[]gene[]score, double min[]average[]splice[]site[
]prob, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 8780--8781


Underfull \hbox (badness 10000) in paragraph at lines 8823--8824
[]\OT1/cmtt/m/n/10.95 void gt[]select[]stream[]set[]drophandler([]GtSelectStrea
m *sstr,

Underfull \hbox (badness 10000) in paragraph at lines 8823--8824

[117]
Underfull \hbox (badness 10000) in paragraph at lines 8837--8838
[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]set[]symbolmap([]GtSeqIterator*, 
const GtUchar

Underfull \hbox (badness 10000) in paragraph at lines 8837--8838


Underfull \hbox (badness 10000) in paragraph at lines 8848--8849


Underfull \hbox (badness 10000) in paragraph at lines 8862--8863
[]\OT1/cmtt/m/n/10.95 int gt[]seq[]iterator[]next([]GtSeqIterator *seqit, const
 GtUchar **sequence,

Underfull \hbox (badness 10000) in paragraph at lines 8862--8863


Underfull \hbox (badness 10000) in paragraph at lines 8876--8877
[]\OT1/cmtt/m/n/10.95 const GtUint64* gt[]seq[]iterator[]getcurrentcounter([]Gt
SeqIterator*,

Underfull \hbox (badness 10000) in paragraph at lines 8876--8877


Underfull \hbox (badness 10000) in paragraph at lines 8885--8886


Underfull \hbox (badness 10000) in paragraph at lines 8895--8896
[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]set[]quality[]buffer([]GtSeqItera
tor *seqit, const

Underfull \hbox (badness 10000) in paragraph at lines 8895--8896


Underfull \hbox (badness 10000) in paragraph at lines 8906--8907

[118]
Underfull \hbox (badness 10000) in paragraph at lines 8918--8919
[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]fastq[]new([]const GtSt
rArray *filenametab,

Underfull \hbox (badness 10000) in paragraph at lines 8918--8919


Underfull \hbox (badness 10000) in paragraph at lines 8929--8930
[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]fastq[]new[]colorspace(
[]const GtStrArray

Underfull \hbox (badness 10000) in paragraph at lines 8929--8930


Underfull \hbox (badness 10000) in paragraph at lines 8939--8940


Overfull \hbox (28.76239pt too wide) in paragraph at lines 8949--8950
[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]fastq[]relax[]check[]of[]quality[
]description([]GtSeqIteratorFastQ

Underfull \hbox (badness 10000) in paragraph at lines 8949--8950

[119]
Underfull \hbox (badness 10000) in paragraph at lines 8963--8964
[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]sequence[]buffer[]new([
]const GtStrArray

Underfull \hbox (badness 10000) in paragraph at lines 8963--8964


Underfull \hbox (badness 10000) in paragraph at lines 8984--8985
[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]sequence[]node[]new([]const char *descr
iption, GtStr

Underfull \hbox (badness 10000) in paragraph at lines 8984--8985


Underfull \hbox (badness 2698) in paragraph at lines 8988--8990
[]\OT1/ptm/m/n/10.95 Create a new \OT1/cmtt/m/n/10.95 GtSequenceNode* \OT1/ptm/
m/n/10.95 rep-re-sent-ing a FASTA en-try with the given

Underfull \hbox (badness 10000) in paragraph at lines 8996--8997
[]\OT1/cmtt/m/n/10.95 const char* gt[]sequence[]node[]get[]description([]const 
GtSequenceNode

Underfull \hbox (badness 10000) in paragraph at lines 8996--8997


Underfull \hbox (badness 10000) in paragraph at lines 9006--9007
[]\OT1/cmtt/m/n/10.95 const char* gt[]sequence[]node[]get[]sequence([]const GtS
equenceNode

Underfull \hbox (badness 10000) in paragraph at lines 9006--9007


Underfull \hbox (badness 10000) in paragraph at lines 9017--9018
[]\OT1/cmtt/m/n/10.95 GtUword gt[]sequence[]node[]get[]sequence[]length([]const
 GtSequenceNode

Underfull \hbox (badness 10000) in paragraph at lines 9017--9018


Underfull \hbox (badness 10000) in paragraph at lines 9026--9027


Underfull \hbox (badness 10000) in paragraph at lines 9038--9039

[120]
Overfull \hbox (58.46886pt too wide) in paragraph at lines 9049--9052
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeVisitor \OT1/ptm/m/
n/10.95 in-ter-face. Used with the \OT1/cmtt/m/n/10.95 GtVisitorStream \OT1/ptm
/m/n/10.95 class, a \OT1/cmtt/m/n/10.95 GtSetSourceVisitor

Underfull \hbox (badness 10000) in paragraph at lines 9057--9058


Underfull \hbox (badness 10000) in paragraph at lines 9075--9076


Underfull \hbox (badness 10000) in paragraph at lines 9094--9095


Underfull \hbox (badness 10000) in paragraph at lines 9104--9105
[]\OT1/cmtt/m/n/10.95 void gt[]splitter[]split([]GtSplitter *splitter, char *st
ring, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 9104--9105


Underfull \hbox (badness 10000) in paragraph at lines 9115--9116
[]\OT1/cmtt/m/n/10.95 void gt[]splitter[]split[]non[]empty([]GtSplitter *s, cha
r *string, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 9115--9116


Underfull \hbox (badness 10000) in paragraph at lines 9126--9127


Underfull \hbox (badness 10000) in paragraph at lines 9136--9137


Underfull \hbox (badness 10000) in paragraph at lines 9145--9146


Underfull \hbox (badness 10000) in paragraph at lines 9154--9155


Underfull \hbox (badness 10000) in paragraph at lines 9163--9164

[121]
Overfull \hbox (31.52028pt too wide) in paragraph at lines 9173--9176
\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. A \OT1/cmtt/m/n/10.95 GtStatStream \OT1/ptm/m/n/10.95 gath-
ers statis-tics about the \OT1/cmtt/m/n/10.95 GtGenomeNode

Underfull \hbox (badness 10000) in paragraph at lines 9188--9189
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]stat[]stream[]new([]GtNodeStream *in[]s
tream, bool

Underfull \hbox (badness 10000) in paragraph at lines 9188--9189
\OT1/cmtt/m/n/10.95 gene[]length[]distribution, bool gene[]score[]distribution,
 bool

Underfull \hbox (badness 10000) in paragraph at lines 9188--9189
\OT1/cmtt/m/n/10.95 exon[]length[]distribution, bool exon[]number[]distribution
, bool

Underfull \hbox (badness 10000) in paragraph at lines 9188--9189
\OT1/cmtt/m/n/10.95 intron[]length[]distribution, bool cds[]length[]distributio
n, bool

Underfull \hbox (badness 10000) in paragraph at lines 9188--9189


Underfull \hbox (badness 3668) in paragraph at lines 9192--9200
\OT1/ptm/m/n/10.95 ment equals \OT1/cmtt/m/n/10.95 true\OT1/ptm/m/n/10.95 : \OT
1/cmtt/m/n/10.95 gene[]length[]distribution\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/n/1
0.95 gene[]score[]distribution\OT1/ptm/m/n/10.95 ,

Underfull \hbox (badness 10000) in paragraph at lines 9192--9200
\OT1/cmtt/m/n/10.95 exon[]length[]distribution\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/
n/10.95 exon[]number[]distribution\OT1/ptm/m/n/10.95 ,

Underfull \hbox (badness 10000) in paragraph at lines 9205--9206

[122]
Underfull \hbox (badness 10000) in paragraph at lines 9221--9222


Underfull \hbox (badness 10000) in paragraph at lines 9230--9231


Underfull \hbox (badness 10000) in paragraph at lines 9239--9240


Underfull \hbox (badness 10000) in paragraph at lines 9248--9249


Underfull \hbox (badness 10000) in paragraph at lines 9258--9259


Underfull \hbox (badness 10000) in paragraph at lines 9268--9269


Underfull \hbox (badness 10000) in paragraph at lines 9277--9278


Underfull \hbox (badness 10000) in paragraph at lines 9286--9287


Underfull \hbox (badness 10000) in paragraph at lines 9295--9296


Underfull \hbox (badness 10000) in paragraph at lines 9305--9306


Underfull \hbox (badness 10000) in paragraph at lines 9314--9315


Underfull \hbox (badness 10000) in paragraph at lines 9323--9324


Underfull \hbox (badness 10000) in paragraph at lines 9333--9334


Underfull \hbox (badness 10000) in paragraph at lines 9342--9343


Underfull \hbox (badness 10000) in paragraph at lines 9351--9352


Underfull \hbox (badness 10000) in paragraph at lines 9360--9361


Underfull \hbox (badness 5667) in paragraph at lines 9364--9366
[]\OT1/ptm/m/n/10.95 Set length of \OT1/cmtt/m/n/10.95 str \OT1/ptm/m/n/10.95 t
o \OT1/cmtt/m/n/10.95 length\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 length \OT
1/ptm/m/n/10.95 must be smaller or equal than

Underfull \hbox (badness 10000) in paragraph at lines 9370--9371


Underfull \hbox (badness 10000) in paragraph at lines 9379--9380


Underfull \hbox (badness 10000) in paragraph at lines 9388--9389


Underfull \hbox (badness 10000) in paragraph at lines 9397--9398

[123]
Underfull \hbox (badness 10000) in paragraph at lines 9414--9415


Underfull \hbox (badness 10000) in paragraph at lines 9423--9424


Underfull \hbox (badness 10000) in paragraph at lines 9432--9433


Underfull \hbox (badness 10000) in paragraph at lines 9442--9443
[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]add[]cstr[]nt([]GtStrArray *str[]arr
ay, const char *cstr,

Underfull \hbox (badness 10000) in paragraph at lines 9442--9443


Underfull \hbox (badness 10000) in paragraph at lines 9452--9453


Underfull \hbox (badness 10000) in paragraph at lines 9462--9463


Underfull \hbox (badness 10000) in paragraph at lines 9473--9474
[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]set[]cstr([]GtStrArray *str[]array, 
GtUword strnum, const

Underfull \hbox (badness 10000) in paragraph at lines 9473--9474


Underfull \hbox (badness 10000) in paragraph at lines 9483--9484
[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]set([]GtStrArray *str[]array, GtUwor
d strnum, const GtStr

Underfull \hbox (badness 10000) in paragraph at lines 9483--9484


Underfull \hbox (badness 10000) in paragraph at lines 9492--9493


Underfull \hbox (badness 2564) in paragraph at lines 9496--9498
[]\OT1/ptm/m/n/10.95 Set the size of \OT1/cmtt/m/n/10.95 str[]array \OT1/ptm/m/
n/10.95 to \OT1/cmtt/m/n/10.95 size\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 siz
e \OT1/ptm/m/n/10.95 must be smaller or equal than

Underfull \hbox (badness 10000) in paragraph at lines 9502--9503


Underfull \hbox (badness 10000) in paragraph at lines 9511--9512


Underfull \hbox (badness 10000) in paragraph at lines 9520--9521

[124]
Overfull \hbox (21.75429pt too wide) in paragraph at lines 9530--9533
\OT1/ptm/m/n/10.95 This enum type de-fines the pos-si-ble strands. The fol-low-
ing strands are de-fined: \OT1/cmtt/m/n/10.95 GT[]STRAND[]FORWARD\OT1/ptm/m/n/1
0.95 ,

Underfull \hbox (badness 10000) in paragraph at lines 9538--9539


Underfull \hbox (badness 10000) in paragraph at lines 9547--9548


Underfull \hbox (badness 10000) in paragraph at lines 9551--9553
[]\OT1/ptm/m/n/10.95 Map \OT1/cmtt/m/n/10.95 strand[]char \OT1/ptm/m/n/10.95 to
 the cor-re-spond-ing strand enum type. Re-turns

Underfull \hbox (badness 10000) in paragraph at lines 9568--9569


Underfull \hbox (badness 10000) in paragraph at lines 9577--9578


Underfull \hbox (badness 10000) in paragraph at lines 9586--9587


Underfull \hbox (badness 10000) in paragraph at lines 9595--9596


Underfull \hbox (badness 10000) in paragraph at lines 9604--9605


Underfull \hbox (badness 10000) in paragraph at lines 9613--9614


Underfull \hbox (badness 10000) in paragraph at lines 9622--9623


Underfull \hbox (badness 10000) in paragraph at lines 9632--9633


Underfull \hbox (badness 10000) in paragraph at lines 9642--9643


Underfull \hbox (badness 10000) in paragraph at lines 9652--9653


Underfull \hbox (badness 10000) in paragraph at lines 9662--9663
[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]color([]GtStyle*, const char *sectio
n, const char *key,

Underfull \hbox (badness 10000) in paragraph at lines 9662--9663


Underfull \hbox (badness 10000) in paragraph at lines 9674--9675
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]color([]const GtStyle 
*style, const char

Underfull \hbox (badness 10000) in paragraph at lines 9674--9675
\OT1/cmtt/m/n/10.95 *section, const char *key, GtColor *result, GtFeatureNode *
fn, GtError

Underfull \hbox (badness 10000) in paragraph at lines 9674--9675


Underfull \hbox (badness 10000) in paragraph at lines 9700--9701
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]color[]with[]track([]c
onst GtStyle *style,

Underfull \hbox (badness 10000) in paragraph at lines 9700--9701
\OT1/cmtt/m/n/10.95 const char *section, const char *key, GtColor *result, GtFe
atureNode

Underfull \hbox (badness 10000) in paragraph at lines 9700--9701


Underfull \hbox (badness 10000) in paragraph at lines 9711--9712
[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]str([]GtStyle*, const char *section,
 const char *key,

Underfull \hbox (badness 10000) in paragraph at lines 9711--9712


Underfull \hbox (badness 10000) in paragraph at lines 9722--9723
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]str([]const GtStyle *s
tyle, const char

Underfull \hbox (badness 10000) in paragraph at lines 9722--9723
\OT1/cmtt/m/n/10.95 *section, const char *key, GtStr *result, GtFeatureNode *fn
, GtError

Underfull \hbox (badness 10000) in paragraph at lines 9722--9723


Underfull \hbox (badness 10000) in paragraph at lines 9747--9748
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]str[]with[]track([]con
st GtStyle *style, const

Underfull \hbox (badness 10000) in paragraph at lines 9747--9748
\OT1/cmtt/m/n/10.95 char *section, const char *key, GtStr *result, GtFeatureNod
e *fn, const

Underfull \hbox (badness 10000) in paragraph at lines 9747--9748


Underfull \hbox (badness 10000) in paragraph at lines 9758--9759
[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]num([]GtStyle*, const char *section,
 const char *key,

Underfull \hbox (badness 10000) in paragraph at lines 9758--9759


Underfull \hbox (badness 10000) in paragraph at lines 9769--9770
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]num([]const GtStyle *s
tyle, const char

Underfull \hbox (badness 10000) in paragraph at lines 9769--9770
\OT1/cmtt/m/n/10.95 *section, const char *key, double *result, GtFeatureNode *f
n, GtError

Underfull \hbox (badness 10000) in paragraph at lines 9769--9770


Underfull \hbox (badness 10000) in paragraph at lines 9794--9795
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]num[]with[]track([]con
st GtStyle *style, const

Underfull \hbox (badness 10000) in paragraph at lines 9794--9795
\OT1/cmtt/m/n/10.95 char *section, const char *key, double *result, GtFeatureNo
de *fn, const

Underfull \hbox (badness 10000) in paragraph at lines 9794--9795


Underfull \hbox (badness 10000) in paragraph at lines 9805--9806
[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]bool([]GtStyle*, const char *section
, const char *key,

Underfull \hbox (badness 10000) in paragraph at lines 9805--9806


Underfull \hbox (badness 10000) in paragraph at lines 9816--9817
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]bool([]const GtStyle *
style, const char

Underfull \hbox (badness 10000) in paragraph at lines 9816--9817
\OT1/cmtt/m/n/10.95 *section, const char *key, bool *result, GtFeatureNode *fn,
 GtError

Underfull \hbox (badness 10000) in paragraph at lines 9816--9817


Underfull \hbox (badness 10000) in paragraph at lines 9841--9842
[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]bool[]with[]track([]co
nst GtStyle *style,

Underfull \hbox (badness 10000) in paragraph at lines 9841--9842
\OT1/cmtt/m/n/10.95 const char *section, const char *key, bool *result, GtFeatu
reNode *fn,

Underfull \hbox (badness 10000) in paragraph at lines 9841--9842


Underfull \hbox (badness 10000) in paragraph at lines 9852--9853


Underfull \hbox (badness 10000) in paragraph at lines 9861--9862

[125] [126] [127] [128]
Underfull \hbox (badness 10000) in paragraph at lines 9885--9886
[]\OT1/cmtt/m/n/10.95 void GtTagValueMapIteratorFunc([]const char *tag, const c
har *value, void

Underfull \hbox (badness 10000) in paragraph at lines 9885--9886


Underfull \hbox (badness 10000) in paragraph at lines 9895--9896


Underfull \hbox (badness 10000) in paragraph at lines 9907--9908
[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]add([]GtTagValueMap *tag[]value
[]map, const char *tag,

Underfull \hbox (badness 10000) in paragraph at lines 9907--9908


Underfull \hbox (badness 10000) in paragraph at lines 9918--9919
[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]set([]GtTagValueMap *tag[]value
[]map, const char *tag,

Underfull \hbox (badness 10000) in paragraph at lines 9918--9919


Underfull \hbox (badness 10000) in paragraph at lines 9928--9929
[]\OT1/cmtt/m/n/10.95 const char* gt[]tag[]value[]map[]get([]const GtTagValueMa
p tag[]value[]map, const

Underfull \hbox (badness 10000) in paragraph at lines 9928--9929


Underfull \hbox (badness 10000) in paragraph at lines 9938--9939


Underfull \hbox (badness 10000) in paragraph at lines 9948--9949
[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]remove([]GtTagValueMap *tag[]va
lue[]map, const char

Underfull \hbox (badness 10000) in paragraph at lines 9948--9949


Underfull \hbox (badness 10000) in paragraph at lines 9961--9962
[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]foreach([]const GtTagValueMap t
ag[]value[]map,

Underfull \hbox (badness 10000) in paragraph at lines 9961--9962


Underfull \hbox (badness 10000) in paragraph at lines 9971--9972


Underfull \hbox (badness 10000) in paragraph at lines 9980--9981

[129]
Overfull \hbox (6.45749pt too wide) in paragraph at lines 9999--10000
[]\OT1/cmtt/m/n/10.95 GtTextWidthCalculator* gt[]text[]width[]calculator[]ref([
]GtTextWidthCalculator*[]) 

Underfull \hbox (badness 10000) in paragraph at lines 9999--10000


Underfull \hbox (badness 10000) in paragraph at lines 10010--10011
[]\OT1/cmtt/m/n/10.95 double gt[]text[]width[]calculator[]get[]text[]width([]Gt
TextWidthCalculator*,

Underfull \hbox (badness 10000) in paragraph at lines 10010--10011


Underfull \hbox (badness 10000) in paragraph at lines 10021--10022


Overfull \hbox (83.5338pt too wide) in paragraph at lines 10031--10037
\OT1/cmtt/m/n/10.95 cairo[]t \OT1/ptm/m/n/10.95 and which should be used later 
via a \OT1/cmtt/m/n/10.95 GtCanvasCairoContext\OT1/ptm/m/n/10.95 , cre-ate a \O
T1/cmtt/m/n/10.95 GtTextWidthCalculatorCairo

Underfull \hbox (badness 10000) in paragraph at lines 10043--10044
[]\OT1/cmtt/m/n/10.95 GtTextWidthCalculator* gt[]text[]width[]calculator[]cairo
[]new([]cairo[]t*,

Underfull \hbox (badness 10000) in paragraph at lines 10043--10044


Underfull \hbox (badness 10000) in paragraph at lines 10062--10063


Underfull \hbox (badness 10000) in paragraph at lines 10071--10072


Underfull \hbox (badness 10000) in paragraph at lines 10082--10083


Underfull \hbox (badness 10000) in paragraph at lines 10091--10092

[130]
Underfull \hbox (badness 10000) in paragraph at lines 10109--10110


Underfull \hbox (badness 10000) in paragraph at lines 10118--10119


Underfull \hbox (badness 10000) in paragraph at lines 10127--10128


Underfull \hbox (badness 10000) in paragraph at lines 10136--10137


Underfull \hbox (badness 10000) in paragraph at lines 10145--10146


Underfull \hbox (badness 3168) in paragraph at lines 10149--10153
[]\OT1/ptm/m/n/10.95 Output the cur-rent state of \OT1/cmtt/m/n/10.95 timer \OT
1/ptm/m/n/10.95 in the for-mat ""GT[]WD".pointer \OT1/cmtt/m/n/10.95 fp \OT1/pt
m/m/n/10.95 (see

Underfull \hbox (badness 10000) in paragraph at lines 10157--10158


Underfull \hbox (badness 10000) in paragraph at lines 10169--10170


Underfull \hbox (badness 10000) in paragraph at lines 10178--10179


Underfull \hbox (badness 10000) in paragraph at lines 10182--10186
[]\OT1/ptm/m/n/10.95 Output the cur-rent state of \OT1/cmtt/m/n/10.95 timer \OT
1/ptm/m/n/10.95 on \OT1/cmtt/m/n/10.95 fp \OT1/ptm/m/n/10.95 since the last cal
l of

Underfull \hbox (badness 1292) in paragraph at lines 10182--10186
\OT1/cmtt/m/n/10.95 gt[]timer[]show[]progress() \OT1/ptm/m/n/10.95 or the last 
start of \OT1/cmtt/m/n/10.95 timer\OT1/ptm/m/n/10.95 , along with the cur-rent

Underfull \hbox (badness 10000) in paragraph at lines 10191--10192
[]\OT1/cmtt/m/n/10.95 void gt[]timer[]show[]progress[]formatted([]GtTimer *time
r, FILE *fp, const

Underfull \hbox (badness 10000) in paragraph at lines 10191--10192


Underfull \hbox (badness 10000) in paragraph at lines 10202--10203
[]\OT1/cmtt/m/n/10.95 void gt[]timer[]show[]progress[]va([]GtTimer *timer, FILE
 *fp, const char

Underfull \hbox (badness 10000) in paragraph at lines 10202--10203


Underfull \hbox (badness 10000) in paragraph at lines 10212--10213


Underfull \hbox (badness 10000) in paragraph at lines 10221--10222


Underfull \hbox (badness 10000) in paragraph at lines 10231--10232


Underfull \hbox (badness 10000) in paragraph at lines 10240--10241

[131]
Underfull \hbox (badness 10000) in paragraph at lines 10257--10258


Underfull \hbox (badness 10000) in paragraph at lines 10267--10268


Underfull \hbox (badness 10000) in paragraph at lines 10277--10278


Underfull \hbox (badness 10000) in paragraph at lines 10289--10290
[]\OT1/cmtt/m/n/10.95 int GtToolArgumentsCheck([]int rest[]argc, void *tool[]ar
guments, GtError

Underfull \hbox (badness 10000) in paragraph at lines 10289--10290


Underfull \hbox (badness 10000) in paragraph at lines 10303--10304
[]\OT1/cmtt/m/n/10.95 int GtToolRunner([]int argc, const char **argv, int parse
d[]args, void

Underfull \hbox (badness 10000) in paragraph at lines 10303--10304


Underfull \hbox (badness 10000) in paragraph at lines 10319--10320


Underfull \hbox (badness 10000) in paragraph at lines 10332--10333
[]\OT1/cmtt/m/n/10.95 GtTool* gt[]tool[]new([]GtToolArgumentsNew tool[]argument
s[]new,

Underfull \hbox (badness 10000) in paragraph at lines 10332--10333
\OT1/cmtt/m/n/10.95 GtToolArgumentsDelete tool[]arguments[]delete, GtToolOption
ParserNew

Underfull \hbox (badness 10000) in paragraph at lines 10332--10333
\OT1/cmtt/m/n/10.95 tool[]option[]parser[]new, GtToolArgumentsCheck tool[]argum
ents[]check,

Underfull \hbox (badness 10000) in paragraph at lines 10332--10333


Underfull \hbox (badness 10000) in paragraph at lines 10348--10349


Underfull \hbox (badness 10000) in paragraph at lines 10367--10368

[132]
Underfull \hbox (badness 10000) in paragraph at lines 10384--10385


Underfull \hbox (badness 10000) in paragraph at lines 10394--10395
[]\OT1/cmtt/m/n/10.95 void gt[]toolbox[]add[]tool([]GtToolbox *toolbox, const c
har *toolname, GtTool

Underfull \hbox (badness 10000) in paragraph at lines 10394--10395


Underfull \hbox (badness 10000) in paragraph at lines 10404--10405
[]\OT1/cmtt/m/n/10.95 void gt[]toolbox[]add[]hidden[]tool([]GtToolbox *toolbox,
 const char *toolname,

Underfull \hbox (badness 10000) in paragraph at lines 10404--10405


Underfull \hbox (badness 10000) in paragraph at lines 10414--10415


Underfull \hbox (badness 10000) in paragraph at lines 10424--10425


Underfull \hbox (badness 10000) in paragraph at lines 10434--10435

[133]
Underfull \hbox (badness 10000) in paragraph at lines 10445--10446


Underfull \hbox (badness 2035) in paragraph at lines 10449--10453
[]\OT1/ptm/m/n/10.95 Returns a \OT1/cmtt/m/n/10.95 GtStrArray \OT1/ptm/m/n/10.9
5 of trans-la-tion scheme de-scrip-tions, each of the for-mat

Underfull \hbox (badness 10000) in paragraph at lines 10457--10458


Underfull \hbox (badness 10000) in paragraph at lines 10470--10471


Underfull \hbox (badness 10000) in paragraph at lines 10479--10480


Underfull \hbox (badness 10000) in paragraph at lines 10490--10491
[]\OT1/cmtt/m/n/10.95 int gt[]trans[]table[]translate[]codon([]const GtTransTab
le *tt, char c1, char

Underfull \hbox (badness 10000) in paragraph at lines 10490--10491


Underfull \hbox (badness 10000) in paragraph at lines 10502--10503

[134]
Underfull \hbox (badness 10000) in paragraph at lines 10520--10521
[]\OT1/cmtt/m/n/10.95 GtTranslator* gt[]translator[]new[]with[]table([]GtTransT
able *tt,

Underfull \hbox (badness 10000) in paragraph at lines 10520--10521


Underfull \hbox (badness 10000) in paragraph at lines 10531--10532


Underfull \hbox (badness 10000) in paragraph at lines 10543--10544
[]\OT1/cmtt/m/n/10.95 void gt[]translator[]set[]codon[]iterator([]GtTranslator 
*translator,

Underfull \hbox (badness 10000) in paragraph at lines 10543--10544


Underfull \hbox (badness 10000) in paragraph at lines 10554--10555
[]\OT1/cmtt/m/n/10.95 void gt[]translator[]set[]translation[]table([]GtTranslat
or *translator,

Underfull \hbox (badness 10000) in paragraph at lines 10554--10555


Underfull \hbox (badness 10000) in paragraph at lines 10567--10568
[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]next([]GtTranslator *t
ranslator, char

Underfull \hbox (badness 10000) in paragraph at lines 10567--10568


Underfull \hbox (badness 10000) in paragraph at lines 10584--10585
[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]find[]startcodon([]GtT
ranslator

Underfull \hbox (badness 10000) in paragraph at lines 10584--10585


Underfull \hbox (badness 10000) in paragraph at lines 10602--10603
[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]find[]stopcodon([]GtTr
anslator *translator,

Underfull \hbox (badness 10000) in paragraph at lines 10602--10603


Underfull \hbox (badness 10000) in paragraph at lines 10621--10622
[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]find[]codon([]GtTransl
ator *translator,

Underfull \hbox (badness 10000) in paragraph at lines 10621--10622


Underfull \hbox (badness 10000) in paragraph at lines 10636--10637

[135]
Underfull \hbox (badness 10000) in paragraph at lines 10653--10654


Underfull \hbox (badness 10000) in paragraph at lines 10662--10663


Underfull \hbox (badness 10000) in paragraph at lines 10672--10673
[]\OT1/cmtt/m/n/10.95 bool gt[]type[]checker[]is[]valid([]GtTypeChecker *type[]
checker, const char

Underfull \hbox (badness 10000) in paragraph at lines 10672--10673


Underfull \hbox (badness 10000) in paragraph at lines 10684--10685
[]\OT1/cmtt/m/n/10.95 bool gt[]type[]checker[]is[]partof([]GtTypeChecker *type[
]checker, const char

Underfull \hbox (badness 10000) in paragraph at lines 10684--10685


Underfull \hbox (badness 10000) in paragraph at lines 10695--10696
[]\OT1/cmtt/m/n/10.95 bool gt[]type[]checker[]is[]a([]GtTypeChecker *type[]chec
ker, const char

Underfull \hbox (badness 10000) in paragraph at lines 10695--10696


Underfull \hbox (badness 10000) in paragraph at lines 10704--10705

[136]
Underfull \hbox (badness 10000) in paragraph at lines 10721--10722
[]\OT1/cmtt/m/n/10.95 GtTypeChecker* gt[]type[]checker[]obo[]new([]const char *
obo[]file[]path, GtError

Underfull \hbox (badness 10000) in paragraph at lines 10721--10722


Underfull \hbox (badness 10000) in paragraph at lines 10740--10741


Underfull \hbox (badness 10000) in paragraph at lines 10764--10765
[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]visitor[]stream[]new([]GtNodeStream *in
[]stream,

Underfull \hbox (badness 10000) in paragraph at lines 10764--10765

[137]
Underfull \hbox (badness 10000) in paragraph at lines 10783--10784


Underfull \hbox (badness 10000) in paragraph at lines 10793--10794


Underfull \hbox (badness 10000) in paragraph at lines 10803--10804
[]\OT1/cmtt/m/n/10.95 bool gt[]xrf[]checker[]is[]valid([]GtXRFChecker *xrf[]che
cker, const char *value,

Underfull \hbox (badness 10000) in paragraph at lines 10803--10804


Underfull \hbox (badness 10000) in paragraph at lines 10814--10815


Underfull \hbox (badness 10000) in paragraph at lines 10825--10826


Underfull \hbox (badness 10000) in paragraph at lines 10837--10838


Underfull \hbox (badness 10000) in paragraph at lines 10850--10851


Underfull \hbox (badness 10000) in paragraph at lines 10859--10860


Underfull \hbox (badness 10000) in paragraph at lines 10871--10872

[138]
Underfull \hbox (badness 10000) in paragraph at lines 10886--10887
[]\OT1/cmtt/m/n/10.95 void* gt[]bsearch[]data([]const void *key, const void *ba
se, size[]t nmemb,

Underfull \hbox (badness 10000) in paragraph at lines 10886--10887


Underfull \hbox (badness 10000) in paragraph at lines 10897--10898
[]\OT1/cmtt/m/n/10.95 void gt[]bsearch[]all([]GtArray *members, const void *key
, const void *base,

Underfull \hbox (badness 10000) in paragraph at lines 10897--10898


Underfull \hbox (badness 10000) in paragraph at lines 10910--10911
[]\OT1/cmtt/m/n/10.95 void gt[]bsearch[]all[]mark([]GtArray *members, const voi
d *key, const

Underfull \hbox (badness 10000) in paragraph at lines 10910--10911
\OT1/cmtt/m/n/10.95 void *base, size[]t nmemb, size[]t size, GtCompareWithData,
 void *data,

Underfull \hbox (badness 10000) in paragraph at lines 10910--10911


Underfull \hbox (badness 10000) in paragraph at lines 10923--10924


Underfull \hbox (badness 10000) in paragraph at lines 10935--10936


Underfull \hbox (badness 10000) in paragraph at lines 10950--10951
[]\OT1/cmtt/m/n/10.95 void gt[]countingsort([]void *out, const void *in, size[]
t elem[]size, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 10950--10951


Underfull \hbox (badness 10000) in paragraph at lines 10966--10967
[]\OT1/cmtt/m/n/10.95 GtUword gt[]countingsort[]get[]max([]const void *in, size
[]t elem[]size, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 10966--10967

[139]
Underfull \hbox (badness 10000) in paragraph at lines 10977--10978


Underfull \hbox (badness 10000) in paragraph at lines 10987--10988


Underfull \hbox (badness 10000) in paragraph at lines 10999--11000


Underfull \hbox (badness 10000) in paragraph at lines 11010--11011


Underfull \hbox (badness 10000) in paragraph at lines 11019--11020


Underfull \hbox (badness 10000) in paragraph at lines 11029--11030


Underfull \hbox (badness 10000) in paragraph at lines 11039--11040


Underfull \hbox (badness 10000) in paragraph at lines 11050--11051

[140]
Underfull \hbox (badness 10000) in paragraph at lines 11063--11064


Underfull \hbox (badness 10000) in paragraph at lines 11075--11076
[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry([]const char *description, co
nst char *sequence,

Underfull \hbox (badness 10000) in paragraph at lines 11075--11076


Underfull \hbox (badness 10000) in paragraph at lines 11087--11088
[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry[]nt([]const char *description
, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 11087--11088
\OT1/cmtt/m/n/10.95 description[]length, const char *sequence, GtUword sequence
[]length,

Underfull \hbox (badness 10000) in paragraph at lines 11087--11088


Underfull \hbox (badness 3364) in paragraph at lines 11091--11096
[]\OT1/ptm/m/n/10.95 Print a fasta en-try with op-tional \OT1/cmtt/m/n/10.95 de
scription \OT1/ptm/m/n/10.95 and manda-tory \OT1/cmtt/m/n/10.95 sequence \OT1/p
tm/m/n/10.95 to

Underfull \hbox (badness 10000) in paragraph at lines 11102--11103
[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry[]str([]const char *descriptio
n, const char

Underfull \hbox (badness 10000) in paragraph at lines 11102--11103


Underfull \hbox (badness 10000) in paragraph at lines 11117--11118
[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry[]nt[]str([]const char *descri
ption, GtUword

Underfull \hbox (badness 10000) in paragraph at lines 11117--11118
\OT1/cmtt/m/n/10.95 description[]length, const char *sequence, GtUword sequence
[]length,

Underfull \hbox (badness 10000) in paragraph at lines 11117--11118


Underfull \hbox (badness 3364) in paragraph at lines 11121--11126
[]\OT1/ptm/m/n/10.95 Print a fasta en-try with op-tional \OT1/cmtt/m/n/10.95 de
scription \OT1/ptm/m/n/10.95 and manda-tory \OT1/cmtt/m/n/10.95 sequence \OT1/p
tm/m/n/10.95 to

Underfull \hbox (badness 10000) in paragraph at lines 11132--11133


Underfull \hbox (badness 10000) in paragraph at lines 11144--11145


Underfull \hbox (badness 10000) in paragraph at lines 11153--11154


Underfull \hbox (badness 10000) in paragraph at lines 11163--11164


Underfull \hbox (badness 10000) in paragraph at lines 11173--11174


Underfull \hbox (badness 10000) in paragraph at lines 11182--11183


Underfull \hbox (badness 10000) in paragraph at lines 11191--11192


Overfull \hbox (183.05757pt too wide) in paragraph at lines 11195--11197
[]\OT1/ptm/m/n/10.95 Find \OT1/cmtt/m/n/10.95 file \OT1/ptm/m/n/10.95 in $\OML/
ztmcm/m/it/10.95 PATH; ifithasnodirname\OT1/ztmcm/m/n/10.95 ; \OML/ztmcm/m/it/1
0.95 set[]todirnameotherwise:Sets[]totheemptystringif[]couldnotbefoundin$\OT1/p
tm/m/n/10.95 PATH. 

Underfull \hbox (badness 10000) in paragraph at lines 11202--11203
[]\OT1/cmtt/m/n/10.95 int gt[]file[]find[]in[]env([]GtStr *path, const char *fi
le, const char *env,

Underfull \hbox (badness 10000) in paragraph at lines 11202--11203


Underfull \hbox (badness 10000) in paragraph at lines 11206--11210
[]\OT1/ptm/m/n/10.95 Find \OT1/cmtt/m/n/10.95 file \OT1/ptm/m/n/10.95 in the ':
'-separated di-rec-tory list (on Win-

Underfull \hbox (badness 10000) in paragraph at lines 11206--11210
\OT1/ptm/m/n/10.95 dows ';'-separated) spec-i-fied in en-vi-ron-ment vari-able

Overfull \hbox (105.20361pt too wide) in paragraph at lines 11206--11210
[]\OML/ztmcm/m/it/10.95 ; ifithasnodirname\OT1/ztmcm/m/n/10.95 ; \OML/ztmcm/m/i
t/10.95 set[]todirnameotherwise:Sets[]totheemptystringif[]couldnotbefoundin$\OT
1/cmtt/m/n/10.95 env\OT1/ptm/m/n/10.95 . 

Underfull \hbox (badness 10000) in paragraph at lines 11214--11215


Underfull \hbox (badness 10000) in paragraph at lines 11225--11226


Underfull \hbox (badness 5091) in paragraph at lines 11229--11231
[]\OT1/ptm/m/n/10.95 Return the (es-ti-mated) to-tal size of all files given in
 \OT1/cmtt/m/n/10.95 filenames\OT1/ptm/m/n/10.95 . Uses

Underfull \hbox (badness 10000) in paragraph at lines 11236--11237
[]\OT1/cmtt/m/n/10.95 int gt[]files[]guess[]if[]protein[]sequences([]const GtSt
rArray *filenames,

Underfull \hbox (badness 10000) in paragraph at lines 11236--11237


Underfull \hbox (badness 10000) in paragraph at lines 11250--11251


Overfull \hbox (344.88547pt too wide) in paragraph at lines 11254--11257
[]\OT1/ptm/m/n/10.95 Find reg-u-lar ex-e-cutable \OT1/cmtt/m/n/10.95 file \OT1/
ptm/m/n/10.95 in $\OML/ztmcm/m/it/10.95 PATH; ifithasnodirname\OT1/ztmcm/m/n/10
.95 ; \OML/ztmcm/m/it/10.95 set[]todirnameotherwise:Sets[]totheemptystringifreg
ularexecutable[]couldnotbefoundin$\OT1/ptm/m/n/10.95 PATH. 

Underfull \hbox (badness 10000) in paragraph at lines 11261--11262


Underfull \hbox (badness 10000) in paragraph at lines 11270--11271

[141] [142]
Underfull \hbox (badness 10000) in paragraph at lines 11282--11283


Underfull \hbox (badness 10000) in paragraph at lines 11295--11296


Underfull \hbox (badness 10000) in paragraph at lines 11304--11305


Underfull \hbox (badness 10000) in paragraph at lines 11315--11316


Underfull \hbox (badness 10000) in paragraph at lines 11325--11326
[]\OT1/cmtt/m/n/10.95 int gt[]grep[]nt([]bool *match, const char *pattern, cons
t char *line, size[]t

Underfull \hbox (badness 10000) in paragraph at lines 11325--11326


Underfull \hbox (badness 10000) in paragraph at lines 11337--11338


Underfull \hbox (badness 10000) in paragraph at lines 11347--11348


Underfull \hbox (badness 10000) in paragraph at lines 11356--11357

[143]
Underfull \hbox (badness 10000) in paragraph at lines 11369--11370


Underfull \hbox (badness 10000) in paragraph at lines 11378--11379


Underfull \hbox (badness 10000) in paragraph at lines 11387--11388


Underfull \hbox (badness 10000) in paragraph at lines 11398--11399


Underfull \hbox (badness 2065) in paragraph at lines 11402--11406
[]\OT1/ptm/m/n/10.95 Prints the log mes-sage ob-tained from for-mat and fol-low
-ing pa-ram-e-ter ac-cord-

Underfull \hbox (badness 4660) in paragraph at lines 11402--11406
\OT1/ptm/m/n/10.95 ing to if log-ging is en-abled ana-log to\OT1/cmtt/m/n/10.95
 gt[]log[]log()\OT1/ptm/m/n/10.95 . But in con-trast to

Underfull \hbox (badness 10000) in paragraph at lines 11410--11411


Underfull \hbox (badness 10000) in paragraph at lines 11419--11420


Underfull \hbox (badness 10000) in paragraph at lines 11430--11431


Underfull \hbox (badness 10000) in paragraph at lines 11443--11444


Underfull \hbox (badness 10000) in paragraph at lines 11454--11455


Underfull \hbox (badness 10000) in paragraph at lines 11465--11466


Underfull \hbox (badness 10000) in paragraph at lines 11476--11477


Underfull \hbox (badness 10000) in paragraph at lines 11486--11487

[144]
Underfull \hbox (badness 10000) in paragraph at lines 11497--11498


Underfull \hbox (badness 10000) in paragraph at lines 11509--11510
[]\OT1/cmtt/m/n/10.95 void gt[]msort[]r([]void *base, size[]t nmemb, size[]t si
ze, void *comparinfo,

Underfull \hbox (badness 10000) in paragraph at lines 11509--11510


Underfull \hbox (badness 10000) in paragraph at lines 11521--11522


Underfull \hbox (badness 10000) in paragraph at lines 11534--11535


Underfull \hbox (badness 2762) in paragraph at lines 11538--11548
[]\OT1/ptm/m/n/10.95 This mod-ule im-ple-ments the func-tion\OT1/cmtt/m/n/10.95
 gt[]basename() \OT1/ptm/m/n/10.95 ac-cord-ing to the spec-i-fi-

Underfull \hbox (badness 2951) in paragraph at lines 11538--11548
\OT1/ptm/m/n/10.95 ca-tions in http://www.unix-systems.org/onlinepubs/7908799/x
sh/basename.html and
[145]
Underfull \hbox (badness 10000) in paragraph at lines 11554--11555


Underfull \hbox (badness 10000) in paragraph at lines 11564--11565


Underfull \hbox (badness 10000) in paragraph at lines 11574--11575


Underfull \hbox (badness 10000) in paragraph at lines 11584--11585


Underfull \hbox (badness 10000) in paragraph at lines 11594--11595


Underfull \hbox (badness 10000) in paragraph at lines 11605--11606
[]\OT1/cmtt/m/n/10.95 int gt[]parse[]range([]GtRange *rng, const char *start, c
onst char *end,

Underfull \hbox (badness 10000) in paragraph at lines 11605--11606


Underfull \hbox (badness 10000) in paragraph at lines 11619--11620
[]\OT1/cmtt/m/n/10.95 int gt[]parse[]range[]tidy([]GtRange *rng, const char *st
art, const char *end,

Underfull \hbox (badness 10000) in paragraph at lines 11619--11620

[146]
Underfull \hbox (badness 10000) in paragraph at lines 11633--11634
[]\OT1/cmtt/m/n/10.95 void gt[]qsort[]r([]void *a, size[]t n, size[]t es, void 
*data,

Underfull \hbox (badness 10000) in paragraph at lines 11633--11634


Underfull \hbox (badness 10000) in paragraph at lines 11637--11639
[]\OT1/ptm/m/n/10.95 Like \OT1/cmtt/m/n/10.95 qsort(3)\OT1/ptm/m/n/10.95 , but 
al-lows an ad-di-tional \OT1/cmtt/m/n/10.95 data \OT1/ptm/m/n/10.95 pointer pas
sed to the

Underfull \hbox (badness 10000) in paragraph at lines 11645--11646


Underfull \hbox (badness 10000) in paragraph at lines 11656--11657


Underfull \hbox (badness 10000) in paragraph at lines 11669--11670


Underfull \hbox (badness 10000) in paragraph at lines 11686--11687


Underfull \hbox (badness 10000) in paragraph at lines 11697--11698


Underfull \hbox (badness 10000) in paragraph at lines 11706--11707


Underfull \hbox (badness 10000) in paragraph at lines 11715--11716


Underfull \hbox (badness 10000) in paragraph at lines 11724--11725


Underfull \hbox (badness 10000) in paragraph at lines 11733--11734


Underfull \hbox (badness 10000) in paragraph at lines 11742--11743


Underfull \hbox (badness 10000) in paragraph at lines 11751--11752


Underfull \hbox (badness 10000) in paragraph at lines 11760--11761


Underfull \hbox (badness 10000) in paragraph at lines 11769--11770


Underfull \hbox (badness 10000) in paragraph at lines 11778--11779


Underfull \hbox (badness 10000) in paragraph at lines 11787--11788

[147]
Underfull \hbox (badness 10000) in paragraph at lines 11798--11799


Underfull \hbox (badness 10000) in paragraph at lines 11812--11813
[]\OT1/cmtt/m/n/10.95 const char* gt[]version[]check([]unsigned int required[]m
ajor, unsigned int

Underfull \hbox (badness 10000) in paragraph at lines 11812--11813


Underfull \hbox (badness 10000) in paragraph at lines 11826--11827

[148]
Underfull \hbox (badness 10000) in paragraph at lines 11837--11838


Underfull \hbox (badness 10000) in paragraph at lines 11846--11847


Underfull \hbox (badness 10000) in paragraph at lines 11855--11856


Underfull \hbox (badness 10000) in paragraph at lines 11865--11866


Underfull \hbox (badness 10000) in paragraph at lines 11875--11876
[]\OT1/cmtt/m/n/10.95 void gt[]warning[]default[]handler([]void *data, const ch
ar *format, va[]list

Underfull \hbox (badness 10000) in paragraph at lines 11875--11876


Underfull \hbox (badness 10000) in paragraph at lines 11886--11887


Underfull \hbox (badness 10000) in paragraph at lines 11895--11896


Underfull \hbox (badness 10000) in paragraph at lines 11907--11908


Underfull \hbox (badness 10000) in paragraph at lines 11916--11917


Underfull \hbox (badness 10000) in paragraph at lines 11925--11926


Underfull \hbox (badness 10000) in paragraph at lines 11934--11935


Underfull \hbox (badness 10000) in paragraph at lines 11943--11944


Underfull \hbox (badness 10000) in paragraph at lines 11952--11953


Underfull \hbox (badness 10000) in paragraph at lines 11961--11962


Underfull \hbox (badness 10000) in paragraph at lines 11970--11971


Underfull \hbox (badness 10000) in paragraph at lines 11979--11980


Underfull \hbox (badness 10000) in paragraph at lines 11988--11989


Underfull \hbox (badness 10000) in paragraph at lines 11997--11998


Underfull \hbox (badness 10000) in paragraph at lines 12007--12008


Underfull \hbox (badness 10000) in paragraph at lines 12016--12017


Underfull \hbox (badness 10000) in paragraph at lines 12025--12026


Underfull \hbox (badness 10000) in paragraph at lines 12034--12035


Underfull \hbox (badness 10000) in paragraph at lines 12044--12045


Underfull \hbox (badness 10000) in paragraph at lines 12053--12054


Underfull \hbox (badness 10000) in paragraph at lines 12062--12063


Underfull \hbox (badness 10000) in paragraph at lines 12071--12072


Underfull \hbox (badness 10000) in paragraph at lines 12080--12081


Underfull \hbox (badness 10000) in paragraph at lines 12089--12090

[149] [150]) [151] (./annotationsketch.aux)

LaTeX Font Warning: Some font shapes were not available, defaults substituted.

 )
(see the transcript file for additional information) </tmp/texfonts/pk/ljfour/p
ublic/cm/cmttb10.864pk> </tmp/texfonts/pk/ljfour/public/cm/cmttb10.480pk>{/usr/
share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmssbx10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmtt8.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/ut
mb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on annotationsketch.pdf (151 pages, 1171088 bytes).
Transcript written on annotationsketch.log.
mv annotationsketch.aux annotationsketch-pdf.aux
test -e annotationsketch.bbl && mv annotationsketch.bbl annotationsketch-pdf.bbl
make[3]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.8+ds/doc/manuals'
make -C /<<BUILDDIR>>/genometools-1.5.8+ds/doc/manuals
make[3]: Entering directory '/<<BUILDDIR>>/genometools-1.5.8+ds/doc/manuals'
test -e readjoiner-pdf.aux && mv readjoiner-pdf.aux readjoiner.aux
Makefile:39: recipe for target 'readjoiner-pdf.aux' failed
make[3]: [readjoiner-pdf.aux] Error 1 (ignored)
pdflatex readjoiner.tex && rm readjoiner.pdf
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./readjoiner.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
No file readjoiner.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]

LaTeX Warning: Citation `MYE:2005' on page 1 undefined on input line 55.


LaTeX Warning: Citation `genometools' on page 1 undefined on input line 58.


Overfull \hbox (6.12744pt too wide) in paragraph at lines 63--73
[] 

Overfull \hbox (19.25665pt too wide) in paragraph at lines 78--81
[]\OT1/ptm/m/n/12 The \OT1/ptm/m/it/12 Read-joiner \OT1/ptm/m/n/12 tools are ru
n us-ing the fol-low-ing syn-tax: \OT1/pcr/m/n/12 gt readjoiner <tool> <argumen
ts>\OT1/ptm/m/n/12 ,
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1]
Underfull \hbox (badness 4132) in paragraph at lines 183--186
[]\OT1/ptm/m/n/12 a single-end li-brary plus an in-ter-leaved
[2]

LaTeX Warning: Citation `MYE:2005' on page 3 undefined on input line 209.

[3]

LaTeX Warning: Citation `MYE:2005' on page 4 undefined on input line 259.

[4]

LaTeX Warning: Citation `Edena' on page 5 undefined on input line 326.

[5] [6] [7] (./readjoiner.aux)

LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
rw/times/utmri8a.pfb>
Output written on readjoiner.pdf (8 pages, 109483 bytes).
Transcript written on readjoiner.log.
mv readjoiner.aux readjoiner-pdf.aux
test -e readjoiner-pdf.aux && mv readjoiner-pdf.aux readjoiner.aux
bibtex readjoiner
This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
The top-level auxiliary file: readjoiner.aux
I found no \bibdata command---while reading file readjoiner.aux
I found no \bibstyle command---while reading file readjoiner.aux
(There were 2 error messages)
Makefile:32: recipe for target 'readjoiner-pdf.bbl' failed
make[3]: [readjoiner-pdf.bbl] Error 2 (ignored)
test -e readjoiner-pdf.bbl || touch readjoiner-pdf.bbl
diff readjoiner-pdf.bbl readjoiner.bbl || mv readjoiner.bbl readjoiner-pdf.bbl && rm -f readjoiner.bbl
mv readjoiner.aux readjoiner-pdf.aux
test -e readjoiner-pdf.aux && mv readjoiner-pdf.aux readjoiner.aux
test -e readjoiner-pdf.bbl && mv readjoiner-pdf.bbl readjoiner.bbl
pdflatex readjoiner.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./readjoiner.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
(./readjoiner.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (6.12744pt too wide) in paragraph at lines 63--73
[] 

Overfull \hbox (19.25665pt too wide) in paragraph at lines 78--81
[]\OT1/ptm/m/n/12 The \OT1/ptm/m/it/12 Read-joiner \OT1/ptm/m/n/12 tools are ru
n us-ing the fol-low-ing syn-tax: \OT1/pcr/m/n/12 gt readjoiner <tool> <argumen
ts>\OT1/ptm/m/n/12 ,
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1]
Underfull \hbox (badness 4132) in paragraph at lines 183--186
[]\OT1/ptm/m/n/12 a single-end li-brary plus an in-ter-leaved
[2] [3] [4] [5] [6] [7] (./readjoiner.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
rw/times/utmri8a.pfb>
Output written on readjoiner.pdf (8 pages, 108816 bytes).
Transcript written on readjoiner.log.
pdflatex readjoiner.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./readjoiner.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
(./readjoiner.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (6.12744pt too wide) in paragraph at lines 63--73
[] 

Overfull \hbox (19.25665pt too wide) in paragraph at lines 78--81
[]\OT1/ptm/m/n/12 The \OT1/ptm/m/it/12 Read-joiner \OT1/ptm/m/n/12 tools are ru
n us-ing the fol-low-ing syn-tax: \OT1/pcr/m/n/12 gt readjoiner <tool> <argumen
ts>\OT1/ptm/m/n/12 ,
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1]
Underfull \hbox (badness 4132) in paragraph at lines 183--186
[]\OT1/ptm/m/n/12 a single-end li-brary plus an in-ter-leaved
[2] [3] [4] [5] [6] [7] (./readjoiner.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
rw/times/utmri8a.pfb>
Output written on readjoiner.pdf (8 pages, 108816 bytes).
Transcript written on readjoiner.log.
mv readjoiner.aux readjoiner-pdf.aux
test -e readjoiner.bbl && mv readjoiner.bbl readjoiner-pdf.bbl
test -e hop-pdf.aux && mv hop-pdf.aux hop.aux
Makefile:39: recipe for target 'hop-pdf.aux' failed
make[3]: [hop-pdf.aux] Error 1 (ignored)
pdflatex hop.tex && rm hop.pdf
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./hop.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
No file hop.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]

LaTeX Warning: Citation `HOP' on page 1 undefined on input line 40.


LaTeX Warning: Citation `genometools' on page 1 undefined on input line 69.

[1]
Overfull \hbox (37.48308pt too wide) in paragraph at lines 130--138
[]\OT1/ptm/m/n/12 It is usu-ally quite easy to pre-pare the map-ping as re-quir
ed. Say the reads to be cor-rected are \OT1/pcr/m/n/12 f[]reads.fastq

Overfull \hbox (32.30313pt too wide) in paragraph at lines 144--144
[]\OT1/pcr/m/n/10 > bwa sampe cognate.fas -f map.sam f_reads.sai r_reads.sai f_
reads.fastq r_reads.fastq[] 
[2] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)
Overfull \hbox (14.55139pt too wide) in paragraph at lines 206--211
\OT1/ptm/m/n/12 The pre-fix added by HOP (in this case \OT1/pcr/m/n/12 hop\OT1/
ptm/m/n/12 , which is the de-fault) can be changed us-ing the \OT1/pcr/m/n/12 -
outprefix
[3] [4] (./hop.aux)

LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courie
r/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></
usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on hop.pdf (5 pages, 74422 bytes).
Transcript written on hop.log.
mv hop.aux hop-pdf.aux
test -e hop-pdf.aux && mv hop-pdf.aux hop.aux
bibtex hop
This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
The top-level auxiliary file: hop.aux
I found no \bibdata command---while reading file hop.aux
I found no \bibstyle command---while reading file hop.aux
(There were 2 error messages)
Makefile:32: recipe for target 'hop-pdf.bbl' failed
make[3]: [hop-pdf.bbl] Error 2 (ignored)
test -e hop-pdf.bbl || touch hop-pdf.bbl
diff hop-pdf.bbl hop.bbl || mv hop.bbl hop-pdf.bbl && rm -f hop.bbl
mv hop.aux hop-pdf.aux
test -e hop-pdf.aux && mv hop-pdf.aux hop.aux
test -e hop-pdf.bbl && mv hop-pdf.bbl hop.bbl
pdflatex hop.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./hop.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
(./hop.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [1]
Overfull \hbox (37.48308pt too wide) in paragraph at lines 130--138
[]\OT1/ptm/m/n/12 It is usu-ally quite easy to pre-pare the map-ping as re-quir
ed. Say the reads to be cor-rected are \OT1/pcr/m/n/12 f[]reads.fastq

Overfull \hbox (32.30313pt too wide) in paragraph at lines 144--144
[]\OT1/pcr/m/n/10 > bwa sampe cognate.fas -f map.sam f_reads.sai r_reads.sai f_
reads.fastq r_reads.fastq[] 
[2] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)
Overfull \hbox (14.55139pt too wide) in paragraph at lines 206--211
\OT1/ptm/m/n/12 The pre-fix added by HOP (in this case \OT1/pcr/m/n/12 hop\OT1/
ptm/m/n/12 , which is the de-fault) can be changed us-ing the \OT1/pcr/m/n/12 -
outprefix
[3] [4] (./hop.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courie
r/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></
usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on hop.pdf (5 pages, 73820 bytes).
Transcript written on hop.log.
pdflatex hop.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./hop.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
(./hop.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [1]
Overfull \hbox (37.48308pt too wide) in paragraph at lines 130--138
[]\OT1/ptm/m/n/12 It is usu-ally quite easy to pre-pare the map-ping as re-quir
ed. Say the reads to be cor-rected are \OT1/pcr/m/n/12 f[]reads.fastq

Overfull \hbox (32.30313pt too wide) in paragraph at lines 144--144
[]\OT1/pcr/m/n/10 > bwa sampe cognate.fas -f map.sam f_reads.sai r_reads.sai f_
reads.fastq r_reads.fastq[] 
[2] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)
Overfull \hbox (14.55139pt too wide) in paragraph at lines 206--211
\OT1/ptm/m/n/12 The pre-fix added by HOP (in this case \OT1/pcr/m/n/12 hop\OT1/
ptm/m/n/12 , which is the de-fault) can be changed us-ing the \OT1/pcr/m/n/12 -
outprefix
[3] [4] (./hop.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courie
r/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></
usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on hop.pdf (5 pages, 73820 bytes).
Transcript written on hop.log.
mv hop.aux hop-pdf.aux
test -e hop.bbl && mv hop.bbl hop-pdf.bbl
test -e ltrharvest-pdf.aux && mv ltrharvest-pdf.aux ltrharvest.aux
Makefile:39: recipe for target 'ltrharvest-pdf.aux' failed
make[3]: [ltrharvest-pdf.aux] Error 1 (ignored)
pdflatex ltrharvest.tex && rm ltrharvest.pdf
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./ltrharvest.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
No file ltrharvest.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]

LaTeX Warning: Citation `LTRharvesturl' on page 1 undefined on input line 49.


LaTeX Warning: Citation `EKW07' on page 1 undefined on input line 51.


LaTeX Warning: Citation `AKO04' on page 1 undefined on input line 55.


LaTeX Warning: Citation `genometools' on page 1 undefined on input line 69.

(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)

LaTeX Warning: Reference `overviewOpt' on page 1 undefined on input line 104.


LaTeX Warning: Reference `Examples' on page 1 undefined on input line 203.

[1] [2]

LaTeX Warning: Citation `gff3' on page 3 undefined on input line 247.

[3] [4] [5]

LaTeX Warning: Reference `different-options' on page 6 undefined on input line 
491.


LaTeX Warning: Reference `Example-genome' on page 6 undefined on input line 492
.


LaTeX Warning: Reference `ExampleCluster' on page 6 undefined on input line 495
.


LaTeX Warning: Citation `vmatch' on page 6 undefined on input line 500.

[6]
Overfull \hbox (38.30313pt too wide) in paragraph at lines 543--543
[]\OT1/pcr/m/n/10 # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) s(rLTR) e(rLTR
) l(rLTR) sim(LTRs) seq-nr[] 

Overfull \hbox (32.30313pt too wide) in paragraph at lines 579--579
[]\OT1/pcr/m/n/10 # args=-index chr02.19970727.fsa -v -out pred-chr02.fsa -outi
nner pred-inner-chr02.fsa[] 
[7]
Overfull \hbox (38.30313pt too wide) in paragraph at lines 603--603
[]\OT1/pcr/m/n/10 # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) s(rLTR) e(rLTR
) l(rLTR) sim(LTRs) seq-nr[] 

Overfull \hbox (38.30313pt too wide) in paragraph at lines 631--631
[]\OT1/pcr/m/n/10 # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) s(rLTR) e(rLTR
) l(rLTR) sim(LTRs) seq-nr[] 

Overfull \hbox (8.30313pt too wide) in paragraph at lines 655--655
[]\OT1/pcr/m/n/10 $ gt ltrharvest -index chr02.19970727.fsa -seed 30 -xdrop 5 -
mat 2 -mis -2 -ins -3 
[8]
Overfull \hbox (266.30313pt too wide) in paragraph at lines 664--664
[]\OT1/pcr/m/n/10 # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) TSD l(TSD) m(l
LTR) s(rLTR) e(rLTR) l(rLTR) TSD l(TSD) m(rLTR) sim(LTRs) seq-nr[] 

LaTeX Warning: Citation `kim:1998' on page 9 undefined on input line 692.


Overfull \hbox (14.30313pt too wide) in paragraph at lines 721--721
[]\OT1/pcr/m/n/10 $ gt ltrharvest -index chrAll.19971001.fsa -seed 100 -minlenl
tr 100 -maxlenltr 1000 
[9]

LaTeX Warning: Citation `vmatch' on page 10 undefined on input line 768.


LaTeX Warning: Reference `parameters-cluster-default' on page 10 undefined on i
nput line 788.


LaTeX Warning: Reference `parameters-cluster-default' on page 10 undefined on i
nput line 789.


LaTeX Warning: Citation `vmatch' on page 10 undefined on input line 790.

[10]
Underfull \hbox (badness 10000) in paragraph at lines 822--824
[]\OT1/ptm/m/sc/12 GFF3\OT1/ptm/m/n/12 , tab de-lim-ited file for-mat for genom
e an-no-ta-tion. $\OT1/pcr/m/n/12 http : / / www .

Overfull \hbox (12.44012pt too wide) in paragraph at lines 859--870
[][]
[11] [12] (./ltrharvest.aux)

LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi6.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi
7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/
texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/t
imes/utmbi8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pf
b></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on ltrharvest.pdf (13 pages, 160860 bytes).
Transcript written on ltrharvest.log.
mv ltrharvest.aux ltrharvest-pdf.aux
test -e ltrharvest-pdf.aux && mv ltrharvest-pdf.aux ltrharvest.aux
bibtex ltrharvest
This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
The top-level auxiliary file: ltrharvest.aux
I found no \bibdata command---while reading file ltrharvest.aux
I found no \bibstyle command---while reading file ltrharvest.aux
(There were 2 error messages)
Makefile:32: recipe for target 'ltrharvest-pdf.bbl' failed
make[3]: [ltrharvest-pdf.bbl] Error 2 (ignored)
test -e ltrharvest-pdf.bbl || touch ltrharvest-pdf.bbl
diff ltrharvest-pdf.bbl ltrharvest.bbl || mv ltrharvest.bbl ltrharvest-pdf.bbl && rm -f ltrharvest.bbl
mv ltrharvest.aux ltrharvest-pdf.aux
test -e ltrharvest-pdf.aux && mv ltrharvest-pdf.aux ltrharvest.aux
test -e ltrharvest-pdf.bbl && mv ltrharvest-pdf.bbl ltrharvest.bbl
pdflatex ltrharvest.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./ltrharvest.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
(./ltrharvest.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1] [2] [3] [4]
[5] [6]
Overfull \hbox (38.30313pt too wide) in paragraph at lines 543--543
[]\OT1/pcr/m/n/10 # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) s(rLTR) e(rLTR
) l(rLTR) sim(LTRs) seq-nr[] 

Overfull \hbox (32.30313pt too wide) in paragraph at lines 579--579
[]\OT1/pcr/m/n/10 # args=-index chr02.19970727.fsa -v -out pred-chr02.fsa -outi
nner pred-inner-chr02.fsa[] 
[7]
Overfull \hbox (38.30313pt too wide) in paragraph at lines 603--603
[]\OT1/pcr/m/n/10 # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) s(rLTR) e(rLTR
) l(rLTR) sim(LTRs) seq-nr[] 

Overfull \hbox (38.30313pt too wide) in paragraph at lines 631--631
[]\OT1/pcr/m/n/10 # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) s(rLTR) e(rLTR
) l(rLTR) sim(LTRs) seq-nr[] 

Overfull \hbox (8.30313pt too wide) in paragraph at lines 655--655
[]\OT1/pcr/m/n/10 $ gt ltrharvest -index chr02.19970727.fsa -seed 30 -xdrop 5 -
mat 2 -mis -2 -ins -3 
[8]
Overfull \hbox (266.30313pt too wide) in paragraph at lines 664--664
[]\OT1/pcr/m/n/10 # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) TSD l(TSD) m(l
LTR) s(rLTR) e(rLTR) l(rLTR) TSD l(TSD) m(rLTR) sim(LTRs) seq-nr[] 

Overfull \hbox (14.30313pt too wide) in paragraph at lines 721--721
[]\OT1/pcr/m/n/10 $ gt ltrharvest -index chrAll.19971001.fsa -seed 100 -minlenl
tr 100 -maxlenltr 1000 
[9] [10]
Underfull \hbox (badness 10000) in paragraph at lines 822--824
[]\OT1/ptm/m/sc/12 GFF3\OT1/ptm/m/n/12 , tab de-lim-ited file for-mat for genom
e an-no-ta-tion. $\OT1/pcr/m/n/12 http : / / www .

Overfull \hbox (12.44012pt too wide) in paragraph at lines 859--870
[][]
[11] [12] (./ltrharvest.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi6.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi
7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/
texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/t
imes/utmbi8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pf
b></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on ltrharvest.pdf (13 pages, 160035 bytes).
Transcript written on ltrharvest.log.
pdflatex ltrharvest.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./ltrharvest.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
(./ltrharvest.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1] [2] [3] [4]
[5] [6]
Overfull \hbox (38.30313pt too wide) in paragraph at lines 543--543
[]\OT1/pcr/m/n/10 # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) s(rLTR) e(rLTR
) l(rLTR) sim(LTRs) seq-nr[] 

Overfull \hbox (32.30313pt too wide) in paragraph at lines 579--579
[]\OT1/pcr/m/n/10 # args=-index chr02.19970727.fsa -v -out pred-chr02.fsa -outi
nner pred-inner-chr02.fsa[] 
[7]
Overfull \hbox (38.30313pt too wide) in paragraph at lines 603--603
[]\OT1/pcr/m/n/10 # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) s(rLTR) e(rLTR
) l(rLTR) sim(LTRs) seq-nr[] 

Overfull \hbox (38.30313pt too wide) in paragraph at lines 631--631
[]\OT1/pcr/m/n/10 # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) s(rLTR) e(rLTR
) l(rLTR) sim(LTRs) seq-nr[] 

Overfull \hbox (8.30313pt too wide) in paragraph at lines 655--655
[]\OT1/pcr/m/n/10 $ gt ltrharvest -index chr02.19970727.fsa -seed 30 -xdrop 5 -
mat 2 -mis -2 -ins -3 
[8]
Overfull \hbox (266.30313pt too wide) in paragraph at lines 664--664
[]\OT1/pcr/m/n/10 # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) TSD l(TSD) m(l
LTR) s(rLTR) e(rLTR) l(rLTR) TSD l(TSD) m(rLTR) sim(LTRs) seq-nr[] 

Overfull \hbox (14.30313pt too wide) in paragraph at lines 721--721
[]\OT1/pcr/m/n/10 $ gt ltrharvest -index chrAll.19971001.fsa -seed 100 -minlenl
tr 100 -maxlenltr 1000 
[9] [10]
Underfull \hbox (badness 10000) in paragraph at lines 822--824
[]\OT1/ptm/m/sc/12 GFF3\OT1/ptm/m/n/12 , tab de-lim-ited file for-mat for genom
e an-no-ta-tion. $\OT1/pcr/m/n/12 http : / / www .

Overfull \hbox (12.44012pt too wide) in paragraph at lines 859--870
[][]
[11] [12] (./ltrharvest.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi6.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi
7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb></usr/share/texlive/
texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/t
imes/utmbi8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pf
b></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on ltrharvest.pdf (13 pages, 160035 bytes).
Transcript written on ltrharvest.log.
mv ltrharvest.aux ltrharvest-pdf.aux
test -e ltrharvest.bbl && mv ltrharvest.bbl ltrharvest-pdf.bbl
test -e ltrdigest-pdf.aux && mv ltrdigest-pdf.aux ltrdigest.aux
Makefile:39: recipe for target 'ltrdigest-pdf.aux' failed
make[3]: [ltrdigest-pdf.aux] Error 1 (ignored)
pdflatex ltrdigest.tex && rm ltrdigest.pdf
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./ltrdigest.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
No file ltrdigest.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd)
Underfull \hbox (badness 10000) in paragraph at lines 45--45
[]$\OT1/pcr/m/n/14.4 http : / / nar . oxfordjournals . org / cgi / content /
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]

LaTeX Warning: Citation `EKW07' on page 1 undefined on input line 52.


Overfull \hbox (12.44974pt too wide) in paragraph at lines 50--54
\OT1/ptm/m/n/12 se-quence fea-tures of LTR retro-trans-posons in pre-dicted can
-di-dates, like those re-ported by\OT1/ptm/m/it/12 LTRharvest \OT1/ptm/m/n/12 [
[]].
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)

LaTeX Warning: Citation `gff3' on page 1 undefined on input line 67.


LaTeX Warning: Citation `genometools' on page 1 undefined on input line 73.


LaTeX Warning: Citation `hmmer' on page 1 undefined on input line 76.


LaTeX Warning: Citation `pfam' on page 1 undefined on input line 78.


LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 104.

[1]

LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 118.


LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 125.


LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 132.


LaTeX Warning: Reference `overviewOpt' on page 2 undefined on input line 164.

[2] [3] [4]
Overfull \hbox (18.22491pt too wide) in paragraph at lines 281--289
\OT1/ptm/m/n/12 trans-po-son it-self (\OT1/pcr/m/n/12 LTR[]retrotransposon \OT1
/ptm/m/n/12 type) and the pre-dicted LTRs (\OT1/pcr/m/n/12 long[]terminal[]repe
at

Underfull \hbox (badness 10000) in paragraph at lines 281--289

[5] [6] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omspcr.fd) [7] [8]
Overfull \hbox (34.70291pt too wide) in paragraph at lines 562--563
[]\OT1/pcr/m/n/12 gt suffixerator -tis -des -dna -ssp -db genome.fas -indexname
 genome.fas 

Overfull \hbox (6.71515pt too wide) in paragraph at lines 568--574
[]\OT1/ptm/m/n/12 We will also as-sume that the HMM files to be used are called
 \OT1/pcr/m/n/12 HMM1.hmm\OT1/ptm/m/n/12 , \OT1/pcr/m/n/12 HMM2.hmm \OT1/ptm/m/
n/12 and \OT1/pcr/m/n/12 HMM3.hmm\OT1/ptm/m/n/12 ,

Overfull \hbox (24.62292pt too wide) in paragraph at lines 575--585
\OT1/pcr/m/n/12 -hmms HMM*.hmm -outfileprefix mygenome-ltrs ltrs[]sorted.gff3 g
enome.fas
[9] [10] (./ltrdigest.aux)

LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmm
i6.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist
/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmsy8.pfb></usr/share/texlive/texmf-dist/fonts/type1/
urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utm
b8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/t
exmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on ltrdigest.pdf (11 pages, 185695 bytes).
Transcript written on ltrdigest.log.
mv ltrdigest.aux ltrdigest-pdf.aux
test -e ltrdigest-pdf.aux && mv ltrdigest-pdf.aux ltrdigest.aux
bibtex ltrdigest
This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
The top-level auxiliary file: ltrdigest.aux
The style file: unsrt.bst
I found no \bibdata command---while reading file ltrdigest.aux
Warning--I didn't find a database entry for "EKW07"
Warning--I didn't find a database entry for "gff3"
Warning--I didn't find a database entry for "genometools"
Warning--I didn't find a database entry for "hmmer"
Warning--I didn't find a database entry for "pfam"
(There was 1 error message)
Makefile:32: recipe for target 'ltrdigest-pdf.bbl' failed
make[3]: [ltrdigest-pdf.bbl] Error 2 (ignored)
test -e ltrdigest-pdf.bbl || touch ltrdigest-pdf.bbl
diff ltrdigest-pdf.bbl ltrdigest.bbl || mv ltrdigest.bbl ltrdigest-pdf.bbl && rm -f ltrdigest.bbl
0a1,3
> \begin{thebibliography}{}
> 
> \end{thebibliography}
mv ltrdigest.aux ltrdigest-pdf.aux
test -e ltrdigest-pdf.aux && mv ltrdigest-pdf.aux ltrdigest.aux
test -e ltrdigest-pdf.bbl && mv ltrdigest-pdf.bbl ltrdigest.bbl
pdflatex ltrdigest.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./ltrdigest.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
(./ltrdigest.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd)
Underfull \hbox (badness 10000) in paragraph at lines 45--45
[]$\OT1/pcr/m/n/14.4 http : / / nar . oxfordjournals . org / cgi / content /
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (12.44974pt too wide) in paragraph at lines 50--54
\OT1/ptm/m/n/12 se-quence fea-tures of LTR retro-trans-posons in pre-dicted can
-di-dates, like those re-ported by\OT1/ptm/m/it/12 LTRharvest \OT1/ptm/m/n/12 [
[]].
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)

LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 104.

[1]

LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 118.


LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 125.


LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 132.

[2] [3] [4]
Overfull \hbox (18.22491pt too wide) in paragraph at lines 281--289
\OT1/ptm/m/n/12 trans-po-son it-self (\OT1/pcr/m/n/12 LTR[]retrotransposon \OT1
/ptm/m/n/12 type) and the pre-dicted LTRs (\OT1/pcr/m/n/12 long[]terminal[]repe
at

Underfull \hbox (badness 10000) in paragraph at lines 281--289

[5] [6] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omspcr.fd) [7] [8]
Overfull \hbox (34.70291pt too wide) in paragraph at lines 562--563
[]\OT1/pcr/m/n/12 gt suffixerator -tis -des -dna -ssp -db genome.fas -indexname
 genome.fas 

Overfull \hbox (6.71515pt too wide) in paragraph at lines 568--574
[]\OT1/ptm/m/n/12 We will also as-sume that the HMM files to be used are called
 \OT1/pcr/m/n/12 HMM1.hmm\OT1/ptm/m/n/12 , \OT1/pcr/m/n/12 HMM2.hmm \OT1/ptm/m/
n/12 and \OT1/pcr/m/n/12 HMM3.hmm\OT1/ptm/m/n/12 ,

Overfull \hbox (24.62292pt too wide) in paragraph at lines 575--585
\OT1/pcr/m/n/12 -hmms HMM*.hmm -outfileprefix mygenome-ltrs ltrs[]sorted.gff3 g
enome.fas
[9] [10] (./ltrdigest.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmm
i6.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist
/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmsy8.pfb></usr/share/texlive/texmf-dist/fonts/type1/
urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utm
b8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/t
exmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on ltrdigest.pdf (11 pages, 185011 bytes).
Transcript written on ltrdigest.log.
pdflatex ltrdigest.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./ltrdigest.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
(./ltrdigest.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd)
Underfull \hbox (badness 10000) in paragraph at lines 45--45
[]$\OT1/pcr/m/n/14.4 http : / / nar . oxfordjournals . org / cgi / content /
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (12.44974pt too wide) in paragraph at lines 50--54
\OT1/ptm/m/n/12 se-quence fea-tures of LTR retro-trans-posons in pre-dicted can
-di-dates, like those re-ported by\OT1/ptm/m/it/12 LTRharvest \OT1/ptm/m/n/12 [
[]].
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)

LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 104.

[1]

LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 118.


LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 125.


LaTeX Warning: Characters dropped after `\end{verbatim}' on input line 132.

[2] [3] [4]
Overfull \hbox (18.22491pt too wide) in paragraph at lines 281--289
\OT1/ptm/m/n/12 trans-po-son it-self (\OT1/pcr/m/n/12 LTR[]retrotransposon \OT1
/ptm/m/n/12 type) and the pre-dicted LTRs (\OT1/pcr/m/n/12 long[]terminal[]repe
at

Underfull \hbox (badness 10000) in paragraph at lines 281--289

[5] [6] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omspcr.fd) [7] [8]
Overfull \hbox (34.70291pt too wide) in paragraph at lines 562--563
[]\OT1/pcr/m/n/12 gt suffixerator -tis -des -dna -ssp -db genome.fas -indexname
 genome.fas 

Overfull \hbox (6.71515pt too wide) in paragraph at lines 568--574
[]\OT1/ptm/m/n/12 We will also as-sume that the HMM files to be used are called
 \OT1/pcr/m/n/12 HMM1.hmm\OT1/ptm/m/n/12 , \OT1/pcr/m/n/12 HMM2.hmm \OT1/ptm/m/
n/12 and \OT1/pcr/m/n/12 HMM3.hmm\OT1/ptm/m/n/12 ,

Overfull \hbox (24.62292pt too wide) in paragraph at lines 575--585
\OT1/pcr/m/n/12 -hmms HMM*.hmm -outfileprefix mygenome-ltrs ltrs[]sorted.gff3 g
enome.fas
[9] [10] (./ltrdigest.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmm
i6.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi8.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr7.pfb></usr/share/texlive/te
xmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/share/texlive/texmf-dist
/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmsy8.pfb></usr/share/texlive/texmf-dist/fonts/type1/
urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utm
b8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/t
exmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on ltrdigest.pdf (11 pages, 185011 bytes).
Transcript written on ltrdigest.log.
mv ltrdigest.aux ltrdigest-pdf.aux
test -e ltrdigest.bbl && mv ltrdigest.bbl ltrdigest-pdf.bbl
test -e uniquesub-pdf.aux && mv uniquesub-pdf.aux uniquesub.aux
Makefile:39: recipe for target 'uniquesub-pdf.aux' failed
make[3]: [uniquesub-pdf.aux] Error 1 (ignored)
pdflatex uniquesub.tex && rm uniquesub.pdf
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./uniquesub.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (./optionman.sty)
No file uniquesub.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)

LaTeX Warning: Citation `GRAE:NIE:KUR:HUY:BIR:STU:FLI:2007' on page 1 undefined
 on input line 62.

[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (8.18253pt too wide) in paragraph at lines 127--131
\OT1/ptm/m/n/12 loaded from $\OT1/pcr/m/n/12 ftp : / / ftp . ensembl . org / pu
b / current _ fasta / homo _ sapiens _ 47 _ 36i /
[2] [3] (./uniquesub.aux)

LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti
12.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive
/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/ti
mes/utmri8a.pfb>
Output written on uniquesub.pdf (3 pages, 98747 bytes).
Transcript written on uniquesub.log.
mv uniquesub.aux uniquesub-pdf.aux
test -e uniquesub-pdf.aux && mv uniquesub-pdf.aux uniquesub.aux
bibtex uniquesub
This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
The top-level auxiliary file: uniquesub.aux
I found no \bibdata command---while reading file uniquesub.aux
I found no \bibstyle command---while reading file uniquesub.aux
(There were 2 error messages)
Makefile:32: recipe for target 'uniquesub-pdf.bbl' failed
make[3]: [uniquesub-pdf.bbl] Error 2 (ignored)
test -e uniquesub-pdf.bbl || touch uniquesub-pdf.bbl
diff uniquesub-pdf.bbl uniquesub.bbl || mv uniquesub.bbl uniquesub-pdf.bbl && rm -f uniquesub.bbl
mv uniquesub.aux uniquesub-pdf.aux
test -e uniquesub-pdf.aux && mv uniquesub-pdf.aux uniquesub.aux
test -e uniquesub-pdf.bbl && mv uniquesub-pdf.bbl uniquesub.bbl
pdflatex uniquesub.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./uniquesub.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (./optionman.sty)
(./uniquesub.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (8.18253pt too wide) in paragraph at lines 127--131
\OT1/ptm/m/n/12 loaded from $\OT1/pcr/m/n/12 ftp : / / ftp . ensembl . org / pu
b / current _ fasta / homo _ sapiens _ 47 _ 36i /
[2] [3] (./uniquesub.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti
12.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive
/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/ti
mes/utmri8a.pfb>
Output written on uniquesub.pdf (3 pages, 97739 bytes).
Transcript written on uniquesub.log.
pdflatex uniquesub.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./uniquesub.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (./optionman.sty)
(./uniquesub.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (8.18253pt too wide) in paragraph at lines 127--131
\OT1/ptm/m/n/12 loaded from $\OT1/pcr/m/n/12 ftp : / / ftp . ensembl . org / pu
b / current _ fasta / homo _ sapiens _ 47 _ 36i /
[2] [3] (./uniquesub.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti
12.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive
/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/ti
mes/utmri8a.pfb>
Output written on uniquesub.pdf (3 pages, 97739 bytes).
Transcript written on uniquesub.log.
mv uniquesub.aux uniquesub-pdf.aux
test -e uniquesub.bbl && mv uniquesub.bbl uniquesub-pdf.bbl
test -e matstat-pdf.aux && mv matstat-pdf.aux matstat.aux
Makefile:39: recipe for target 'matstat-pdf.aux' failed
make[3]: [matstat-pdf.aux] Error 1 (ignored)
pdflatex matstat.tex && rm matstat.pdf
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./matstat.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (./optionman.sty)
No file matstat.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (8.18253pt too wide) in paragraph at lines 120--124
\OT1/ptm/m/n/12 loaded from $\OT1/pcr/m/n/12 ftp : / / ftp . ensembl . org / pu
b / current _ fasta / homo _ sapiens _ 47 _ 36i /
[2] (./matstat.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti
12.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive
/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/ti
mes/utmri8a.pfb>
Output written on matstat.pdf (2 pages, 92615 bytes).
Transcript written on matstat.log.
mv matstat.aux matstat-pdf.aux
test -e matstat-pdf.aux && mv matstat-pdf.aux matstat.aux
bibtex matstat
This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
The top-level auxiliary file: matstat.aux
I found no \citation commands---while reading file matstat.aux
I found no \bibdata command---while reading file matstat.aux
I found no \bibstyle command---while reading file matstat.aux
(There were 3 error messages)
Makefile:32: recipe for target 'matstat-pdf.bbl' failed
make[3]: [matstat-pdf.bbl] Error 2 (ignored)
test -e matstat-pdf.bbl || touch matstat-pdf.bbl
diff matstat-pdf.bbl matstat.bbl || mv matstat.bbl matstat-pdf.bbl && rm -f matstat.bbl
mv matstat.aux matstat-pdf.aux
test -e matstat-pdf.aux && mv matstat-pdf.aux matstat.aux
test -e matstat-pdf.bbl && mv matstat-pdf.bbl matstat.bbl
pdflatex matstat.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./matstat.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (./optionman.sty)
(./matstat.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (8.18253pt too wide) in paragraph at lines 120--124
\OT1/ptm/m/n/12 loaded from $\OT1/pcr/m/n/12 ftp : / / ftp . ensembl . org / pu
b / current _ fasta / homo _ sapiens _ 47 _ 36i /
[2] (./matstat.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti
12.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive
/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/ti
mes/utmri8a.pfb>
Output written on matstat.pdf (2 pages, 92615 bytes).
Transcript written on matstat.log.
pdflatex matstat.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./matstat.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (./optionman.sty)
(./matstat.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (8.18253pt too wide) in paragraph at lines 120--124
\OT1/ptm/m/n/12 loaded from $\OT1/pcr/m/n/12 ftp : / / ftp . ensembl . org / pu
b / current _ fasta / homo _ sapiens _ 47 _ 36i /
[2] (./matstat.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti
12.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive
/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/ti
mes/utmri8a.pfb>
Output written on matstat.pdf (2 pages, 92615 bytes).
Transcript written on matstat.log.
mv matstat.aux matstat-pdf.aux
test -e matstat.bbl && mv matstat.bbl matstat-pdf.bbl
test -e mgth-pdf.aux && mv mgth-pdf.aux mgth.aux
Makefile:39: recipe for target 'mgth-pdf.aux' failed
make[3]: [mgth-pdf.aux] Error 1 (ignored)
pdflatex mgth.tex && rm mgth.pdf
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./mgth.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/dvipsnam.def)
No file mgth.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]

LaTeX Warning: Citation `krause' on page 1 undefined on input line 49.

(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd)

LaTeX Warning: Citation `genometools' on page 1 undefined on input line 56.

(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)

LaTeX Warning: Citation `genometools' on page 1 undefined on input line 96.


Overfull \hbox (1.48183pt too wide) in paragraph at lines 95--106
\OT1/ptm/m/it/12 Tools \OT1/ptm/m/n/12 (see [[]] for in-stal-la-tion in-struc-t
ions). There are two dif-fer-ent in-stal-la-tion op-tions for the \OT1/ptm/m/it
/12 Genome-
[1]

LaTeX Warning: Reference `overviewOpt' on page 2 undefined on input line 121.


Overfull \hbox (0.98593pt too wide) in paragraph at lines 113--123
[]\OT1/pcr/m/n/10.95 BLAST-Filename \OT1/ptm/m/n/12 de-notes the XML for-mat-te
d BLAST-hit file, \OT1/pcr/m/n/10.95 Metagenome-Filename \OT1/ptm/m/n/12 the FA
STA
[2]
Overfull \hbox (1.2452pt too wide) in paragraph at lines 254--255
[]\OT1/ptm/m/n/12 . If this op-

LaTeX Warning: Reference `Examples' on page 3 undefined on input line 261.

[3] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omlptm.fd) [4]
Overfull \hbox (13.12135pt too wide) in paragraph at lines 437--437
[]\OT1/ptm/m/n/10.95 tataaaatagccaaatctgagcctaaaagcccttggatatccatgatttagaacgaac
catcccctcttattcaggagaagttttctgaactcttcaacatcctcga...| 

Overfull \hbox (7.99995pt too wide) in paragraph at lines 427--441
[] 
[5]
Overfull \hbox (13.12135pt too wide) in paragraph at lines 450--450
[]\OT1/ptm/m/n/10.95 tataaaatagccaaatctgagcctaaaagcccttggatatccatgatttagaacgaac
catcccctcttattcaggagaagttttctgaactcttcaacatcctcga...| 

Overfull \hbox (12.18396pt too wide) in paragraph at lines 454--454
[]\OT1/ptm/m/n/10.95 MLLREVTREERKNFYTNEWKVKDIPDFIVKTLELREFGFDHSGEGPSDRKNQYTDIRD
LEDYIRATA...| 

Overfull \hbox (7.99995pt too wide) in paragraph at lines 442--466
[][] 

Overfull \hbox (12.88672pt too wide) in paragraph at lines 468--470
[]\OT1/ptm/m/n/12 Content:| 

Overfull \hbox (1.15051pt too wide) in paragraph at lines 476--476
[][]| 

Overfull \hbox (1.15051pt too wide) in paragraph at lines 478--478
[][]| 

Overfull \hbox (1.15051pt too wide) in paragraph at lines 480--480
[][]| 

Overfull \hbox (38.49402pt too wide) in paragraph at lines 502--504
[]\OT1/ptm/m/n/12 Content:| 

Overfull \hbox (1.15051pt too wide) in paragraph at lines 504--504
[]\OT1/ptm/m/n/12 -

Overfull \hbox (1.15051pt too wide) in paragraph at lines 507--507
[]\OT1/ptm/m/n/12 -
[6] [7] (./mgth.aux)

LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr1
2.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/
texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/font
s/type1/urw/times/utmbi8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/ti
mes/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb
>
Output written on mgth.pdf (8 pages, 131900 bytes).
Transcript written on mgth.log.
mv mgth.aux mgth-pdf.aux
test -e mgth-pdf.aux && mv mgth-pdf.aux mgth.aux
bibtex mgth
This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
The top-level auxiliary file: mgth.aux
I found no \bibdata command---while reading file mgth.aux
I found no \bibstyle command---while reading file mgth.aux
(There were 2 error messages)
Makefile:32: recipe for target 'mgth-pdf.bbl' failed
make[3]: [mgth-pdf.bbl] Error 2 (ignored)
test -e mgth-pdf.bbl || touch mgth-pdf.bbl
diff mgth-pdf.bbl mgth.bbl || mv mgth.bbl mgth-pdf.bbl && rm -f mgth.bbl
mv mgth.aux mgth-pdf.aux
test -e mgth-pdf.aux && mv mgth-pdf.aux mgth.aux
test -e mgth-pdf.bbl && mv mgth-pdf.bbl mgth.bbl
pdflatex mgth.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./mgth.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/dvipsnam.def) (./mgth.aux)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)
Overfull \hbox (1.48183pt too wide) in paragraph at lines 95--106
\OT1/ptm/m/it/12 Tools \OT1/ptm/m/n/12 (see [[]] for in-stal-la-tion in-struc-t
ions). There are two dif-fer-ent in-stal-la-tion op-tions for the \OT1/ptm/m/it
/12 Genome-
[1]
Overfull \hbox (0.98593pt too wide) in paragraph at lines 113--123
[]\OT1/pcr/m/n/10.95 BLAST-Filename \OT1/ptm/m/n/12 de-notes the XML for-mat-te
d BLAST-hit file, \OT1/pcr/m/n/10.95 Metagenome-Filename \OT1/ptm/m/n/12 the FA
STA
[2]
Overfull \hbox (1.2452pt too wide) in paragraph at lines 254--255
[]\OT1/ptm/m/n/12 . If this op-
[3] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omlptm.fd) [4]
Overfull \hbox (13.12135pt too wide) in paragraph at lines 437--437
[]\OT1/ptm/m/n/10.95 tataaaatagccaaatctgagcctaaaagcccttggatatccatgatttagaacgaac
catcccctcttattcaggagaagttttctgaactcttcaacatcctcga...| 

Overfull \hbox (7.99995pt too wide) in paragraph at lines 427--441
[] 
[5]
Overfull \hbox (13.12135pt too wide) in paragraph at lines 450--450
[]\OT1/ptm/m/n/10.95 tataaaatagccaaatctgagcctaaaagcccttggatatccatgatttagaacgaac
catcccctcttattcaggagaagttttctgaactcttcaacatcctcga...| 

Overfull \hbox (12.18396pt too wide) in paragraph at lines 454--454
[]\OT1/ptm/m/n/10.95 MLLREVTREERKNFYTNEWKVKDIPDFIVKTLELREFGFDHSGEGPSDRKNQYTDIRD
LEDYIRATA...| 

Overfull \hbox (7.99995pt too wide) in paragraph at lines 442--466
[][] 

Overfull \hbox (12.88672pt too wide) in paragraph at lines 468--470
[]\OT1/ptm/m/n/12 Content:| 

Overfull \hbox (1.15051pt too wide) in paragraph at lines 476--476
[][]| 

Overfull \hbox (1.15051pt too wide) in paragraph at lines 478--478
[][]| 

Overfull \hbox (1.15051pt too wide) in paragraph at lines 480--480
[][]| 

Overfull \hbox (38.49402pt too wide) in paragraph at lines 502--504
[]\OT1/ptm/m/n/12 Content:| 

Overfull \hbox (1.15051pt too wide) in paragraph at lines 504--504
[]\OT1/ptm/m/n/12 -

Overfull \hbox (1.15051pt too wide) in paragraph at lines 507--507
[]\OT1/ptm/m/n/12 -
[6] [7] (./mgth.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr1
2.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/
texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/font
s/type1/urw/times/utmbi8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/ti
mes/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb
>
Output written on mgth.pdf (8 pages, 131233 bytes).
Transcript written on mgth.log.
pdflatex mgth.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./mgth.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/dvipsnam.def) (./mgth.aux)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)
Overfull \hbox (1.48183pt too wide) in paragraph at lines 95--106
\OT1/ptm/m/it/12 Tools \OT1/ptm/m/n/12 (see [[]] for in-stal-la-tion in-struc-t
ions). There are two dif-fer-ent in-stal-la-tion op-tions for the \OT1/ptm/m/it
/12 Genome-
[1]
Overfull \hbox (0.98593pt too wide) in paragraph at lines 113--123
[]\OT1/pcr/m/n/10.95 BLAST-Filename \OT1/ptm/m/n/12 de-notes the XML for-mat-te
d BLAST-hit file, \OT1/pcr/m/n/10.95 Metagenome-Filename \OT1/ptm/m/n/12 the FA
STA
[2]
Overfull \hbox (1.2452pt too wide) in paragraph at lines 254--255
[]\OT1/ptm/m/n/12 . If this op-
[3] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omlptm.fd) [4]
Overfull \hbox (13.12135pt too wide) in paragraph at lines 437--437
[]\OT1/ptm/m/n/10.95 tataaaatagccaaatctgagcctaaaagcccttggatatccatgatttagaacgaac
catcccctcttattcaggagaagttttctgaactcttcaacatcctcga...| 

Overfull \hbox (7.99995pt too wide) in paragraph at lines 427--441
[] 
[5]
Overfull \hbox (13.12135pt too wide) in paragraph at lines 450--450
[]\OT1/ptm/m/n/10.95 tataaaatagccaaatctgagcctaaaagcccttggatatccatgatttagaacgaac
catcccctcttattcaggagaagttttctgaactcttcaacatcctcga...| 

Overfull \hbox (12.18396pt too wide) in paragraph at lines 454--454
[]\OT1/ptm/m/n/10.95 MLLREVTREERKNFYTNEWKVKDIPDFIVKTLELREFGFDHSGEGPSDRKNQYTDIRD
LEDYIRATA...| 

Overfull \hbox (7.99995pt too wide) in paragraph at lines 442--466
[][] 

Overfull \hbox (12.88672pt too wide) in paragraph at lines 468--470
[]\OT1/ptm/m/n/12 Content:| 

Overfull \hbox (1.15051pt too wide) in paragraph at lines 476--476
[][]| 

Overfull \hbox (1.15051pt too wide) in paragraph at lines 478--478
[][]| 

Overfull \hbox (1.15051pt too wide) in paragraph at lines 480--480
[][]| 

Overfull \hbox (38.49402pt too wide) in paragraph at lines 502--504
[]\OT1/ptm/m/n/12 Content:| 

Overfull \hbox (1.15051pt too wide) in paragraph at lines 504--504
[]\OT1/ptm/m/n/12 -

Overfull \hbox (1.15051pt too wide) in paragraph at lines 507--507
[]\OT1/ptm/m/n/12 -
[6] [7] (./mgth.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr1
2.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/
texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/font
s/type1/urw/times/utmbi8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/ti
mes/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb
>
Output written on mgth.pdf (8 pages, 131233 bytes).
Transcript written on mgth.log.
mv mgth.aux mgth-pdf.aux
test -e mgth.bbl && mv mgth.bbl mgth-pdf.bbl
test -e packedindex-pdf.aux && mv packedindex-pdf.aux packedindex.aux
Makefile:39: recipe for target 'packedindex-pdf.aux' failed
make[3]: [packedindex-pdf.aux] Error 1 (ignored)
pdflatex packedindex.tex && rm packedindex.pdf
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./packedindex.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/comment/comment.sty
Excluding comment 'comment') (./optionman.sty)
No file packedindex.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]

LaTeX Warning: Citation `oai:CiteSeerPSU:481302' on page 1 undefined on input l
ine 49.


LaTeX Warning: Citation `journals/talg/FerraginaMMN07' on page 1 undefined on i
nput line 51.


LaTeX Warning: Citation `genometools' on page 1 undefined on input line 54.

(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1] [2]
Overfull \hbox (5.0115pt too wide) in paragraph at lines 250--255
\OT1/ptm/m/n/12 The \OT1/pcr/b/n/12 mkctxmap \OT1/ptm/m/n/12 sub-tool fa-cil-i-
tates late build-ing of a re-verse lookup ta-ble, it can use the \OT1/pcr/m/sl/
12 prefix.suf

LaTeX Warning: Reference `sec:packedindex:mkindex' on page 3 undefined on input
 line 276.

[3]

LaTeX Warning: Reference `sec:packedindex:examples' on page 4 undefined on inpu
t line 308.

[4]

LaTeX Warning: Citation `gttestdata' on page 5 undefined on input line 430.


Overfull \hbox (37.00337pt too wide) in paragraph at lines 439--443
[]\OT1/ptm/m/n/12 First com-pute the \OT1/ptm/m/it/12 packedin-dex \OT1/ptm/m/n
/12 in-dex file (this as-sumes \OT1/pcr/m/sl/12 chr01.19960731.fsa.gz \OT1/ptm/
m/n/12 has been copied/linked
[5]
No file packedindex.bbl.
[6] (./packedindex.aux)

LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi
8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/sha
re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/share/texlive/texmf-di
st/fonts/type1/urw/courier/ucrbo8a.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courie
r/ucrro8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist
/fonts/type1/urw/times/utmri8a.pfb>
Output written on packedindex.pdf (7 pages, 157363 bytes).
Transcript written on packedindex.log.
mv packedindex.aux packedindex-pdf.aux
test -e packedindex-pdf.aux && mv packedindex-pdf.aux packedindex.aux
bibtex packedindex
This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
The top-level auxiliary file: packedindex.aux
The style file: unsrt.bst
Database file #1: gtmanuals.bib
test -e packedindex-pdf.bbl || touch packedindex-pdf.bbl
diff packedindex-pdf.bbl packedindex.bbl || mv packedindex.bbl packedindex-pdf.bbl && rm -f packedindex.bbl
0a1,21
> \begin{thebibliography}{1}
> 
> \bibitem{oai:CiteSeerPSU:481302}
> Paolo Ferragina and Giovanni Manzini.
> \newblock Opportunistic data structures with applications, September~03 2000.
> 
> \bibitem{journals/talg/FerraginaMMN07}
> Paolo Ferragina, Giovanni Manzini, Veli M{\"a}kinen, and Gonzalo Navarro.
> \newblock Compressed representations of sequences and full-text indexes.
> \newblock {\em ACM Transactions on Algorithms}, 3(2), 2007.
> 
> \bibitem{genometools}
> Gordon Gremme.
> \newblock The \textsc{GenomeTools} genome analysis system.
> \newblock \url{http://genometools.org}.
> 
> \bibitem{gttestdata}
> \textsc{GenomeTools} test data set.
> \newblock \url{git://genometools.org/gttestdata.git}.
> 
> \end{thebibliography}
mv packedindex.aux packedindex-pdf.aux
test -e packedindex-pdf.aux && mv packedindex-pdf.aux packedindex.aux
test -e packedindex-pdf.bbl && mv packedindex-pdf.bbl packedindex.bbl
pdflatex packedindex.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./packedindex.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/comment/comment.sty
Excluding comment 'comment') (./optionman.sty) (./packedindex.aux)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]

LaTeX Warning: Citation `oai:CiteSeerPSU:481302' on page 1 undefined on input l
ine 49.


LaTeX Warning: Citation `journals/talg/FerraginaMMN07' on page 1 undefined on i
nput line 51.


LaTeX Warning: Citation `genometools' on page 1 undefined on input line 54.

(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1] [2]
Overfull \hbox (5.0115pt too wide) in paragraph at lines 250--255
\OT1/ptm/m/n/12 The \OT1/pcr/b/n/12 mkctxmap \OT1/ptm/m/n/12 sub-tool fa-cil-i-
tates late build-ing of a re-verse lookup ta-ble, it can use the \OT1/pcr/m/sl/
12 prefix.suf
[3] [4]

LaTeX Warning: Citation `gttestdata' on page 5 undefined on input line 430.


Overfull \hbox (37.00337pt too wide) in paragraph at lines 439--443
[]\OT1/ptm/m/n/12 First com-pute the \OT1/ptm/m/it/12 packedin-dex \OT1/ptm/m/n
/12 in-dex file (this as-sumes \OT1/pcr/m/sl/12 chr01.19960731.fsa.gz \OT1/ptm/
m/n/12 has been copied/linked
[5] (./packedindex.bbl) [6] (./packedindex.aux)

LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi
8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/sha
re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/share/texlive/texmf-di
st/fonts/type1/urw/courier/ucrbo8a.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courie
r/ucrro8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist
/fonts/type1/urw/times/utmri8a.pfb>
Output written on packedindex.pdf (7 pages, 159320 bytes).
Transcript written on packedindex.log.
pdflatex packedindex.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./packedindex.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/comment/comment.sty
Excluding comment 'comment') (./optionman.sty) (./packedindex.aux)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1] [2]
Overfull \hbox (5.0115pt too wide) in paragraph at lines 250--255
\OT1/ptm/m/n/12 The \OT1/pcr/b/n/12 mkctxmap \OT1/ptm/m/n/12 sub-tool fa-cil-i-
tates late build-ing of a re-verse lookup ta-ble, it can use the \OT1/pcr/m/sl/
12 prefix.suf
[3] [4]
Overfull \hbox (37.00337pt too wide) in paragraph at lines 439--443
[]\OT1/ptm/m/n/12 First com-pute the \OT1/ptm/m/it/12 packedin-dex \OT1/ptm/m/n
/12 in-dex file (this as-sumes \OT1/pcr/m/sl/12 chr01.19960731.fsa.gz \OT1/ptm/
m/n/12 has been copied/linked
[5] (./packedindex.bbl) [6] (./packedindex.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi
8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/sha
re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/share/texlive/texmf-di
st/fonts/type1/urw/courier/ucrbo8a.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courie
r/ucrro8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist
/fonts/type1/urw/times/utmri8a.pfb>
Output written on packedindex.pdf (7 pages, 158685 bytes).
Transcript written on packedindex.log.
mv packedindex.aux packedindex-pdf.aux
test -e packedindex.bbl && mv packedindex.bbl packedindex-pdf.bbl
test -e repfind-pdf.aux && mv repfind-pdf.aux repfind.aux
Makefile:39: recipe for target 'repfind-pdf.aux' failed
make[3]: [repfind-pdf.aux] Error 1 (ignored)
pdflatex repfind.tex && rm repfind.pdf
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./repfind.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (./optionman.sty)
No file repfind.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [2]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)
Overfull \hbox (72.74506pt too wide) in paragraph at lines 124--127
[]\OT1/ptm/m/n/12 Suppose the in-put se-quence $\OML/cmm/m/it/12 S \OT1/cmr/m/n
/12 = \OML/cmm/m/it/12 gagctcgagcgctgct$ \OT1/ptm/m/n/12 is con-tained in the f
ile \OT1/pcr/m/n/12 Repfind-example.fna\OT1/ptm/m/n/12 .

Overfull \hbox (91.74632pt too wide) in paragraph at lines 128--128
[]\OT1/pcr/m/n/10 gt suffixerator -db repfinf-sample.seq -indexname repidx -dna
 -suf -tis -lcp -ssp -pl 
[3]
Overfull \hbox (5.17455pt too wide) in paragraph at lines 161--164
[]\OT1/ptm/m/n/12 Kurtz, S., Choud-huri, J. V., Ohle-busch, E., Schleier-ma-che
r, C., Stoye, J., Giegerich,

LaTeX Warning: Reference `forwardEQ' on page 4 undefined on input line 194.


LaTeX Warning: Reference `reversedEQ' on page 4 undefined on input line 194.


LaTeX Warning: Reference `forwardEQ' on page 4 undefined on input line 198.


LaTeX Warning: Reference `reversedEQ' on page 4 undefined on input line 198.

[4] (./repfind.aux)

LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy8.pfb></
usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist
/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/ur
w/times/utmri8a.pfb>
Output written on repfind.pdf (4 pages, 103910 bytes).
Transcript written on repfind.log.
mv repfind.aux repfind-pdf.aux
test -e repfind-pdf.aux && mv repfind-pdf.aux repfind.aux
bibtex repfind
This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
The top-level auxiliary file: repfind.aux
I found no \citation commands---while reading file repfind.aux
I found no \bibdata command---while reading file repfind.aux
I found no \bibstyle command---while reading file repfind.aux
(There were 3 error messages)
Makefile:32: recipe for target 'repfind-pdf.bbl' failed
make[3]: [repfind-pdf.bbl] Error 2 (ignored)
test -e repfind-pdf.bbl || touch repfind-pdf.bbl
diff repfind-pdf.bbl repfind.bbl || mv repfind.bbl repfind-pdf.bbl && rm -f repfind.bbl
mv repfind.aux repfind-pdf.aux
test -e repfind-pdf.aux && mv repfind-pdf.aux repfind.aux
test -e repfind-pdf.bbl && mv repfind-pdf.bbl repfind.bbl
pdflatex repfind.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./repfind.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (./optionman.sty)
(./repfind.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [2]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)
Overfull \hbox (72.74506pt too wide) in paragraph at lines 124--127
[]\OT1/ptm/m/n/12 Suppose the in-put se-quence $\OML/cmm/m/it/12 S \OT1/cmr/m/n
/12 = \OML/cmm/m/it/12 gagctcgagcgctgct$ \OT1/ptm/m/n/12 is con-tained in the f
ile \OT1/pcr/m/n/12 Repfind-example.fna\OT1/ptm/m/n/12 .

Overfull \hbox (91.74632pt too wide) in paragraph at lines 128--128
[]\OT1/pcr/m/n/10 gt suffixerator -db repfinf-sample.seq -indexname repidx -dna
 -suf -tis -lcp -ssp -pl 
[3]
Overfull \hbox (5.17455pt too wide) in paragraph at lines 161--164
[]\OT1/ptm/m/n/12 Kurtz, S., Choud-huri, J. V., Ohle-busch, E., Schleier-ma-che
r, C., Stoye, J., Giegerich,
[4] (./repfind.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy8.pfb></
usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist
/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/ur
w/times/utmri8a.pfb>
Output written on repfind.pdf (4 pages, 103243 bytes).
Transcript written on repfind.log.
pdflatex repfind.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./repfind.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (./optionman.sty)
(./repfind.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [2]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)
Overfull \hbox (72.74506pt too wide) in paragraph at lines 124--127
[]\OT1/ptm/m/n/12 Suppose the in-put se-quence $\OML/cmm/m/it/12 S \OT1/cmr/m/n
/12 = \OML/cmm/m/it/12 gagctcgagcgctgct$ \OT1/ptm/m/n/12 is con-tained in the f
ile \OT1/pcr/m/n/12 Repfind-example.fna\OT1/ptm/m/n/12 .

Overfull \hbox (91.74632pt too wide) in paragraph at lines 128--128
[]\OT1/pcr/m/n/10 gt suffixerator -db repfinf-sample.seq -indexname repidx -dna
 -suf -tis -lcp -ssp -pl 
[3]
Overfull \hbox (5.17455pt too wide) in paragraph at lines 161--164
[]\OT1/ptm/m/n/12 Kurtz, S., Choud-huri, J. V., Ohle-busch, E., Schleier-ma-che
r, C., Stoye, J., Giegerich,
[4] (./repfind.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy8.pfb></
usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist
/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/ur
w/times/utmri8a.pfb>
Output written on repfind.pdf (4 pages, 103243 bytes).
Transcript written on repfind.log.
mv repfind.aux repfind-pdf.aux
test -e repfind.bbl && mv repfind.bbl repfind-pdf.bbl
head -n 6999 ../../testdata/at1MB > read1.fna
echo ">" > read2.fna
tail -n 6945 ../../testdata/at1MB >> read2.fna
cp ../../testdata/U89959_genomic.fas U89959.fna
./findemptyoutfiles.sh
./execcommand.pl tallymer.tex > tallymer-tmp.tex
# file output/gt-suffixerator--dna--pl--tis--suf--lcp--v--parts-4--db-read1.fna-read2.fna--indexname-reads.out already exists
# file output/gt-tallymer-occratio--output-unique-nonunique--minmersize-10--maxmersize-20--esa-reads.out already exists
# file output/gt-tallymer-occratio--output-unique-relative--minmersize-10--maxmersize-20--esa-reads.out already exists
# file output/gt-tallymer-occratio--output-unique-nonunique--mersizes-10-13-17--esa-reads.out already exists
# file output/gt-tallymer-mkindex--mersize-19--minocc-40--esa-reads.out already exists
# file output/gt-tallymer-mkindex--mersize-19--minocc-4--indexname-tyr-reads--counts--pl--esa-reads.out already exists
# file output/gt-tallymer-search--output-qseqnum-qpos-counts-sequence--tyr-tyr-reads--q-U89959.fna.out already exists
pdflatex tallymer-tmp
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./tallymer-tmp.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
No file tallymer-tmp.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex

LaTeX Warning: Citation `KUR:NER:STE:WAR:2008' on page 1 undefined on input lin
e 103.

(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd)

LaTeX Warning: Reference `Examples' on page 1 undefined on input line 114.

[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1phv.fd)
Overfull \hbox (49.67761pt too wide) in paragraph at lines 168--168
[]\OT1/pcr/m/n/12 gt tallymer occratio: error: fopen(): cannot open file 'reads
.prj':
[2]

LaTeX Warning: Reference `Examples' on page 3 undefined on input line 192.

[3]
Overfull \hbox (49.67761pt too wide) in paragraph at lines 255--255
[]\OT1/pcr/m/n/12 gt tallymer occratio: error: fopen(): cannot open file 'reads
.prj':
[4] [5] [6] [7] [8] [9] (./tallymer-tmp.aux)

LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr1
2.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></
usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/share/texlive/t
exmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw
/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.p
fb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on tallymer-tmp.pdf (9 pages, 139957 bytes).
Transcript written on tallymer-tmp.log.
pdflatex tallymer-tmp
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./tallymer-tmp.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
(./tallymer-tmp.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)

*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1phv.fd)
Overfull \hbox (49.67761pt too wide) in paragraph at lines 168--168
[]\OT1/pcr/m/n/12 gt tallymer occratio: error: fopen(): cannot open file 'reads
.prj':
[2] [3]
Overfull \hbox (49.67761pt too wide) in paragraph at lines 255--255
[]\OT1/pcr/m/n/12 gt tallymer occratio: error: fopen(): cannot open file 'reads
.prj':
[4] [5] [6] [7] [8] [9] (./tallymer-tmp.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmex10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr1
2.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></
usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/share/texlive/t
exmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/urw/helvetic/uhvr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw
/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.p
fb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on tallymer-tmp.pdf (9 pages, 139321 bytes).
Transcript written on tallymer-tmp.log.
mv tallymer-tmp.pdf tallymer.pdf
../../bin/gt packedindex mkindex -dna -dir rev -parts 12 -bsize 10 \
                      -sprank -locfreq 32 -tis -ssp -indexname pck-human\
                      -db ../../testdata/at1MB
cp ../../testdata/Q1.gz Q1.gz
./findemptyoutfiles.sh
./execcommand.pl tagerator.tex > tagerator-tmp.tex
# file output/gt-tagerator--q-Q1.gz--maxocc-10--pck-pck-human.out already exists
# file output/gt-tagerator--q-Q1.gz--pck-pck-human--e-2.out already exists
# file output/gt-tagerator--q-Q1.gz--pck-pck-human--e-1--maxocc-5.out already exists
pdflatex tagerator-tmp
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./tagerator-tmp.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (./optionman.sty)
No file tagerator-tmp.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [2] [3] [4]
Overfull \hbox (5.90344pt too wide) in paragraph at lines 263--263
[]\OT1/pcr/m/n/8 # computing prefix matches with up to 1 differences and at mos
t 5 occurrences in the subject sequences[] 
[5] (./tagerator-tmp.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.
pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></
usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-di
st/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/
urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri
8a.pfb>
Output written on tagerator-tmp.pdf (5 pages, 112678 bytes).
Transcript written on tagerator-tmp.log.
pdflatex tagerator-tmp
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./tagerator-tmp.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (./optionman.sty)
(./tagerator-tmp.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd
)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [2] [3] [4]
Overfull \hbox (5.90344pt too wide) in paragraph at lines 263--263
[]\OT1/pcr/m/n/8 # computing prefix matches with up to 1 differences and at mos
t 5 occurrences in the subject sequences[] 
[5] (./tagerator-tmp.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.
pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></
usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-di
st/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/
urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri
8a.pfb>
Output written on tagerator-tmp.pdf (5 pages, 112678 bytes).
Transcript written on tagerator-tmp.log.
mv tagerator-tmp.pdf tagerator.pdf
test -e genomediff-pdf.aux && mv genomediff-pdf.aux genomediff.aux
Makefile:39: recipe for target 'genomediff-pdf.aux' failed
make[3]: [genomediff-pdf.aux] Error 1 (ignored)
pdflatex genomediff.tex && rm genomediff.pdf
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./genomediff.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(./optionman.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty)
(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
No file genomediff.aux.
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd)

LaTeX Warning: Citation `HAU:DOM:WIE:2008' on page 1 undefined on input line 88
.


LaTeX Warning: Citation `HAU:PFA:DOM:WIE:2009' on page 1 undefined on input lin
e 88.


LaTeX Warning: Citation `HAU:REE:PFA:2011' on page 1 undefined on input line 88
.


LaTeX Warning: Citation `genometools' on page 1 undefined on input line 96.

[1]

LaTeX Warning: Reference `tab:gdopts' on page 2 undefined on input line 163.

[2]

LaTeX Warning: Reference `code:lua' on page 3 undefined on input line 239.

[3] [4]
Overfull \hbox (35.00766pt too wide) in paragraph at lines 322--323
[][][][][][][][][][][][][][][][][][][][][][][][] 
No file genomediff.bbl.
[5] (./genomediff.aux)

LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmbxti10.pfb></usr/share/texlive/texmf-dist/fonts/
type1/public/amsfonts/cm/cmitt10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmmi8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo
nts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/
cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.p
fb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></u
sr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/sha
re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti12.pfb></usr/share/tex
live/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/t
exmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on genomediff.pdf (6 pages, 163510 bytes).
Transcript written on genomediff.log.
mv genomediff.aux genomediff-pdf.aux
test -e genomediff-pdf.aux && mv genomediff-pdf.aux genomediff.aux
bibtex genomediff
This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
The top-level auxiliary file: genomediff.aux
The style file: unsrt.bst
Database file #1: gtmanuals.bib
test -e genomediff-pdf.bbl || touch genomediff-pdf.bbl
diff genomediff-pdf.bbl genomediff.bbl || mv genomediff.bbl genomediff-pdf.bbl && rm -f genomediff.bbl
0a1,25
> \begin{thebibliography}{1}
> 
> \bibitem{HAU:DOM:WIE:2008}
> Bernhard Haubold, Mirjana Domazet-Loso, and Thomas Wiehe.
> \newblock An alignment-free distance measure for closely related genomes.
> \newblock In {\em RECOMB-CG ’08: Proceedings of the international workshop on
>   Comparative Genomics}, pages 87--99, Berlin, Heidelberg, 2008.
>   Springer-Verlag.
> 
> \bibitem{HAU:PFA:DOM:WIE:2009}
> B.~Haubold, P.~Pfaffelhuber, M.~Domazet-Loso, and T.~Wiehe.
> \newblock Estimating mutation distances from unaligned genomes.
> \newblock {\em J. Comput. Biol.}, 16:1487--1500, "Oct" 2009.
> 
> \bibitem{HAU:REE:PFA:2011}
> Bernhard Haubold, Floyd~A. Reed, and Peter Pfaffelhuber.
> \newblock Alignment-free estimation of nucleotide diversity.
> \newblock {\em Bioinformatics}, 27(4):449--455, 2011.
> 
> \bibitem{genometools}
> Gordon Gremme.
> \newblock The \textsc{GenomeTools} genome analysis system.
> \newblock \url{http://genometools.org}.
> 
> \end{thebibliography}
mv genomediff.aux genomediff-pdf.aux
test -e genomediff-pdf.aux && mv genomediff-pdf.aux genomediff.aux
test -e genomediff-pdf.bbl && mv genomediff-pdf.bbl genomediff.bbl
pdflatex genomediff.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./genomediff.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(./optionman.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty)
(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(./genomediff.aux)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd)

LaTeX Warning: Citation `HAU:DOM:WIE:2008' on page 1 undefined on input line 88
.


LaTeX Warning: Citation `HAU:PFA:DOM:WIE:2009' on page 1 undefined on input lin
e 88.


LaTeX Warning: Citation `HAU:REE:PFA:2011' on page 1 undefined on input line 88
.


LaTeX Warning: Citation `genometools' on page 1 undefined on input line 96.

[1] [2] [3] [4]
Overfull \hbox (35.00766pt too wide) in paragraph at lines 322--323
[][][][][][][][][][][][][][][][][][][][][][][][] 
(./genomediff.bbl) [5] (./genomediff.aux)

LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmbxti10.pfb></usr/share/texlive/texmf-dist/fonts/
type1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmitt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.pfb></
usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti12.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on genomediff.pdf (6 pages, 176742 bytes).
Transcript written on genomediff.log.
pdflatex genomediff.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./genomediff.tex
LaTeX2e <2016/02/01>
Babel <3.9n> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(./optionman.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty)
(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(./genomediff.aux)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [1] [2] [3] [4]
Overfull \hbox (35.00766pt too wide) in paragraph at lines 322--323
[][][][][][][][][][][][][][][][][][][][][][][][] 
(./genomediff.bbl) [5] (./genomediff.aux) )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmbxti10.pfb></usr/share/texlive/texmf-dist/fonts/
type1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmitt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.pfb></
usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti12.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on genomediff.pdf (6 pages, 176515 bytes).
Transcript written on genomediff.log.
mv genomediff.aux genomediff-pdf.aux
test -e genomediff.bbl && mv genomediff.bbl genomediff-pdf.bbl
make[3]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.8+ds/doc/manuals'
make[2]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.8+ds'
make[1]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.8+ds'
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/genometools-1.5.8+ds'
bin/gt -test
seed=781871127
Lua serializer module...ok
MD5 seqid module...ok
PBS finder module...ok
alignment class...ok
alphabet class...ok
array class...ok
array example...ok
array2dim example...ok
array2dim sparse example...ok
array3dim example...ok
basename module...ok
bit pack array class...ok
bit pack string module...ok
bittab class...ok
bittab example...ok
block class...ok
bsearch module...ok
codon iterator class, encoded...ok
codon iterator class, simple...ok
color space module...ok
combinatorics...ok
compactulongstore class...ok
compressed bitsequence...ok
countingsort module...ok
cstr module...ok
cstr table class...ok
database feature index class (GFF-like)...ok
description buffer class...ok
diagram class...ok
disc distri class...ok
dlist class...ok
dlist example...ok
dynamic bittab class...ok
editscript class...ok
element class...ok
elias gamma class...ok
encdesc class...ok
encseq builder class...ok
encseq gc module...ok
evaluator class...ok
feature in stream class...ok
feature node class...ok
feature node iterator example...ok
genome node class...ok
gff3 escaping module...ok
golomb class...ok
grep module...ok
hashmap class...ok
hashtable class...ok
hmm class...ok
huffman coding class...ok
imageinfo class...ok
interval tree class...ok
intset classes...ok
kmer_database class...ok
line class...ok
mathsupport module...ok
memory allocator module...ok
memory feature index class...ok
multieoplist...ok
popcount sorted tab...ok
priority queue class...ok
quality module...ok
queue class...ok
range class...ok
range minimum query class...ok
ranked list class...ok
rdj: string graph class...ok
rdj: suffix-prefix matches list module...ok
red-black tree class...ok
safearith example...ok
safearith module...ok
sequence buffer class...ok
splicedseq class...ok
splitter class...ok
string class...ok
string matching module...ok
style class...ok
symbol module...ok
tag value map class...ok
tag value map example...ok
tokenizer class...ok
track class...ok
translator class...ok
transtable class...ok
uint64hashtable...ok
xdrop...ok
cd testsuite; ./testsuite.rb -keywords 'gt_sketch and not gt_python and not gt_ruby' -threads 3
seed=1066253395
1364: gt sketch short test (unknown output format)                : ok
1362: gt sketch short test                                        : ok
1363: gt sketch short test (stdin)                                : ok
1365: gt sketch short test (unwriteable PNG file)                 : ok
1367: gt sketch short test (nonexistant style file)               : ok
1369: gt sketch prob 1                                            : ok
1368: gt sketch short test (invalid style file)                   : ok
1366: gt sketch short test (unwriteable PDF file)                 : ok
1370: gt sketch prob 2                                            : ok
1372: gt sketch multiline without parent                          : ok
1371: gt sketch track IDs to style file                           : ok
1373: gt sketch pipe                                              : ok
1376: gt sketch -showrecmaps (normal text size)                   : ok
1375: gt sketch -showrecmaps                                      : ok
1377: gt sketch -showrecmaps (narrow image)                       : ok
1378: gt sketch -showrecmaps (large text size)                    : ok
1379: gt sketch for transcript (neg. coords in ruler)             : ok
1381: sketch_constructed (C)                                      : ok
1382: sketch_parsed (C)                                           : ok
1383: sketch_parsed reverse order (C)                             : ok
1384: sketch_constructed (Lua)                                    : ok
1385: sketch_parsed (Lua)                                         : ok
1374: gt sketch streams <-> file output                           : ok
1380: gt sketch runtime Lua failures                              : ok
make[1]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.8+ds'
 fakeroot debian/rules binary-arch
dh binary-arch --with python2
   dh_testroot -a
   dh_prep -a
   debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/genometools-1.5.8+ds'
dh_auto_install -- installmanpages useshared=yes \
  x32=no 64bit=no errorcheck=no prefix=/<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr
	make -j1 install DESTDIR=/<<BUILDDIR>>/genometools-1.5.8\+ds/debian/tmp AM_UPDATE_INFO_DIR=no installmanpages useshared=yes x32=no 64bit=no errorcheck=no prefix=/<<BUILDDIR>>/genometools-1.5.8\+ds/debian/tmp/usr
make[2]: Entering directory '/<<BUILDDIR>>/genometools-1.5.8+ds'
[link libgenometools.so]
test -d /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/bin || mkdir -p /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/bin
cp bin/gt /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/bin
strip /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/bin/gt
cp -r gtdata /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/bin
test -d /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/include/genometools/core \
  || mkdir -p /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/include/genometools/core
cp src/core/*_api.h /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/include/genometools/core
test -d /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/include/genometools/extended \
          || mkdir -p /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/include/genometools/extended
cp src/extended/*_api.h /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/include/genometools/extended
test -d /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/include/genometools/annotationsketch \
          || mkdir -p /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/include/genometools/annotationsketch
cp src/annotationsketch/*_api.h \
          /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/include/genometools/annotationsketch
test -d /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/include/genometools/ltr \
          || mkdir -p /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/include/genometools/ltr
cp src/ltr/*_api.h /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/include/genometools/ltr
cp obj/gt_config.h /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/include/genometools
cp src/genometools.h /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/include/genometools
test -d /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/lib || mkdir -p /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/lib
cp lib/libgenometools.a /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/lib
cp lib/libgenometools.so.0 /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/lib
ln -fs /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/lib/libgenometools.so.0 /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/lib/libgenometools.so
[build config script install]
sed -e 's!@CC@!cc!' -e 's!@CFLAGS@!-g -O2 -fstack-protector-strong -Wformat -Werror=format-security!' \
  -e 's!@CPPFLAGS@!-I\\"/<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/include\\" -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DHAVE_MEMMOVE -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN -DLUA_USE_MKSTEMP -DHAVE_SQLITE!' \
  -e 's!@CXX@!g++!' -e 's!@CXXFLAGS@!-g -O2 -fstack-protector-strong -Wformat -Werror=format-security!' \
  -e 's!@LDFLAGS@!-L/<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/lib -Wl,-z,relro -L/usr/local/lib!' \
  -e 's!@LIBS@! -lm -lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 -llua5.1-filesystem -llua5.1-des56 -ltre -lm -lpthread -ldl -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo -lsqlite3!' -e "s!@VERSION@!`cat VERSION`!" \
  -e 's!@BUILDSTAMP@!"2016-03-17 06:15:15"!' \
  -e 's!@SYSTEM@!Linux!' <src/genometools-config.in \
  >/<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/bin/genometools-config
chmod 755 /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/bin/genometools-config
bin/gt -createman /tmp/gtmanpages
warning: skipping tool 'mgth' in iterator (not a GtTool object)
warning: skipping tool 'mkfmindex' in iterator (not a GtTool object)
warning: skipping tool 'suffixerator' in iterator (not a GtTool object)
warning: skipping tool 'chkintegrity' in iterator (not a GtTool object)
warning: skipping tool 'chksearch' in iterator (not a GtTool object)
warning: skipping tool 'mkctxmap' in iterator (not a GtTool object)
warning: skipping tool 'mkindex' in iterator (not a GtTool object)
warning: skipping tool 'trsuftab' in iterator (not a GtTool object)
test -d /<<BUILDDIR>>/genometools-1.5.8+ds/doc/manpages || mkdir -p /<<BUILDDIR>>/genometools-1.5.8+ds/doc/manpages
rm -f /<<BUILDDIR>>/genometools-1.5.8+ds/doc/manpages/*
scripts/create_manpages /tmp/gtmanpages /<<BUILDDIR>>/genometools-1.5.8+ds/doc/manpages
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
.a2x: WARNING: --destination-dir option is only applicable to HTML based outputs

test ! -d /<<BUILDDIR>>/genometools-1.5.8+ds/doc/manpages || \
  ((test -d /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/share/man/man1 || mkdir -p /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/share/man/man1) \
    && cp /<<BUILDDIR>>/genometools-1.5.8+ds/doc/manpages/* /<<BUILDDIR>>/genometools-1.5.8+ds/debian/tmp/usr/share/man/man1)
make[2]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.8+ds'
dh_auto_install --sourcedirectory=gtpython \
  --destdir=/<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools
pyversions: missing X(S)-Python-Version in control file, fall back to debian/pyversions
pyversions: missing debian/pyversions file, fall back to supported versions
	python setup.py install --force --root=/<<BUILDDIR>>/genometools-1.5.8\+ds/debian/python-genometools --no-compile -O0 --install-layout=deb
running install
running build
running build_py
creating build
creating build/lib.linux-armv7l-2.7
creating build/lib.linux-armv7l-2.7/gt
copying gt/props.py -> build/lib.linux-armv7l-2.7/gt
copying gt/__init__.py -> build/lib.linux-armv7l-2.7/gt
copying gt/version.py -> build/lib.linux-armv7l-2.7/gt
copying gt/dlload.py -> build/lib.linux-armv7l-2.7/gt
creating build/lib.linux-armv7l-2.7/gt/core
copying gt/core/array.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/gtrange.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/alphabet.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/gtstr.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/warning.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/str_array.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/encseq.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/__init__.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/error.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/readmode.py -> build/lib.linux-armv7l-2.7/gt/core
creating build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/color.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/custom_track.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/feature_stream.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/diagram.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/graphics.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/canvas.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/custom_track_example.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/__init__.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/layout.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/feature_index.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/image_info.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/block.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/style.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/rec_map.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
creating build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/gff3_visitor.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/custom_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/region_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/feature_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/sequence_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/anno_db.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/sort_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/eof_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/genome_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/merge_feature_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/meta_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/strand.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/gff3_out_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/add_introns_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/gff3_in_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/dup_feature_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/custom_visitor_example.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/rdb.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/__init__.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/custom_visitor.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/genome_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/feature_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/feature_index.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/custom_stream_example.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/inter_feature_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/comment_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/node_visitor.py -> build/lib.linux-armv7l-2.7/gt/extended
running install_lib
creating /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools
creating /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr
creating /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib
creating /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7
creating /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages
creating /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
copying build/lib.linux-armv7l-2.7/gt/props.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
copying build/lib.linux-armv7l-2.7/gt/__init__.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
copying build/lib.linux-armv7l-2.7/gt/version.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
copying build/lib.linux-armv7l-2.7/gt/dlload.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
creating /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/array.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/gtrange.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/alphabet.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/gtstr.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/warning.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/str_array.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/encseq.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/__init__.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/error.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/readmode.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
creating /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/color.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/custom_track.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/feature_stream.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/diagram.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/graphics.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/canvas.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/custom_track_example.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/__init__.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/layout.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/feature_index.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/image_info.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/block.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/style.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/rec_map.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
creating /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/gff3_visitor.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_stream.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/region_node.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/feature_stream.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/sequence_node.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/anno_db.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/sort_stream.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/eof_node.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/genome_node.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/merge_feature_stream.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/meta_node.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/strand.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/gff3_out_stream.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/add_introns_stream.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/gff3_in_stream.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/dup_feature_stream.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_visitor_example.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/rdb.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/__init__.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_visitor.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/genome_stream.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/feature_node.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/feature_index.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_stream_example.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/inter_feature_stream.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/comment_node.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/node_visitor.py -> /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
running install_egg_info
Writing /<<BUILDDIR>>/genometools-1.5.8+ds/debian/python-genometools/usr/lib/python2.7/dist-packages/GenomeTools-1.5.8.egg-info
make[1]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.8+ds'
   dh_install -a
   dh_installdocs -a
   dh_installchangelogs -a
   dh_installman -a
   dh_python2 -a
   dh_perl -a
   dh_link -a
   dh_strip_nondeterminism -a
   dh_compress -a
   dh_fixperms -a
   debian/rules override_dh_strip
make[1]: Entering directory '/<<BUILDDIR>>/genometools-1.5.8+ds'
dh_strip --dbg-package=genometools-dbg
make[1]: Leaving directory '/<<BUILDDIR>>/genometools-1.5.8+ds'
   dh_makeshlibs -a
   dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/genometools/usr/bin/gt was not linked against libglib-2.0.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/genometools/usr/bin/gt was not linked against libdl.so.2 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libgenometools0/usr/lib/libgenometools.so.0 was not linked against libglib-2.0.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libgenometools0/usr/lib/libgenometools.so.0 was not linked against liblua5.1-filesystem.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libgenometools0/usr/lib/libgenometools.so.0 was not linked against liblua5.1-des56.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libgenometools0/usr/lib/libgenometools.so.0 was not linked against liblua5.1-lpeg.so.2 (it uses none of the library's symbols)
   dh_installdeb -a
   dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: Depends field of package libgenometools0-dev: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: Depends field of package genometools-dbg: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
   dh_md5sums -a
   dh_builddeb -a
dpkg-deb: building package 'libgenometools0-dev' in '../libgenometools0-dev_1.5.8+ds-2_armhf.deb'.
dpkg-deb: building package 'genometools-dbg' in '../genometools-dbg_1.5.8+ds-2_armhf.deb'.
dpkg-deb: building package 'genometools' in '../genometools_1.5.8+ds-2_armhf.deb'.
dpkg-deb: building package 'libgenometools0' in '../libgenometools0_1.5.8+ds-2_armhf.deb'.
 dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../genometools_1.5.8+ds-2_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build genometools-1.5.8+ds
dpkg-buildpackage: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160317-0732

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


genometools_1.5.8+ds-2_armhf.changes:
-------------------------------------

Format: 1.8
Date: Fri, 11 Mar 2016 16:10:42 +0000
Source: genometools
Binary: genometools genometools-common libgenometools0 libgenometools0-dev genometools-doc genometools-dbg python-genometools
Architecture: armhf
Version: 1.5.8+ds-2
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <sascha@steinbiss.name>
Description:
 genometools - versatile genome analysis toolkit
 genometools-common - shared data files for GenomeTools
 genometools-dbg - versatile genome analysis toolkit, with debug symbols
 genometools-doc - documentation for GenomeTools
 libgenometools0 - versatile genome analysis library
 libgenometools0-dev - development files for GenomeTools
 python-genometools - Python bindings for genometools
Changes:
 genometools (1.5.8+ds-2) unstable; urgency=medium
 .
   * Fix locale (LC_PAPER) for LaTeX runs (reproducibility).
   * Patch documentation generation to gather API symbols in
     deterministic order.
   * Do not delete two docu files in clean step.
Checksums-Sha1:
 5f48e94f736805d7bd283904fd49c3ff8656b04f 4127480 genometools-dbg_1.5.8+ds-2_armhf.deb
 8beb113a973417a270aa6bb9218052a34c13a87c 1727022 genometools_1.5.8+ds-2_armhf.deb
 49ecd014d0815f45385e1e82c6d18a823b4085fb 77754 libgenometools0-dev_1.5.8+ds-2_armhf.deb
 eae3ba902bc416731d3f7b0560d4b7db90116f65 1601114 libgenometools0_1.5.8+ds-2_armhf.deb
Checksums-Sha256:
 7b775276f07d34be0b6c283895fbf2213a5af14594095f6a752d65bf4f892885 4127480 genometools-dbg_1.5.8+ds-2_armhf.deb
 5dd823dddce889858a35a5deed3b1977db98b763173c15850c411286b6fe2737 1727022 genometools_1.5.8+ds-2_armhf.deb
 06ec3a26cf9bd9d7babf5c10165bd37ba54bf315904bba5d7964abc888594e09 77754 libgenometools0-dev_1.5.8+ds-2_armhf.deb
 3336d1134bd17cd0f82aa2a1c4c5bc9bea0aeacddea52e2ecfde4bbd4e762572 1601114 libgenometools0_1.5.8+ds-2_armhf.deb
Files:
 c6131f6afd39e03cc660a5ecca5f5d47 4127480 debug extra genometools-dbg_1.5.8+ds-2_armhf.deb
 fb2b15986be5d8b73872f37ade1f252c 1727022 science optional genometools_1.5.8+ds-2_armhf.deb
 eee1ffc13f3082f0d0356c740a546ad8 77754 libdevel optional libgenometools0-dev_1.5.8+ds-2_armhf.deb
 84a906693cc4a293466ed4e5c5f3fe4d 1601114 libs optional libgenometools0_1.5.8+ds-2_armhf.deb

+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


genometools-dbg_1.5.8+ds-2_armhf.deb
------------------------------------

 new debian package, version 2.0.
 size 4127480 bytes: control archive=712 bytes.
     632 bytes,    15 lines      control              
     341 bytes,     4 lines      md5sums              
 Package: genometools-dbg
 Source: genometools
 Version: 1.5.8+ds-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 4598
 Depends: genometools (= 1.5.8+ds-2) | libgenometools0 (= 1.5.8+ds-2)
 Section: debug
 Priority: extra
 Homepage: http://genometools.org
 Description: versatile genome analysis toolkit, with debug symbols
  This package contains debug information stripped from the GenomeTools.
  You may decide to install it to help identifying issues, typically
  to help communication with upstream developers.
 Build-Ids: 9645f4d5e2029cf366c4484761b5567487a304f2

drwxr-xr-x root/root         0 2016-03-17 07:31 ./
drwxr-xr-x root/root         0 2016-03-17 07:31 ./usr/
drwxr-xr-x root/root         0 2016-03-17 07:31 ./usr/lib/
drwxr-xr-x root/root         0 2016-03-17 07:31 ./usr/lib/debug/
drwxr-xr-x root/root         0 2016-03-17 07:31 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2016-03-17 07:31 ./usr/lib/debug/.build-id/96/
-rw-r--r-- root/root   4682796 2016-03-17 07:31 ./usr/lib/debug/.build-id/96/45f4d5e2029cf366c4484761b5567487a304f2.debug
drwxr-xr-x root/root         0 2016-03-17 07:30 ./usr/share/
drwxr-xr-x root/root         0 2016-03-17 07:30 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-03-17 07:31 ./usr/share/doc/genometools-dbg/
-rw-r--r-- root/root      2738 2016-03-11 16:10 ./usr/share/doc/genometools-dbg/changelog.Debian.gz
-rw-r--r-- root/root      6081 2016-01-07 19:56 ./usr/share/doc/genometools-dbg/changelog.gz
-rw-r--r-- root/root      5106 2016-03-11 09:51 ./usr/share/doc/genometools-dbg/copyright


genometools_1.5.8+ds-2_armhf.deb
--------------------------------

 new debian package, version 2.0.
 size 1727022 bytes: control archive=3569 bytes.
     890 bytes,    16 lines      control              
    7249 bytes,   101 lines      md5sums              
 Package: genometools
 Version: 1.5.8+ds-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 5507
 Depends: libbz2-1.0, libc6 (>= 2.15), libcairo2 (>= 1.2.4), libexpat1 (>= 2.0.1), libglib2.0-0 (>= 2.12.0), liblua5.1-0, libpango-1.0-0 (>= 1.14.0), libpangocairo-1.0-0 (>= 1.14.0), libsqlite3-0 (>= 3.5.9), libtre5, lua-filesystem, lua-lpeg, lua-md5, zlib1g (>= 1:1.2.3.3), genometools-common
 Section: science
 Priority: optional
 Homepage: http://genometools.org
 Description: versatile genome analysis toolkit
  The GenomeTools contains a collection of useful tools for biological
  sequence analysis and -presentation combined into a single binary.
  .
  The toolkit contains binaries for sequence and annotation handling, sequence
  compression, index structure generation and access, annotation visualization,
  and much more.

drwxr-xr-x root/root         0 2016-03-17 07:31 ./
drwxr-xr-x root/root         0 2016-03-17 07:30 ./usr/
drwxr-xr-x root/root         0 2016-03-17 07:31 ./usr/bin/
-rwxr-xr-x root/root   5472628 2016-03-17 07:31 ./usr/bin/gt
drwxr-xr-x root/root         0 2016-03-17 07:31 ./usr/share/
drwxr-xr-x root/root         0 2016-03-17 07:30 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-03-17 07:31 ./usr/share/doc/genometools/
-rw-r--r-- root/root       833 2016-01-07 19:56 ./usr/share/doc/genometools/CONTRIBUTORS
-rw-r--r-- root/root      1772 2016-01-07 19:56 ./usr/share/doc/genometools/README
-rw-r--r-- root/root         6 2016-01-07 19:56 ./usr/share/doc/genometools/VERSION
-rw-r--r-- root/root      2738 2016-03-11 16:10 ./usr/share/doc/genometools/changelog.Debian.gz
-rw-r--r-- root/root      6081 2016-01-07 19:56 ./usr/share/doc/genometools/changelog.gz
-rw-r--r-- root/root      5106 2016-03-11 09:51 ./usr/share/doc/genometools/copyright
drwxr-xr-x root/root         0 2016-03-17 07:31 ./usr/share/man/
drwxr-xr-x root/root         0 2016-03-17 07:31 ./usr/share/man/man1/
-rw-r--r-- root/root       835 2016-03-17 07:31 ./usr/share/man/man1/gt-bed_to_gff3.1.gz
-rw-r--r-- root/root      1621 2016-03-17 07:31 ./usr/share/man/man1/gt-cds.1.gz
-rw-r--r-- root/root      1250 2016-03-17 07:31 ./usr/share/man/man1/gt-chain2dim.1.gz
-rw-r--r-- root/root      1071 2016-03-17 07:31 ./usr/share/man/man1/gt-chseqids.1.gz
-rw-r--r-- root/root       667 2016-03-17 07:31 ./usr/share/man/man1/gt-clean.1.gz
-rw-r--r-- root/root      1037 2016-03-17 07:31 ./usr/share/man/man1/gt-compreads-compress.1.gz
-rw-r--r-- root/root      1009 2016-03-17 07:31 ./usr/share/man/man1/gt-compreads-decompress.1.gz
-rw-r--r-- root/root      1079 2016-03-17 07:31 ./usr/share/man/man1/gt-compreads-refcompress.1.gz
-rw-r--r-- root/root       876 2016-03-17 07:31 ./usr/share/man/man1/gt-compreads-refdecompress.1.gz
-rw-r--r-- root/root       737 2016-03-17 07:31 ./usr/share/man/man1/gt-compreads.1.gz
-rw-r--r-- root/root       771 2016-03-17 07:31 ./usr/share/man/man1/gt-condenseq.1.gz
-rw-r--r-- root/root       775 2016-03-17 07:31 ./usr/share/man/man1/gt-congruence-spacedseed.1.gz
-rw-r--r-- root/root       790 2016-03-17 07:31 ./usr/share/man/man1/gt-congruence.1.gz
-rw-r--r-- root/root       969 2016-03-17 07:31 ./usr/share/man/man1/gt-convertseq.1.gz
-rw-r--r-- root/root      1412 2016-03-17 07:31 ./usr/share/man/man1/gt-csa.1.gz
-rw-r--r-- root/root       648 2016-03-17 07:31 ./usr/share/man/man1/gt-dot.1.gz
-rw-r--r-- root/root       813 2016-03-17 07:31 ./usr/share/man/man1/gt-dupfeat.1.gz
-rw-r--r-- root/root       787 2016-03-17 07:31 ./usr/share/man/man1/gt-encseq-bench.1.gz
-rw-r--r-- root/root       840 2016-03-17 07:31 ./usr/share/man/man1/gt-encseq-bitextract.1.gz
-rw-r--r-- root/root       824 2016-03-17 07:31 ./usr/share/man/man1/gt-encseq-check.1.gz
-rw-r--r-- root/root      1052 2016-03-17 07:31 ./usr/share/man/man1/gt-encseq-decode.1.gz
-rw-r--r-- root/root      1069 2016-03-17 07:31 ./usr/share/man/man1/gt-encseq-encode.1.gz
-rw-r--r-- root/root       939 2016-03-17 07:31 ./usr/share/man/man1/gt-encseq-info.1.gz
-rw-r--r-- root/root       801 2016-03-17 07:31 ./usr/share/man/man1/gt-encseq-md5.1.gz
-rw-r--r-- root/root      1029 2016-03-17 07:31 ./usr/share/man/man1/gt-encseq-sample.1.gz
-rw-r--r-- root/root       784 2016-03-17 07:31 ./usr/share/man/man1/gt-encseq.1.gz
-rw-r--r-- root/root       913 2016-03-17 07:31 ./usr/share/man/man1/gt-encseq2spm.1.gz
-rw-r--r-- root/root      1174 2016-03-17 07:31 ./usr/share/man/man1/gt-eval.1.gz
-rw-r--r-- root/root      2045 2016-03-17 07:31 ./usr/share/man/man1/gt-extractfeat.1.gz
-rw-r--r-- root/root      2122 2016-03-17 07:31 ./usr/share/man/man1/gt-extractseq.1.gz
-rw-r--r-- root/root       804 2016-03-17 07:31 ./usr/share/man/man1/gt-fastq_sample.1.gz
-rw-r--r-- root/root       869 2016-03-17 07:31 ./usr/share/man/man1/gt-featureindex.1.gz
-rw-r--r-- root/root      1584 2016-03-17 07:31 ./usr/share/man/man1/gt-fingerprint.1.gz
-rw-r--r-- root/root      1712 2016-03-17 07:31 ./usr/share/man/man1/gt-genomediff.1.gz
-rw-r--r-- root/root      1924 2016-03-17 07:31 ./usr/share/man/man1/gt-gff3.1.gz
-rw-r--r-- root/root       775 2016-03-17 07:31 ./usr/share/man/man1/gt-gff3_to_gtf.1.gz
-rw-r--r-- root/root       993 2016-03-17 07:31 ./usr/share/man/man1/gt-gff3validator.1.gz
-rw-r--r-- root/root       804 2016-03-17 07:31 ./usr/share/man/man1/gt-gtf_to_gff3.1.gz
-rw-r--r-- root/root      2417 2016-03-17 07:31 ./usr/share/man/man1/gt-hop.1.gz
-rw-r--r-- root/root      1528 2016-03-17 07:31 ./usr/share/man/man1/gt-id_to_md5.1.gz
-rw-r--r-- root/root      1146 2016-03-17 07:31 ./usr/share/man/man1/gt-inlineseq_add.1.gz
-rw-r--r-- root/root       759 2016-03-17 07:31 ./usr/share/man/man1/gt-inlineseq_split.1.gz
-rw-r--r-- root/root       828 2016-03-17 07:31 ./usr/share/man/man1/gt-interfeat.1.gz
-rw-r--r-- root/root       665 2016-03-17 07:31 ./usr/share/man/man1/gt-loccheck.1.gz
-rw-r--r-- root/root       877 2016-03-17 07:31 ./usr/share/man/man1/gt-ltrclustering.1.gz
-rw-r--r-- root/root      2165 2016-03-17 07:31 ./usr/share/man/man1/gt-ltrdigest.1.gz
-rw-r--r-- root/root      1564 2016-03-17 07:31 ./usr/share/man/man1/gt-ltrharvest.1.gz
-rw-r--r-- root/root       939 2016-03-17 07:31 ./usr/share/man/man1/gt-matchtool.1.gz
-rw-r--r-- root/root       893 2016-03-17 07:31 ./usr/share/man/man1/gt-matstat.1.gz
-rw-r--r-- root/root       831 2016-03-17 07:31 ./usr/share/man/man1/gt-md5_to_id.1.gz
-rw-r--r-- root/root       886 2016-03-17 07:31 ./usr/share/man/man1/gt-merge.1.gz
-rw-r--r-- root/root       801 2016-03-17 07:31 ./usr/share/man/man1/gt-mergefeat.1.gz
-rw-r--r-- root/root       843 2016-03-17 07:31 ./usr/share/man/man1/gt-mkfeatureindex.1.gz
-rw-r--r-- root/root       666 2016-03-17 07:31 ./usr/share/man/man1/gt-mmapandread.1.gz
-rw-r--r-- root/root      1294 2016-03-17 07:31 ./usr/share/man/man1/gt-orffinder.1.gz
-rw-r--r-- root/root       832 2016-03-17 07:31 ./usr/share/man/man1/gt-packedindex.1.gz
-rw-r--r-- root/root       742 2016-03-17 07:31 ./usr/share/man/man1/gt-prebwt.1.gz
-rw-r--r-- root/root      1071 2016-03-17 07:31 ./usr/share/man/man1/gt-readjoiner-assembly.1.gz
-rw-r--r-- root/root       909 2016-03-17 07:31 ./usr/share/man/man1/gt-readjoiner-overlap.1.gz
-rw-r--r-- root/root      1256 2016-03-17 07:31 ./usr/share/man/man1/gt-readjoiner-prefilter.1.gz
-rw-r--r-- root/root       851 2016-03-17 07:31 ./usr/share/man/man1/gt-readjoiner.1.gz
-rw-r--r-- root/root      1163 2016-03-17 07:31 ./usr/share/man/man1/gt-repfind.1.gz
-rw-r--r-- root/root       757 2016-03-17 07:31 ./usr/share/man/man1/gt-scriptfilter.1.gz
-rw-r--r-- root/root      1241 2016-03-17 07:31 ./usr/share/man/man1/gt-seed_extend.1.gz
-rw-r--r-- root/root      1836 2016-03-17 07:31 ./usr/share/man/man1/gt-select.1.gz
-rw-r--r-- root/root       979 2016-03-17 07:31 ./usr/share/man/man1/gt-seq.1.gz
-rw-r--r-- root/root       998 2016-03-17 07:31 ./usr/share/man/man1/gt-seqfilter.1.gz
-rw-r--r-- root/root       652 2016-03-17 07:31 ./usr/share/man/man1/gt-seqids.1.gz
-rw-r--r-- root/root      1173 2016-03-17 07:31 ./usr/share/man/man1/gt-seqmutate.1.gz
-rw-r--r-- root/root       784 2016-03-17 07:31 ./usr/share/man/man1/gt-seqorder.1.gz
-rw-r--r-- root/root       895 2016-03-17 07:31 ./usr/share/man/man1/gt-seqstat.1.gz
-rw-r--r-- root/root       894 2016-03-17 07:31 ./usr/share/man/man1/gt-seqtransform.1.gz
-rw-r--r-- root/root       854 2016-03-17 07:31 ./usr/share/man/man1/gt-seqtranslate.1.gz
-rw-r--r-- root/root       945 2016-03-17 07:31 ./usr/share/man/man1/gt-sequniq.1.gz
-rw-r--r-- root/root      1429 2016-03-17 07:31 ./usr/share/man/man1/gt-shredder.1.gz
-rw-r--r-- root/root       772 2016-03-17 07:31 ./usr/share/man/man1/gt-shulengthdist.1.gz
-rw-r--r-- root/root      1021 2016-03-17 07:31 ./usr/share/man/man1/gt-simreads.1.gz
-rw-r--r-- root/root      1093 2016-03-17 07:31 ./usr/share/man/man1/gt-sketch.1.gz
-rw-r--r-- root/root      1028 2016-03-17 07:31 ./usr/share/man/man1/gt-sketch_page.1.gz
-rw-r--r-- root/root      1950 2016-03-17 07:31 ./usr/share/man/man1/gt-snpper.1.gz
-rw-r--r-- root/root      1526 2016-03-17 07:31 ./usr/share/man/man1/gt-speck.1.gz
-rw-r--r-- root/root      1527 2016-03-17 07:31 ./usr/share/man/man1/gt-splicesiteinfo.1.gz
-rw-r--r-- root/root       862 2016-03-17 07:31 ./usr/share/man/man1/gt-splitfasta.1.gz
-rw-r--r-- root/root       973 2016-03-17 07:31 ./usr/share/man/man1/gt-stat.1.gz
-rw-r--r-- root/root      1250 2016-03-17 07:31 ./usr/share/man/man1/gt-tagerator.1.gz
-rw-r--r-- root/root      1038 2016-03-17 07:31 ./usr/share/man/man1/gt-tallymer-mkindex.1.gz
-rw-r--r-- root/root      1014 2016-03-17 07:31 ./usr/share/man/man1/gt-tallymer-occratio.1.gz
-rw-r--r-- root/root       904 2016-03-17 07:31 ./usr/share/man/man1/gt-tallymer-search.1.gz
-rw-r--r-- root/root       803 2016-03-17 07:31 ./usr/share/man/man1/gt-tallymer.1.gz
-rw-r--r-- root/root      1518 2016-03-17 07:31 ./usr/share/man/man1/gt-tirvish.1.gz
-rw-r--r-- root/root      1151 2016-03-17 07:31 ./usr/share/man/man1/gt-uniq.1.gz
-rw-r--r-- root/root       892 2016-03-17 07:31 ./usr/share/man/man1/gt-uniquesub.1.gz
-rw-r--r-- root/root       728 2016-03-17 07:31 ./usr/share/man/man1/gt-wtree.1.gz
-rw-r--r-- root/root      1616 2016-03-17 07:31 ./usr/share/man/man1/gt.1.gz


libgenometools0-dev_1.5.8+ds-2_armhf.deb
----------------------------------------

 new debian package, version 2.0.
 size 77754 bytes: control archive=5118 bytes.
     678 bytes,    18 lines      control              
   13509 bytes,   160 lines      md5sums              
 Package: libgenometools0-dev
 Source: genometools
 Version: 1.5.8+ds-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 560
 Depends: libgenometools0 (= 1.5.8+ds-2)
 Section: libdevel
 Priority: optional
 Homepage: http://genometools.org
 Description: development files for GenomeTools
  This package contains the GenomeTools static library and necessary
  header files.
  .
  Besides basic bioinformatics data structures, the library contains components
  for sequence and annotation handling, sequence compression, index structure
  generation and access, efficient matching, annotation visualization and much
  more.

drwxr-xr-x root/root         0 2016-03-17 07:31 ./
drwxr-xr-x root/root         0 2016-03-17 07:31 ./usr/
drwxr-xr-x root/root         0 2016-03-17 06:15 ./usr/include/
drwxr-xr-x root/root         0 2016-03-17 06:15 ./usr/include/genometools/
drwxr-xr-x root/root         0 2016-03-17 07:30 ./usr/include/genometools/annotationsketch/
-rw-r--r-- root/root      3569 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/block_api.h
-rw-r--r-- root/root      1358 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/canvas_api.h
-rw-r--r-- root/root      2045 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/canvas_cairo_context_api.h
-rw-r--r-- root/root      2467 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/canvas_cairo_file_api.h
-rw-r--r-- root/root      1807 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/color_api.h
-rw-r--r-- root/root      1415 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/custom_track_api.h
-rw-r--r-- root/root      1976 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/custom_track_gc_content_api.h
-rw-r--r-- root/root      2624 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/custom_track_script_wrapper_api.h
-rw-r--r-- root/root      3528 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/diagram_api.h
-rw-r--r-- root/root      1026 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/feature_index_api.h
-rw-r--r-- root/root      1033 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/feature_index_memory_api.h
-rw-r--r-- root/root      1028 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/feature_stream_api.h
-rw-r--r-- root/root     10107 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/graphics_api.h
-rw-r--r-- root/root      2517 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/graphics_cairo_api.h
-rw-r--r-- root/root      2192 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/image_info_api.h
-rw-r--r-- root/root      3965 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/layout_api.h
-rw-r--r-- root/root      2722 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/rec_map_api.h
-rw-r--r-- root/root     10124 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/style_api.h
-rw-r--r-- root/root      2005 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/text_width_calculator_api.h
-rw-r--r-- root/root      1937 2016-03-17 06:15 ./usr/include/genometools/annotationsketch/text_width_calculator_cairo_api.h
drwxr-xr-x root/root         0 2016-03-17 07:30 ./usr/include/genometools/core/
-rw-r--r-- root/root      8585 2016-03-17 06:15 ./usr/include/genometools/core/alphabet_api.h
-rw-r--r-- root/root      3104 2016-03-17 06:15 ./usr/include/genometools/core/array2dim_api.h
-rw-r--r-- root/root      5199 2016-03-17 06:15 ./usr/include/genometools/core/array_api.h
-rw-r--r-- root/root      2711 2016-03-17 06:15 ./usr/include/genometools/core/assert_api.h
-rw-r--r-- root/root      2047 2016-03-17 06:15 ./usr/include/genometools/core/basename_api.h
-rw-r--r-- root/root      4047 2016-03-17 06:15 ./usr/include/genometools/core/bittab_api.h
-rw-r--r-- root/root      2014 2016-03-17 06:15 ./usr/include/genometools/core/bsearch_api.h
-rw-r--r-- root/root      1102 2016-03-17 06:15 ./usr/include/genometools/core/byte_popcount_api.h
-rw-r--r-- root/root      1218 2016-03-17 06:15 ./usr/include/genometools/core/byte_select_api.h
-rw-r--r-- root/root       962 2016-03-17 06:15 ./usr/include/genometools/core/codon_api.h
-rw-r--r-- root/root      3140 2016-03-17 06:15 ./usr/include/genometools/core/codon_iterator_api.h
-rw-r--r-- root/root      2432 2016-03-17 06:15 ./usr/include/genometools/core/codon_iterator_encseq_api.h
-rw-r--r-- root/root      1579 2016-03-17 06:15 ./usr/include/genometools/core/codon_iterator_simple_api.h
-rw-r--r-- root/root      2127 2016-03-17 06:15 ./usr/include/genometools/core/countingsort_api.h
-rw-r--r-- root/root      2313 2016-03-17 06:15 ./usr/include/genometools/core/cstr_api.h
-rw-r--r-- root/root      1990 2016-03-17 06:15 ./usr/include/genometools/core/cstr_table_api.h
-rw-r--r-- root/root      1838 2016-03-17 06:15 ./usr/include/genometools/core/deprecated_api.h
-rw-r--r-- root/root      2925 2016-03-17 06:15 ./usr/include/genometools/core/disc_distri_api.h
-rw-r--r-- root/root      3102 2016-03-17 06:15 ./usr/include/genometools/core/dlist_api.h
-rw-r--r-- root/root     34137 2016-03-17 06:15 ./usr/include/genometools/core/encseq_api.h
-rw-r--r-- root/root      1058 2016-03-17 06:15 ./usr/include/genometools/core/endianess_api.h
-rw-r--r-- root/root      3140 2016-03-17 06:15 ./usr/include/genometools/core/error_api.h
-rw-r--r-- root/root      2910 2016-03-17 06:15 ./usr/include/genometools/core/fasta_api.h
-rw-r--r-- root/root      2992 2016-03-17 06:15 ./usr/include/genometools/core/file_api.h
-rw-r--r-- root/root      4369 2016-03-17 06:15 ./usr/include/genometools/core/fileutils_api.h
-rw-r--r-- root/root      1534 2016-03-17 06:15 ./usr/include/genometools/core/fptr_api.h
-rw-r--r-- root/root      1364 2016-03-17 06:15 ./usr/include/genometools/core/grep_api.h
-rw-r--r-- root/root      4098 2016-03-17 06:15 ./usr/include/genometools/core/hashmap_api.h
-rw-r--r-- root/root      1345 2016-03-17 06:15 ./usr/include/genometools/core/init_api.h
-rw-r--r-- root/root      4805 2016-03-17 06:15 ./usr/include/genometools/core/interval_tree_api.h
-rw-r--r-- root/root      1844 2016-03-17 06:15 ./usr/include/genometools/core/log_api.h
-rw-r--r-- root/root      2556 2016-03-17 06:15 ./usr/include/genometools/core/logger_api.h
-rw-r--r-- root/root      2538 2016-03-17 06:15 ./usr/include/genometools/core/ma_api.h
-rw-r--r-- root/root      2076 2016-03-17 06:15 ./usr/include/genometools/core/md5_encoder_api.h
-rw-r--r-- root/root      1204 2016-03-17 06:15 ./usr/include/genometools/core/md5_fingerprint_api.h
-rw-r--r-- root/root      1481 2016-03-17 06:15 ./usr/include/genometools/core/msort_api.h
-rw-r--r-- root/root      1237 2016-03-17 06:15 ./usr/include/genometools/core/multithread_api.h
-rw-r--r-- root/root     23711 2016-03-17 06:15 ./usr/include/genometools/core/option_api.h
-rw-r--r-- root/root      2007 2016-03-17 06:15 ./usr/include/genometools/core/output_file_api.h
-rw-r--r-- root/root      3072 2016-03-17 06:15 ./usr/include/genometools/core/parseutils_api.h
-rw-r--r-- root/root      1528 2016-03-17 06:15 ./usr/include/genometools/core/phase_api.h
-rw-r--r-- root/root      1196 2016-03-17 06:15 ./usr/include/genometools/core/qsort_r_api.h
-rw-r--r-- root/root      2080 2016-03-17 06:15 ./usr/include/genometools/core/queue_api.h
-rw-r--r-- root/root      3040 2016-03-17 06:15 ./usr/include/genometools/core/range_api.h
-rw-r--r-- root/root      1882 2016-03-17 06:15 ./usr/include/genometools/core/readmode_api.h
-rw-r--r-- root/root      3188 2016-03-17 06:15 ./usr/include/genometools/core/seq_iterator_api.h
-rw-r--r-- root/root      2169 2016-03-17 06:15 ./usr/include/genometools/core/seq_iterator_fastq_api.h
-rw-r--r-- root/root      1667 2016-03-17 06:15 ./usr/include/genometools/core/seq_iterator_sequence_buffer_api.h
-rw-r--r-- root/root      2444 2016-03-17 06:15 ./usr/include/genometools/core/splitter_api.h
-rw-r--r-- root/root      3458 2016-03-17 06:15 ./usr/include/genometools/core/str_api.h
-rw-r--r-- root/root      2923 2016-03-17 06:15 ./usr/include/genometools/core/str_array_api.h
-rw-r--r-- root/root      1588 2016-03-17 06:15 ./usr/include/genometools/core/strand_api.h
-rw-r--r-- root/root      1135 2016-03-17 06:15 ./usr/include/genometools/core/strcmp_api.h
-rw-r--r-- root/root      1449 2016-03-17 06:15 ./usr/include/genometools/core/symbol_api.h
-rw-r--r-- root/root      3473 2016-03-17 06:15 ./usr/include/genometools/core/thread_api.h
-rw-r--r-- root/root      3688 2016-03-17 06:15 ./usr/include/genometools/core/timer_api.h
-rw-r--r-- root/root      4458 2016-03-17 06:15 ./usr/include/genometools/core/tool_api.h
-rw-r--r-- root/root      2170 2016-03-17 06:15 ./usr/include/genometools/core/toolbox_api.h
-rw-r--r-- root/root      2855 2016-03-17 06:15 ./usr/include/genometools/core/trans_table_api.h
-rw-r--r-- root/root      5419 2016-03-17 06:15 ./usr/include/genometools/core/translator_api.h
-rw-r--r-- root/root      3366 2016-03-17 06:15 ./usr/include/genometools/core/types_api.h
-rw-r--r-- root/root      1862 2016-03-17 06:15 ./usr/include/genometools/core/undef_api.h
-rw-r--r-- root/root      1089 2016-03-17 06:15 ./usr/include/genometools/core/unused_api.h
-rw-r--r-- root/root      1643 2016-03-17 06:15 ./usr/include/genometools/core/version_api.h
-rw-r--r-- root/root      2069 2016-03-17 06:15 ./usr/include/genometools/core/warning_api.h
-rw-r--r-- root/root      3511 2016-03-17 06:15 ./usr/include/genometools/core/xansi_api.h
drwxr-xr-x root/root         0 2016-03-17 07:30 ./usr/include/genometools/extended/
-rw-r--r-- root/root      1441 2016-03-17 06:15 ./usr/include/genometools/extended/add_introns_stream_api.h
-rw-r--r-- root/root      1766 2016-03-17 06:15 ./usr/include/genometools/extended/anno_db_gfflike_api.h
-rw-r--r-- root/root      1627 2016-03-17 06:15 ./usr/include/genometools/extended/anno_db_schema_api.h
-rw-r--r-- root/root      1626 2016-03-17 06:15 ./usr/include/genometools/extended/array_in_stream_api.h
-rw-r--r-- root/root      1862 2016-03-17 06:15 ./usr/include/genometools/extended/array_out_stream_api.h
-rw-r--r-- root/root      2181 2016-03-17 06:15 ./usr/include/genometools/extended/bed_in_stream_api.h
-rw-r--r-- root/root      2461 2016-03-17 06:15 ./usr/include/genometools/extended/cds_stream_api.h
-rw-r--r-- root/root      1212 2016-03-17 06:15 ./usr/include/genometools/extended/check_boundaries_visitor_api.h
-rw-r--r-- root/root      2229 2016-03-17 06:15 ./usr/include/genometools/extended/comment_node_api.h
-rw-r--r-- root/root      1529 2016-03-17 06:15 ./usr/include/genometools/extended/csa_stream_api.h
-rw-r--r-- root/root      1213 2016-03-17 06:15 ./usr/include/genometools/extended/dup_feature_stream_api.h
-rw-r--r-- root/root      1541 2016-03-17 06:15 ./usr/include/genometools/extended/eof_node_api.h
-rw-r--r-- root/root      2838 2016-03-17 06:15 ./usr/include/genometools/extended/extract_feature_stream_api.h
-rw-r--r-- root/root      1579 2016-03-17 06:15 ./usr/include/genometools/extended/feature_in_stream_api.h
-rw-r--r-- root/root      5890 2016-03-17 06:15 ./usr/include/genometools/extended/feature_index_api.h
-rw-r--r-- root/root      1751 2016-03-17 06:15 ./usr/include/genometools/extended/feature_index_memory_api.h
-rw-r--r-- root/root     13753 2016-03-17 06:15 ./usr/include/genometools/extended/feature_node_api.h
-rw-r--r-- root/root      2151 2016-03-17 06:15 ./usr/include/genometools/extended/feature_node_iterator_api.h
-rw-r--r-- root/root      1201 2016-03-17 06:15 ./usr/include/genometools/extended/feature_out_stream_api.h
-rw-r--r-- root/root      1327 2016-03-17 06:15 ./usr/include/genometools/extended/feature_stream_api.h
-rw-r--r-- root/root      4674 2016-03-17 06:15 ./usr/include/genometools/extended/genome_node_api.h
-rw-r--r-- root/root      3512 2016-03-17 06:15 ./usr/include/genometools/extended/gff3_in_stream_api.h
-rw-r--r-- root/root      2339 2016-03-17 06:15 ./usr/include/genometools/extended/gff3_out_stream_api.h
-rw-r--r-- root/root      4984 2016-03-17 06:15 ./usr/include/genometools/extended/gff3_parser_api.h
-rw-r--r-- root/root      2207 2016-03-17 06:15 ./usr/include/genometools/extended/gff3_visitor_api.h
-rw-r--r-- root/root      1393 2016-03-17 06:15 ./usr/include/genometools/extended/gtf_in_stream_api.h
-rw-r--r-- root/root      1333 2016-03-17 06:15 ./usr/include/genometools/extended/gtf_out_stream_api.h
-rw-r--r-- root/root      1673 2016-03-17 06:15 ./usr/include/genometools/extended/id_to_md5_stream_api.h
-rw-r--r-- root/root      1597 2016-03-17 06:15 ./usr/include/genometools/extended/inter_feature_stream_api.h
-rw-r--r-- root/root      4263 2016-03-17 06:15 ./usr/include/genometools/extended/match_api.h
-rw-r--r-- root/root      2712 2016-03-17 06:15 ./usr/include/genometools/extended/match_blast_api.h
-rw-r--r-- root/root      1942 2016-03-17 06:15 ./usr/include/genometools/extended/match_iterator_api.h
-rw-r--r-- root/root      2105 2016-03-17 06:15 ./usr/include/genometools/extended/match_last_api.h
-rw-r--r-- root/root      1898 2016-03-17 06:15 ./usr/include/genometools/extended/match_open_api.h
-rw-r--r-- root/root      2446 2016-03-17 06:15 ./usr/include/genometools/extended/match_sw_api.h
-rw-r--r-- root/root      1798 2016-03-17 06:15 ./usr/include/genometools/extended/match_visitor_api.h
-rw-r--r-- root/root      1495 2016-03-17 06:15 ./usr/include/genometools/extended/md5_to_id_stream_api.h
-rw-r--r-- root/root      1416 2016-03-17 06:15 ./usr/include/genometools/extended/merge_feature_stream_api.h
-rw-r--r-- root/root      1363 2016-03-17 06:15 ./usr/include/genometools/extended/merge_stream_api.h
-rw-r--r-- root/root      2483 2016-03-17 06:15 ./usr/include/genometools/extended/meta_node_api.h
-rw-r--r-- root/root      4900 2016-03-17 06:15 ./usr/include/genometools/extended/node_stream_api.h
-rw-r--r-- root/root      4404 2016-03-17 06:15 ./usr/include/genometools/extended/node_visitor_api.h
-rw-r--r-- root/root      2770 2016-03-17 06:15 ./usr/include/genometools/extended/orf_iterator_api.h
-rw-r--r-- root/root      3077 2016-03-17 06:15 ./usr/include/genometools/extended/rdb_api.h
-rw-r--r-- root/root      1861 2016-03-17 06:15 ./usr/include/genometools/extended/rdb_mysql_api.h
-rw-r--r-- root/root      1646 2016-03-17 06:15 ./usr/include/genometools/extended/rdb_sqlite_api.h
-rw-r--r-- root/root      1683 2016-03-17 06:15 ./usr/include/genometools/extended/rdb_visitor_api.h
-rw-r--r-- root/root      5500 2016-03-17 06:15 ./usr/include/genometools/extended/region_mapping_api.h
-rw-r--r-- root/root      2146 2016-03-17 06:15 ./usr/include/genometools/extended/region_node_api.h
-rw-r--r-- root/root      1110 2016-03-17 06:15 ./usr/include/genometools/extended/reverse_api.h
-rw-r--r-- root/root      2708 2016-03-17 06:15 ./usr/include/genometools/extended/script_filter_api.h
-rw-r--r-- root/root      1734 2016-03-17 06:15 ./usr/include/genometools/extended/script_wrapper_stream_api.h
-rw-r--r-- root/root      2623 2016-03-17 06:15 ./usr/include/genometools/extended/script_wrapper_visitor_api.h
-rw-r--r-- root/root      4475 2016-03-17 06:15 ./usr/include/genometools/extended/select_stream_api.h
-rw-r--r-- root/root      2762 2016-03-17 06:15 ./usr/include/genometools/extended/sequence_node_api.h
-rw-r--r-- root/root      1344 2016-03-17 06:15 ./usr/include/genometools/extended/set_source_visitor_api.h
-rw-r--r-- root/root      1349 2016-03-17 06:15 ./usr/include/genometools/extended/sort_stream_api.h
-rw-r--r-- root/root      2496 2016-03-17 06:15 ./usr/include/genometools/extended/stat_stream_api.h
-rw-r--r-- root/root      3661 2016-03-17 06:15 ./usr/include/genometools/extended/tag_value_map_api.h
-rw-r--r-- root/root      2269 2016-03-17 06:15 ./usr/include/genometools/extended/type_checker_api.h
-rw-r--r-- root/root      1181 2016-03-17 06:15 ./usr/include/genometools/extended/type_checker_builtin_api.h
-rw-r--r-- root/root      1352 2016-03-17 06:15 ./usr/include/genometools/extended/type_checker_obo_api.h
-rw-r--r-- root/root      1750 2016-03-17 06:15 ./usr/include/genometools/extended/uniq_stream_api.h
-rw-r--r-- root/root      1386 2016-03-17 06:15 ./usr/include/genometools/extended/visitor_stream_api.h
-rw-r--r-- root/root      1761 2016-03-17 06:15 ./usr/include/genometools/extended/xrf_checker_api.h
-rw-r--r-- root/root      6539 2016-03-17 06:15 ./usr/include/genometools/genometools.h
-rw-r--r-- root/root      1369 2016-03-17 06:15 ./usr/include/genometools/gt_config.h
drwxr-xr-x root/root         0 2016-03-17 07:30 ./usr/include/genometools/ltr/
-rw-r--r-- root/root      1449 2016-03-17 06:15 ./usr/include/genometools/ltr/ltr_classify_stream_api.h
-rw-r--r-- root/root      2109 2016-03-17 06:15 ./usr/include/genometools/ltr/ltr_cluster_stream_api.h
-rw-r--r-- root/root      1821 2016-03-17 06:15 ./usr/include/genometools/ltr/ltr_orf_annotator_stream_api.h
-rw-r--r-- root/root      3939 2016-03-17 06:15 ./usr/include/genometools/ltr/ltr_refseq_match_stream_api.h
drwxr-xr-x root/root         0 2016-03-17 07:31 ./usr/lib/
lrwxrwxrwx root/root         0 2016-03-17 07:31 ./usr/lib/libgenometools.so -> libgenometools.so.0
drwxr-xr-x root/root         0 2016-03-17 07:30 ./usr/share/
drwxr-xr-x root/root         0 2016-03-17 07:30 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-03-17 07:31 ./usr/share/doc/libgenometools0-dev/
-rw-r--r-- root/root      2738 2016-03-11 16:10 ./usr/share/doc/libgenometools0-dev/changelog.Debian.gz
-rw-r--r-- root/root      6081 2016-01-07 19:56 ./usr/share/doc/libgenometools0-dev/changelog.gz
-rw-r--r-- root/root      5106 2016-03-11 09:51 ./usr/share/doc/libgenometools0-dev/copyright


libgenometools0_1.5.8+ds-2_armhf.deb
------------------------------------

 new debian package, version 2.0.
 size 1601114 bytes: control archive=1494 bytes.
    1009 bytes,    19 lines      control              
     297 bytes,     4 lines      md5sums              
     858 bytes,    37 lines   *  postinst             #!/bin/sh
     848 bytes,    38 lines   *  postrm               #!/bin/sh
      33 bytes,     1 lines      shlibs               
      60 bytes,     2 lines      triggers             
 Package: libgenometools0
 Source: genometools
 Version: 1.5.8+ds-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 5364
 Depends: libbz2-1.0, libc6 (>= 2.15), libcairo2 (>= 1.2.4), libexpat1 (>= 2.0.1), libglib2.0-0 (>= 2.12.0), liblua5.1-0, libpango-1.0-0 (>= 1.14.0), libpangocairo-1.0-0 (>= 1.14.0), libsqlite3-0 (>= 3.5.9), libtre5, lua-filesystem, lua-lpeg, lua-md5, zlib1g (>= 1:1.2.3.3), genometools-common
 Section: libs
 Priority: optional
 Homepage: http://genometools.org
 Description: versatile genome analysis library
  This package contains the GenomeTools shared library and header
  files. It offers efficient sequence analysis components, available
  via an object-oriented interface.
  .
  Besides basic bioinformatics data structures, the library contains components
  for sequence and annotation handling, sequence compression, index structure
  generation and access, efficient matching, annotation visualization and much
  more.

drwxr-xr-x root/root         0 2016-03-17 07:31 ./
drwxr-xr-x root/root         0 2016-03-17 07:30 ./usr/
drwxr-xr-x root/root         0 2016-03-17 07:31 ./usr/lib/
-rw-r--r-- root/root   5466800 2016-03-17 07:31 ./usr/lib/libgenometools.so.0
drwxr-xr-x root/root         0 2016-03-17 07:30 ./usr/share/
drwxr-xr-x root/root         0 2016-03-17 07:30 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-03-17 07:31 ./usr/share/doc/libgenometools0/
-rw-r--r-- root/root      2738 2016-03-11 16:10 ./usr/share/doc/libgenometools0/changelog.Debian.gz
-rw-r--r-- root/root      6081 2016-01-07 19:56 ./usr/share/doc/libgenometools0/changelog.gz
-rw-r--r-- root/root      5106 2016-03-11 09:51 ./usr/share/doc/libgenometools0/copyright


+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build-Space: 255144
Build-Time: 6994
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 1695
Job: genometools_1.5.8+ds-2
Machine Architecture: armhf
Package: genometools
Package-Time: 8747
Source-Version: 1.5.8+ds-2
Space: 255144
Status: successful
Version: 1.5.8+ds-2
--------------------------------------------------------------------------------
Finished at 20160317-0732
Build needed 02:25:47, 255144k disc space
Raspbian Package Auto-Building

Build log for genometools (1.5.8+ds-2) on armhf
