Raspbian Package Auto-Building

genometools → 1.5.7-2 → armhf → 2015-10-21 08:21:43

sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on testwandboard

╔══════════════════════════════════════════════════════════════════════════════╗
║ genometools 1.5.7-2 (armhf)                                21 Oct 2015 06:46 ║
╚══════════════════════════════════════════════════════════════════════════════╝

Package: genometools
Version: 1.5.7-2
Source Version: 1.5.7-2
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'build/genometools-RO_ybI/genometools-1.5.7' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/genometools-RO_ybI' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-5b2790aa-d9a9-4949-a516-82ab99da5369' with '«CHROOT»'

┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot                                                                │
└──────────────────────────────────────────────────────────────────────────────┘

Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [8374 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [10.3 MB]
Ign http://172.17.0.1 stretch-staging/main Translation-en
Fetched 18.7 MB in 36s (512 kB/s)
Reading package lists...

┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files                                                           │
└──────────────────────────────────────────────────────────────────────────────┘


Check APT
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Checking available source versions...

Download source files with APT
──────────────────────────────

Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'genometools' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/genometools/trunk/
Need to get 12.9 MB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main genometools 1.5.7-2 (dsc) [2779 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main genometools 1.5.7-2 (tar) [12.9 MB]
Get:3 http://172.17.0.1/private/ stretch-staging/main genometools 1.5.7-2 (diff) [15.0 kB]
Fetched 12.9 MB in 8s (1612 kB/s)
Download complete and in download only mode

Check architectures
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Check dependencies
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-dGDlZv/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
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
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 16 not upgraded.
Need to get 0 B/764 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
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(Reading database ... 12922 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) ...
Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), liblua5.1-0-dev, lua-md5-dev, lua-filesystem-dev, lua-lpeg-dev, libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, libncurses5-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
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), liblua5.1-0-dev, lua-md5-dev, lua-filesystem-dev, lua-lpeg-dev, libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, libncurses5-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
dpkg-deb: building package 'sbuild-build-depends-genometools-dummy' in '/«BUILDDIR»/resolver-qPN58N/apt_archive/sbuild-build-depends-genometools-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
Reading package lists...

┌──────────────────────────────────────────────────────────────────────────────┐
│ Install genometools build dependencies (apt-based resolver)                  │
└──────────────────────────────────────────────────────────────────────────────┘

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
  asciidoc bsdmainutils ca-certificates debhelper 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-droid 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-inconsolata
  fonts-junicode fonts-lato fonts-linuxlibertine fonts-lobster
  fonts-lobstertwo fonts-oflb-asana-math fonts-roboto 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
  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 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 libgnutls-deb0-28
  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 liblua5.1-0 liblua5.1-0-dev liblzo2-2 libmagic1
  libncurses5-dev libnettle6 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 libpoppler46
  libpotrace0 libptexenc1 libpthread-stubs0-dev libpython-stdlib
  libpython2.7-minimal libpython2.7-stdlib libreadline-dev libreadline6-dev
  libruby2.1 libsasl2-2 libsasl2-modules-db libsm-dev libsm6 libsqlite3-0
  libsqlite3-dev libssl1.0.0 libsynctex1 libtasn1-6 libtexlua52 libtexluajit2
  libthai-data libthai0 libtiff5 libtinfo-dev libtre-dev libtre5 libtrio2
  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 ruby ruby2.1 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 libcairo2-doc cups-common libglib2.0-doc gnutls-bin
  krb5-doc krb5-user libice-doc liblcms2-utils ncurses-doc imagemagick
  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 ri ruby-dev bundler
  sgml-base-doc gv postscript-viewer perl-tk xpdf-reader pdf-viewer cm-super
  libfile-which-perl libspreadsheet-parseexcel-perl python-pygments
  texlive-pstricks libtcltk-ruby dot2tex gvfs-bin
Recommended packages:
  dblatex docbook-utils xmlto docbook-xml curl wget lynx-cur bzip2-doc
  shared-mime-info xdg-user-dirs krb5-locales libtool libtool-bin
  libsasl2-modules libx11-doc libmail-sendmail-perl 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 texlive-pictures-doc prerex
  libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils
  x11-xserver-utils
The following NEW packages will be installed:
  asciidoc bsdmainutils ca-certificates debhelper 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-droid 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-inconsolata
  fonts-junicode fonts-lato fonts-linuxlibertine fonts-lobster
  fonts-lobstertwo fonts-oflb-asana-math fonts-roboto 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
  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 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 libgnutls-deb0-28
  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 liblua5.1-0 liblua5.1-0-dev liblzo2-2 libmagic1
  libncurses5-dev libnettle6 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 libpoppler46
  libpotrace0 libptexenc1 libpthread-stubs0-dev libpython-stdlib
  libpython2.7-minimal libpython2.7-stdlib libreadline-dev libreadline6-dev
  libruby2.1 libsasl2-2 libsasl2-modules-db libsm-dev libsm6 libsqlite3-0
  libsqlite3-dev libssl1.0.0 libsynctex1 libtasn1-6 libtexlua52 libtexluajit2
  libthai-data libthai0 libtiff5 libtinfo-dev libtre-dev libtre5 libtrio2
  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 ruby ruby2.1 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
0 upgraded, 231 newly installed, 0 to remove and 16 not upgraded.
Need to get 370 MB/370 MB of archives.
After this operation, 1161 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-1 [1085 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.1-1 [23.9 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.4-1 [974 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libpython2.7-minimal armhf 2.7.10-5 [380 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main python2.7-minimal armhf 2.7.10-5 [1095 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main python-minimal armhf 2.7.9-1 [40.1 kB]
Get:8 http://172.17.0.1/private/ stretch-staging/main mime-support all 3.59 [36.4 kB]
Get:9 http://172.17.0.1/private/ stretch-staging/main libexpat1 armhf 2.1.0-7 [59.8 kB]
Get:10 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.2.1-3 [18.5 kB]
Get:11 http://172.17.0.1/private/ stretch-staging/main libsqlite3-0 armhf 3.8.11.1-1 [391 kB]
Get:12 http://172.17.0.1/private/ stretch-staging/main libssl1.0.0 armhf 1.0.2d-1 [882 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main libpython2.7-stdlib armhf 2.7.10-5 [1813 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main python2.7 armhf 2.7.10-5 [265 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main libpython-stdlib armhf 2.7.9-1 [19.6 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main python armhf 2.7.9-1 [151 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main libfreetype6 armhf 2.6-2 [397 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main ucf all 3.0030 [69.7 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main fonts-dejavu-core all 2.35-1 [1064 kB]
Get:20 http://172.17.0.1/private/ stretch-staging/main fontconfig-config all 2.11.0-6.3 [273 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main libfontconfig1 armhf 2.11.0-6.3 [311 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main fontconfig armhf 2.11.0-6.3 [402 kB]
Get:23 http://172.17.0.1/private/ stretch-staging/main fonts-droid all 1:4.4.4r2-7 [3626 kB]
Get:24 http://172.17.0.1/private/ stretch-staging/main fonts-lato all 2.0-1 [2684 kB]
Get:25 http://172.17.0.1/private/ stretch-staging/main fonts-roboto all 1:4.4.4r2-7 [371 kB]
Get:26 http://172.17.0.1/private/ stretch-staging/main libavahi-common-data armhf 0.6.31-5 [98.8 kB]
Get:27 http://172.17.0.1/private/ stretch-staging/main libavahi-common3 armhf 0.6.31-5 [48.0 kB]
Get:28 http://172.17.0.1/private/ stretch-staging/main libavahi-client3 armhf 0.6.31-5 [50.6 kB]
Get:29 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.46.0-2 [2376 kB]
Get:30 http://172.17.0.1/private/ stretch-staging/main libicu55 armhf 55.1-5 [7378 kB]
Get:31 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.2+zdfsg1-4 [797 kB]
Get:32 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:33 http://172.17.0.1/private/ stretch-staging/main libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:34 http://172.17.0.1/private/ stretch-staging/main liblcms2-2 armhf 2.6-3 [113 kB]
Get:35 http://172.17.0.1/private/ stretch-staging/main liblzo2-2 armhf 2.08-1.2 [47.6 kB]
Get:36 http://172.17.0.1/private/ stretch-staging/main libpaper1 armhf 1.1.24+nmu4 [21.4 kB]
Get:37 http://172.17.0.1/private/ stretch-staging/main libpcrecpp0v5 armhf 2:8.35-7.2 [141 kB]
Get:38 http://172.17.0.1/private/ stretch-staging/main libtre5 armhf 0.8.0-4 [51.3 kB]
Get:39 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:40 http://172.17.0.1/private/ stretch-staging/main libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:41 http://172.17.0.1/private/ stretch-staging/main libxdmcp6 armhf 1:1.1.2-1 [25.0 kB]
Get:42 http://172.17.0.1/private/ stretch-staging/main libxcb1 armhf 1.10-3+b1 [40.6 kB]
Get:43 http://172.17.0.1/private/ stretch-staging/main libx11-data all 2:1.6.3-1 [128 kB]
Get:44 http://172.17.0.1/private/ stretch-staging/main libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:45 http://172.17.0.1/private/ stretch-staging/main libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:46 http://172.17.0.1/private/ stretch-staging/main libxrender1 armhf 1:0.9.8-1+b1 [28.4 kB]
Get:47 http://172.17.0.1/private/ stretch-staging/main libxft2 armhf 2.3.2-1 [48.3 kB]
Get:48 http://172.17.0.1/private/ stretch-staging/main x11-common all 1:7.7+12 [251 kB]
Get:49 http://172.17.0.1/private/ stretch-staging/main libice6 armhf 2:1.0.9-1+b1 [51.9 kB]
Get:50 http://172.17.0.1/private/ stretch-staging/main libsm6 armhf 2:1.2.2-1+b1 [31.2 kB]
Get:51 http://172.17.0.1/private/ stretch-staging/main libxt6 armhf 1:1.1.4-1+b1 [154 kB]
Get:52 http://172.17.0.1/private/ stretch-staging/main libxmu6 armhf 2:1.1.2-1 [50.8 kB]
Get:53 http://172.17.0.1/private/ stretch-staging/main libyaml-0-2 armhf 0.1.6-3 [41.5 kB]
Get:54 http://172.17.0.1/private/ stretch-staging/main libzzip-0-13 armhf 0.13.62-3 [51.3 kB]
Get:55 http://172.17.0.1/private/ stretch-staging/main lua-md5 armhf 1.2+git+1+8d87fee-1 [14.6 kB]
Get:56 http://172.17.0.1/private/ stretch-staging/main lua-md5-dev armhf 1.2+git+1+8d87fee-1 [22.3 kB]
Get:57 http://172.17.0.1/private/ stretch-staging/main poppler-data all 0.4.7-3 [1470 kB]
Get:58 http://172.17.0.1/private/ stretch-staging/main sgml-base all 1.26+nmu4 [14.6 kB]
Get:59 http://172.17.0.1/private/ stretch-staging/main libfaketime armhf 0.9.6-4 [24.9 kB]
Get:60 http://172.17.0.1/private/ stretch-staging/main faketime armhf 0.9.6-4 [13.1 kB]
Get:61 http://172.17.0.1/private/ stretch-staging/main libtrio2 armhf 1.16+dfsg1-3 [39.0 kB]
Get:62 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.25-2 [250 kB]
Get:63 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.25-2 [61.2 kB]
Get:64 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.6-1 [119 kB]
Get:65 http://172.17.0.1/private/ stretch-staging/main libnettle6 armhf 3.1.1-4 [200 kB]
Get:66 http://172.17.0.1/private/ stretch-staging/main libhogweed4 armhf 3.1.1-4 [126 kB]
Get:67 http://172.17.0.1/private/ stretch-staging/main libp11-kit0 armhf 0.23.1-3 [94.2 kB]
Get:68 http://172.17.0.1/private/ stretch-staging/main libtasn1-6 armhf 4.7-2 [44.3 kB]
Get:69 http://172.17.0.1/private/ stretch-staging/main libgnutls-deb0-28 armhf 3.3.18-1 [645 kB]
Get:70 http://172.17.0.1/private/ stretch-staging/main libkeyutils1 armhf 1.5.9-8 [11.5 kB]
Get:71 http://172.17.0.1/private/ stretch-staging/main libkrb5support0 armhf 1.13.2+dfsg-2 [55.9 kB]
Get:72 http://172.17.0.1/private/ stretch-staging/main libk5crypto3 armhf 1.13.2+dfsg-2 [109 kB]
Get:73 http://172.17.0.1/private/ stretch-staging/main libkrb5-3 armhf 1.13.2+dfsg-2 [260 kB]
Get:74 http://172.17.0.1/private/ stretch-staging/main libgssapi-krb5-2 armhf 1.13.2+dfsg-2 [130 kB]
Get:75 http://172.17.0.1/private/ stretch-staging/main libidn11 armhf 1.32-3 [110 kB]
Get:76 http://172.17.0.1/private/ stretch-staging/main libsasl2-modules-db armhf 2.1.26.dfsg1-14 [65.5 kB]
Get:77 http://172.17.0.1/private/ stretch-staging/main libsasl2-2 armhf 2.1.26.dfsg1-14 [96.8 kB]
Get:78 http://172.17.0.1/private/ stretch-staging/main libldap-2.4-2 armhf 2.4.42+dfsg-2+rpi1 [197 kB]
Get:79 http://172.17.0.1/private/ stretch-staging/main asciidoc all 8.6.9-3 [830 kB]
Get:80 http://172.17.0.1/private/ stretch-staging/main openssl armhf 1.0.2d-1 [683 kB]
Get:81 http://172.17.0.1/private/ stretch-staging/main ca-certificates all 20150426 [208 kB]
Get:82 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.6-1 [1393 kB]
Get:83 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:84 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:85 http://172.17.0.1/private/ stretch-staging/main libarchive-zip-perl all 1.53-1 [97.3 kB]
Get:86 http://172.17.0.1/private/ stretch-staging/main libfile-stripnondeterminism-perl all 0.012-1 [10.6 kB]
Get:87 http://172.17.0.1/private/ stretch-staging/main dh-strip-nondeterminism all 0.012-1 [7282 B]
Get:88 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20151005 [817 kB]
Get:89 http://172.17.0.1/private/ stretch-staging/main xml-core all 0.13+nmu2 [24.2 kB]
Get:90 http://172.17.0.1/private/ stretch-staging/main docbook-xsl all 1.78.1+dfsg-1 [2339 kB]
Get:91 http://172.17.0.1/private/ stretch-staging/main fonts-cabin all 1.5-2 [139 kB]
Get:92 http://172.17.0.1/private/ stretch-staging/main fonts-comfortaa all 2.003-1 [133 kB]
Get:93 http://172.17.0.1/private/ stretch-staging/main fonts-crosextra-caladea all 20130214-1 [82.1 kB]
Get:94 http://172.17.0.1/private/ stretch-staging/main fonts-crosextra-carlito all 20130920-1 [745 kB]
Get:95 http://172.17.0.1/private/ stretch-staging/main fonts-dejavu-extra all 2.35-1 [1787 kB]
Get:96 http://172.17.0.1/private/ stretch-staging/main fonts-ebgaramond all 0.015+git20130628-3 [415 kB]
Get:97 http://172.17.0.1/private/ stretch-staging/main fonts-ebgaramond-extra all 0.015+git20130628-3 [680 kB]
Get:98 http://172.17.0.1/private/ stretch-staging/main fonts-font-awesome all 4.4.0~dfsg-1 [493 kB]
Get:99 http://172.17.0.1/private/ stretch-staging/main fonts-freefont-otf all 20120503-4 [3186 kB]
Get:100 http://172.17.0.1/private/ stretch-staging/main fonts-freefont-ttf all 20120503-4 [4262 kB]
Get:101 http://172.17.0.1/private/ stretch-staging/main fonts-gfs-artemisia all 1.1-5 [259 kB]
Get:102 http://172.17.0.1/private/ stretch-staging/main fonts-gfs-complutum all 1.1-6 [41.6 kB]
Get:103 http://172.17.0.1/private/ stretch-staging/main fonts-gfs-didot all 1.1-6 [278 kB]
Get:104 http://172.17.0.1/private/ stretch-staging/main fonts-gfs-neohellenic all 1.1-6 [215 kB]
Get:105 http://172.17.0.1/private/ stretch-staging/main fonts-gfs-olga all 1.1-5 [33.2 kB]
Get:106 http://172.17.0.1/private/ stretch-staging/main fonts-gfs-solomos all 1.1-5 [40.6 kB]
Get:107 http://172.17.0.1/private/ stretch-staging/main fonts-inconsolata all 001.010-5 [61.6 kB]
Get:108 http://172.17.0.1/private/ stretch-staging/main fonts-junicode all 0.7.8-2 [643 kB]
Get:109 http://172.17.0.1/private/ stretch-staging/main fonts-linuxlibertine all 5.3.0-2 [1713 kB]
Get:110 http://172.17.0.1/private/ stretch-staging/main fonts-lobster all 2.0-2 [39.5 kB]
Get:111 http://172.17.0.1/private/ stretch-staging/main fonts-lobstertwo all 2.0-2 [94.0 kB]
Get:112 http://172.17.0.1/private/ stretch-staging/main fonts-oflb-asana-math all 000.907-6 [245 kB]
Get:113 http://172.17.0.1/private/ stretch-staging/main fonts-sil-gentium all 20081126:1.03-1 [251 kB]
Get:114 http://172.17.0.1/private/ stretch-staging/main fonts-sil-gentium-basic all 1.1-7 [382 kB]
Get:115 http://172.17.0.1/private/ stretch-staging/main fonts-sil-gentiumplus all 5.000-1 [2811 kB]
Get:116 http://172.17.0.1/private/ stretch-staging/main libgirepository-1.0-1 armhf 1.46.0-1 [83.3 kB]
Get:117 http://172.17.0.1/private/ stretch-staging/main gir1.2-glib-2.0 armhf 1.46.0-1 [143 kB]
Get:118 http://172.17.0.1/private/ stretch-staging/main libpixman-1-0 armhf 0.33.2-2 [444 kB]
Get:119 http://172.17.0.1/private/ stretch-staging/main libxcb-render0 armhf 1.10-3+b1 [16.9 kB]
Get:120 http://172.17.0.1/private/ stretch-staging/main libxcb-shm0 armhf 1.10-3+b1 [11.4 kB]
Get:121 http://172.17.0.1/private/ stretch-staging/main libcairo2 armhf 1.14.2-2 [672 kB]
Get:122 http://172.17.0.1/private/ stretch-staging/main libcairo-gobject2 armhf 1.14.2-2 [314 kB]
Get:123 http://172.17.0.1/private/ stretch-staging/main gir1.2-freedesktop armhf 1.46.0-1 [22.3 kB]
Get:124 http://172.17.0.1/private/ stretch-staging/main libthai-data all 0.1.22-2 [161 kB]
Get:125 http://172.17.0.1/private/ stretch-staging/main libdatrie1 armhf 0.2.9-3 [31.3 kB]
Get:126 http://172.17.0.1/private/ stretch-staging/main libthai0 armhf 0.1.22-2 [44.8 kB]
Get:127 http://172.17.0.1/private/ stretch-staging/main libpango-1.0-0 armhf 1.38.0-3 [291 kB]
Get:128 http://172.17.0.1/private/ stretch-staging/main libgraphite2-3 armhf 1.3.3-1 [61.1 kB]
Get:129 http://172.17.0.1/private/ stretch-staging/main libharfbuzz0b armhf 1.0.1-1+b1 [501 kB]
Get:130 http://172.17.0.1/private/ stretch-staging/main libpangoft2-1.0-0 armhf 1.38.0-3 [228 kB]
Get:131 http://172.17.0.1/private/ stretch-staging/main libpangocairo-1.0-0 armhf 1.38.0-3 [217 kB]
Get:132 http://172.17.0.1/private/ stretch-staging/main libpangoxft-1.0-0 armhf 1.38.0-3 [212 kB]
Get:133 http://172.17.0.1/private/ stretch-staging/main gir1.2-pango-1.0 armhf 1.38.0-3 [220 kB]
Get:134 http://172.17.0.1/private/ stretch-staging/main libbam-dev armhf 0.1.19-2 [109 kB]
Get:135 http://172.17.0.1/private/ stretch-staging/main libbz2-dev armhf 1.0.6-8 [27.8 kB]
Get:136 http://172.17.0.1/private/ stretch-staging/main libcairo-script-interpreter2 armhf 1.14.2-2 [342 kB]
Get:137 http://172.17.0.1/private/ stretch-staging/main libexpat1-dev armhf 2.1.0-7 [114 kB]
Get:138 http://172.17.0.1/private/ stretch-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:139 http://172.17.0.1/private/ stretch-staging/main libpng12-dev armhf 1.2.50-2+b2 [236 kB]
Get:140 http://172.17.0.1/private/ stretch-staging/main libfreetype6-dev armhf 2.6-2 [936 kB]
Get:141 http://172.17.0.1/private/ stretch-staging/main pkg-config armhf 0.28-1 [55.1 kB]
Get:142 http://172.17.0.1/private/ stretch-staging/main libfontconfig1-dev armhf 2.11.0-6.3 [875 kB]
Get:143 http://172.17.0.1/private/ stretch-staging/main xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:144 http://172.17.0.1/private/ stretch-staging/main x11proto-core-dev all 7.0.27-1 [729 kB]
Get:145 http://172.17.0.1/private/ stretch-staging/main libxau-dev armhf 1:1.0.8-1 [23.0 kB]
Get:146 http://172.17.0.1/private/ stretch-staging/main libxdmcp-dev armhf 1:1.1.2-1 [40.3 kB]
Get:147 http://172.17.0.1/private/ stretch-staging/main x11proto-input-dev all 2.3.1-1 [157 kB]
Get:148 http://172.17.0.1/private/ stretch-staging/main x11proto-kb-dev all 1.0.6-2 [269 kB]
Get:149 http://172.17.0.1/private/ stretch-staging/main xtrans-dev all 1.3.5-1 [100 kB]
Get:150 http://172.17.0.1/private/ stretch-staging/main libpthread-stubs0-dev armhf 0.3-4 [4042 B]
Get:151 http://172.17.0.1/private/ stretch-staging/main libxcb1-dev armhf 1.10-3+b1 [79.5 kB]
Get:152 http://172.17.0.1/private/ stretch-staging/main libx11-dev armhf 2:1.6.3-1 [749 kB]
Get:153 http://172.17.0.1/private/ stretch-staging/main x11proto-render-dev all 2:0.11.1-2 [20.8 kB]
Get:154 http://172.17.0.1/private/ stretch-staging/main libxrender-dev armhf 1:0.9.8-1+b1 [36.0 kB]
Get:155 http://172.17.0.1/private/ stretch-staging/main x11proto-xext-dev all 7.3.0-1 [212 kB]
Get:156 http://172.17.0.1/private/ stretch-staging/main libxext-dev armhf 2:1.3.3-1 [102 kB]
Get:157 http://172.17.0.1/private/ stretch-staging/main libice-dev armhf 2:1.0.9-1+b1 [59.0 kB]
Get:158 http://172.17.0.1/private/ stretch-staging/main libsm-dev armhf 2:1.2.2-1+b1 [33.5 kB]
Get:159 http://172.17.0.1/private/ stretch-staging/main libpixman-1-dev armhf 0.33.2-2 [466 kB]
Get:160 http://172.17.0.1/private/ stretch-staging/main libxcb-render0-dev armhf 1.10-3+b1 [22.3 kB]
Get:161 http://172.17.0.1/private/ stretch-staging/main libxcb-shm0-dev armhf 1.10-3+b1 [12.8 kB]
Get:162 http://172.17.0.1/private/ stretch-staging/main libelf1 armhf 0.163-5.1 [162 kB]
Get:163 http://172.17.0.1/private/ stretch-staging/main libglib2.0-data all 2.46.1-1 [2415 kB]
Get:164 http://172.17.0.1/private/ stretch-staging/main libglib2.0-bin armhf 2.46.0-2 [1458 kB]
Get:165 http://172.17.0.1/private/ stretch-staging/main libpcre16-3 armhf 2:8.35-7.2 [221 kB]
Get:166 http://172.17.0.1/private/ stretch-staging/main libpcre32-3 armhf 2:8.35-7.2 [214 kB]
Get:167 http://172.17.0.1/private/ stretch-staging/main libpcre3-dev armhf 2:8.35-7.2 [546 kB]
Get:168 http://172.17.0.1/private/ stretch-staging/main libglib2.0-dev armhf 2.46.0-2 [2607 kB]
Get:169 http://172.17.0.1/private/ stretch-staging/main libcairo2-dev armhf 1.14.2-2 [795 kB]
Get:170 http://172.17.0.1/private/ stretch-staging/main libcups2 armhf 2.1.0-4 [264 kB]
Get:171 http://172.17.0.1/private/ stretch-staging/main libcupsimage2 armhf 2.1.0-4 [116 kB]
Get:172 http://172.17.0.1/private/ stretch-staging/main libjpeg62-turbo armhf 1:1.4.1-2 [103 kB]
Get:173 http://172.17.0.1/private/ stretch-staging/main libtiff5 armhf 4.0.5-1 [200 kB]
Get:174 http://172.17.0.1/private/ stretch-staging/main libcupsfilters1 armhf 1.0.76-1 [104 kB]
Get:175 http://172.17.0.1/private/ stretch-staging/main libijs-0.35 armhf 0.35-11 [16.1 kB]
Get:176 http://172.17.0.1/private/ stretch-staging/main libjbig2dec0 armhf 0.12+20150918-1 [50.7 kB]
Get:177 http://172.17.0.1/private/ stretch-staging/main libgs9-common all 9.16~dfsg-2 [2983 kB]
Get:178 http://172.17.0.1/private/ stretch-staging/main libgs9 armhf 9.16~dfsg-2 [1699 kB]
Get:179 http://172.17.0.1/private/ stretch-staging/main libharfbuzz-icu0 armhf 1.0.1-1+b1 [390 kB]
Get:180 http://172.17.0.1/private/ stretch-staging/main libharfbuzz-gobject0 armhf 1.0.1-1+b1 [395 kB]
Get:181 http://172.17.0.1/private/ stretch-staging/main libharfbuzz-dev armhf 1.0.1-1+b1 [548 kB]
Get:182 http://172.17.0.1/private/ stretch-staging/main libkpathsea6 armhf 2015.20150524.37493-6 [148 kB]
Get:183 http://172.17.0.1/private/ stretch-staging/main liblua5.1-0 armhf 5.1.5-8 [83.3 kB]
Get:184 http://172.17.0.1/private/ stretch-staging/main libtinfo-dev armhf 6.0+20150810-1 [65.8 kB]
Get:185 http://172.17.0.1/private/ stretch-staging/main libreadline6-dev armhf 6.3-8+b3 [105 kB]
Get:186 http://172.17.0.1/private/ stretch-staging/main libreadline-dev armhf 6.3-8+b3 [958 B]
Get:187 http://172.17.0.1/private/ stretch-staging/main liblua5.1-0-dev armhf 5.1.5-8 [115 kB]
Get:188 http://172.17.0.1/private/ stretch-staging/main libncurses5-dev armhf 6.0+20150810-1 [154 kB]
Get:189 http://172.17.0.1/private/ stretch-staging/main libxft-dev armhf 2.3.2-1 [59.1 kB]
Get:190 http://172.17.0.1/private/ stretch-staging/main libpango1.0-dev armhf 1.38.0-3 [448 kB]
Get:191 http://172.17.0.1/private/ stretch-staging/main libpaper-utils armhf 1.1.24+nmu4 [17.2 kB]
Get:192 http://172.17.0.1/private/ stretch-staging/main libopenjpeg5 armhf 1:1.5.2-3.1 [93.6 kB]
Get:193 http://172.17.0.1/private/ stretch-staging/main libpoppler46 armhf 0.26.5-4 [1084 kB]
Get:194 http://172.17.0.1/private/ stretch-staging/main libpotrace0 armhf 1.12-1 [22.9 kB]
Get:195 http://172.17.0.1/private/ stretch-staging/main libptexenc1 armhf 2015.20150524.37493-6 [53.3 kB]
Get:196 http://172.17.0.1/private/ stretch-staging/main libsqlite3-dev armhf 3.8.11.1-1 [502 kB]
Get:197 http://172.17.0.1/private/ stretch-staging/main libsynctex1 armhf 2015.20150524.37493-6 [55.9 kB]
Get:198 http://172.17.0.1/private/ stretch-staging/main libtexlua52 armhf 2015.20150524.37493-6 [84.2 kB]
Get:199 http://172.17.0.1/private/ stretch-staging/main libtexluajit2 armhf 2015.20150524.37493-6 [185 kB]
Get:200 http://172.17.0.1/private/ stretch-staging/main libtre-dev armhf 0.8.0-4 [27.1 kB]
Get:201 http://172.17.0.1/private/ stretch-staging/main libxpm4 armhf 1:3.5.11-1+b1 [42.4 kB]
Get:202 http://172.17.0.1/private/ stretch-staging/main libxaw7 armhf 2:1.0.13-1 [164 kB]
Get:203 http://172.17.0.1/private/ stretch-staging/main libxi6 armhf 2:1.7.5-1 [75.4 kB]
Get:204 http://172.17.0.1/private/ stretch-staging/main libxml2-utils armhf 2.9.2+zdfsg1-4 [101 kB]
Get:205 http://172.17.0.1/private/ stretch-staging/main libxslt1.1 armhf 1.1.28-2+b2 [211 kB]
Get:206 http://172.17.0.1/private/ stretch-staging/main lua-filesystem armhf 1.6.3-1 [9984 B]
Get:207 http://172.17.0.1/private/ stretch-staging/main lua-filesystem-dev armhf 1.6.3-1 [24.4 kB]
Get:208 http://172.17.0.1/private/ stretch-staging/main lua-lpeg armhf 0.12.2-1 [25.4 kB]
Get:209 http://172.17.0.1/private/ stretch-staging/main lua-lpeg-dev armhf 0.12.2-1 [44.3 kB]
Get:210 http://172.17.0.1/private/ stretch-staging/main tex-common all 6.04 [564 kB]
Get:211 http://172.17.0.1/private/ stretch-staging/main preview-latex-style all 11.87-3+deb8u1 [318 kB]
Get:212 http://172.17.0.1/private/ stretch-staging/main rubygems-integration all 1.9 [4754 B]
Get:213 http://172.17.0.1/private/ stretch-staging/main libruby2.1 armhf 2.1.5-4 [3015 kB]
Get:214 http://172.17.0.1/private/ stretch-staging/main ruby2.1 armhf 2.1.5-4 [276 kB]
Get:215 http://172.17.0.1/private/ stretch-staging/main ruby all 1:2.1.5.1 [9756 B]
Get:216 http://172.17.0.1/private/ stretch-staging/main t1utils armhf 1.38-4 [50.1 kB]
Get:217 http://172.17.0.1/private/ stretch-staging/main xdg-utils all 1.1.1-1 [71.1 kB]
Get:218 http://172.17.0.1/private/ stretch-staging/main texlive-binaries armhf 2015.20150524.37493-6 [6798 kB]
Get:219 http://172.17.0.1/private/ stretch-staging/main texlive-base all 2015.20151016-1 [17.8 MB]
Get:220 http://172.17.0.1/private/ stretch-staging/main fonts-stix all 1.1.1-4 [590 kB]
Get:221 http://172.17.0.1/private/ stretch-staging/main ttf-adf-gillius all 0.20090423-2 [400 kB]
Get:222 http://172.17.0.1/private/ stretch-staging/main ttf-adf-universalis all 0.20090423-2 [221 kB]
Get:223 http://172.17.0.1/private/ stretch-staging/main ttf-adf-accanthis all 0.20090423-2 [401 kB]
Get:224 http://172.17.0.1/private/ stretch-staging/main texlive-fonts-extra all 2015.20151016-1 [221 MB]
Get:225 http://172.17.0.1/private/ stretch-staging/main texlive-fonts-recommended all 2015.20151016-1 [5686 kB]
Get:226 http://172.17.0.1/private/ stretch-staging/main texlive-latex-base all 2015.20151016-1 [897 kB]
Get:227 http://172.17.0.1/private/ stretch-staging/main texlive-latex-recommended all 2015.20151016-1 [8446 kB]
Get:228 http://172.17.0.1/private/ stretch-staging/main texlive-pictures all 2015.20151016-1 [3150 kB]
Get:229 http://172.17.0.1/private/ stretch-staging/main texlive-latex-extra all 2015.20151016-1 [10.8 MB]
Get:230 http://172.17.0.1/private/ stretch-staging/main xsltproc armhf 1.1.28-2+b2 [118 kB]
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Setting up liblzo2-2:armhf (2.08-1.2) ...
Setting up libpaper1:armhf (1.1.24+nmu4) ...

Creating config file /etc/papersize with new version
Setting up libpcrecpp0v5:armhf (2:8.35-7.2) ...
Setting up libtre5:armhf (0.8.0-4) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libxau6:armhf (1:1.0.8-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-1) ...
Setting up libxcb1:armhf (1.10-3+b1) ...
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 libxrender1:armhf (1:0.9.8-1+b1) ...
Setting up libxft2:armhf (2.3.2-1) ...
Setting up x11-common (1:7.7+12) ...
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 libxt6:armhf (1:1.1.4-1+b1) ...
Setting up libxmu6:armhf (2:1.1.2-1) ...
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 (0.4.7-3) ...
Setting up sgml-base (1.26+nmu4) ...
Setting up libfaketime:armhf (0.9.6-4) ...
Setting up faketime (0.9.6-4) ...
Setting up libtrio2:armhf (1.16+dfsg1-3) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.6-1) ...
Setting up libnettle6:armhf (3.1.1-4) ...
Setting up libhogweed4:armhf (3.1.1-4) ...
Setting up libp11-kit0:armhf (0.23.1-3) ...
Setting up libtasn1-6:armhf (4.7-2) ...
Setting up libgnutls-deb0-28:armhf (3.3.18-1) ...
Setting up libkeyutils1:armhf (1.5.9-8) ...
Setting up libkrb5support0:armhf (1.13.2+dfsg-2) ...
Setting up libk5crypto3:armhf (1.13.2+dfsg-2) ...
Setting up libkrb5-3:armhf (1.13.2+dfsg-2) ...
Setting up libgssapi-krb5-2:armhf (1.13.2+dfsg-2) ...
Setting up libidn11:armhf (1.32-3) ...
Setting up libsasl2-modules-db:armhf (2.1.26.dfsg1-14) ...
Setting up libsasl2-2:armhf (2.1.26.dfsg1-14) ...
Setting up libldap-2.4-2:armhf (2.4.42+dfsg-2+rpi1) ...
Setting up asciidoc (8.6.9-3) ...
Setting up openssl (1.0.2d-1) ...
Setting up ca-certificates (20150426) ...
Setting up gettext (0.19.6-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.18) ...
Setting up libarchive-zip-perl (1.53-1) ...
Setting up libfile-stripnondeterminism-perl (0.012-1) ...
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 (4.4.0~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-inconsolata (001.010-5) ...
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-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 (1.46.0-1) ...
Setting up gir1.2-glib-2.0:armhf (1.46.0-1) ...
Setting up libpixman-1-0:armhf (0.33.2-2) ...
Setting up libxcb-render0:armhf (1.10-3+b1) ...
Setting up libxcb-shm0:armhf (1.10-3+b1) ...
Setting up libcairo2:armhf (1.14.2-2) ...
Setting up libcairo-gobject2:armhf (1.14.2-2) ...
Setting up gir1.2-freedesktop:armhf (1.46.0-1) ...
Setting up libthai-data (0.1.22-2) ...
Setting up libdatrie1:armhf (0.2.9-3) ...
Setting up libthai0:armhf (0.1.22-2) ...
Setting up libpango-1.0-0:armhf (1.38.0-3) ...
Setting up libgraphite2-3:armhf (1.3.3-1) ...
Setting up libharfbuzz0b:armhf (1.0.1-1+b1) ...
Setting up libpangoft2-1.0-0:armhf (1.38.0-3) ...
Setting up libpangocairo-1.0-0:armhf (1.38.0-3) ...
Setting up libpangoxft-1.0-0:armhf (1.38.0-3) ...
Setting up gir1.2-pango-1.0:armhf (1.38.0-3) ...
Setting up libbam-dev (0.1.19-2) ...
Setting up libbz2-dev:armhf (1.0.6-8) ...
Setting up libcairo-script-interpreter2:armhf (1.14.2-2) ...
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 (1.2.50-2+b2) ...
Setting up libfreetype6-dev (2.6-2) ...
Setting up pkg-config (0.28-1) ...
Setting up libfontconfig1-dev:armhf (2.11.0-6.3) ...
Setting up xorg-sgml-doctools (1:1.11-1) ...
Setting up x11proto-core-dev (7.0.27-1) ...
Setting up libxau-dev:armhf (1:1.0.8-1) ...
Setting up libxdmcp-dev:armhf (1:1.1.2-1) ...
Setting up x11proto-input-dev (2.3.1-1) ...
Setting up x11proto-kb-dev (1.0.6-2) ...
Setting up xtrans-dev (1.3.5-1) ...
Setting up libpthread-stubs0-dev:armhf (0.3-4) ...
Setting up libxcb1-dev:armhf (1.10-3+b1) ...
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 (1:0.9.8-1+b1) ...
Setting up x11proto-xext-dev (7.3.0-1) ...
Setting up libxext-dev:armhf (2:1.3.3-1) ...
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 (0.33.2-2) ...
Setting up libxcb-render0-dev:armhf (1.10-3+b1) ...
Setting up libxcb-shm0-dev:armhf (1.10-3+b1) ...
Setting up libelf1:armhf (0.163-5.1) ...
Setting up libglib2.0-data (2.46.1-1) ...
Setting up libglib2.0-bin (2.46.0-2) ...
Setting up libpcre16-3:armhf (2:8.35-7.2) ...
Setting up libpcre32-3:armhf (2:8.35-7.2) ...
Setting up libpcre3-dev:armhf (2:8.35-7.2) ...
Setting up libglib2.0-dev (2.46.0-2) ...
Setting up libcairo2-dev (1.14.2-2) ...
Setting up libcups2:armhf (2.1.0-4) ...
Setting up libjpeg62-turbo:armhf (1:1.4.1-2) ...
Setting up libtiff5:armhf (4.0.5-1) ...
Setting up libijs-0.35:armhf (0.35-11) ...
Setting up libjbig2dec0 (0.12+20150918-1) ...
Setting up libgs9-common (9.16~dfsg-2) ...
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 (2015.20150524.37493-6) ...
Setting up liblua5.1-0:armhf (5.1.5-8) ...
Setting up libtinfo-dev:armhf (6.0+20150810-1) ...
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 libncurses5-dev:armhf (6.0+20150810-1) ...
Setting up libxft-dev (2.3.2-1) ...
Setting up libpango1.0-dev (1.38.0-3) ...
Setting up libpaper-utils (1.1.24+nmu4) ...
Setting up libopenjpeg5:armhf (1:1.5.2-3.1) ...
Setting up libpoppler46:armhf (0.26.5-4) ...
Setting up libpotrace0 (1.12-1) ...
Setting up libptexenc1 (2015.20150524.37493-6) ...
Setting up libsqlite3-dev:armhf (3.8.11.1-1) ...
Setting up libsynctex1 (2015.20150524.37493-6) ...
Setting up libtexlua52 (2015.20150524.37493-6) ...
Setting up libtexluajit2 (2015.20150524.37493-6) ...
Setting up libtre-dev (0.8.0-4) ...
Setting up libxpm4:armhf (1:3.5.11-1+b1) ...
Setting up libxaw7:armhf (2:1.0.13-1) ...
Setting up libxi6:armhf (2:1.7.5-1) ...
Setting up libxml2-utils (2.9.2+zdfsg1-4) ...
Setting up libxslt1.1:armhf (1.1.28-2+b2) ...
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 (1.9) ...
Setting up libruby2.1:armhf (2.1.5-4) ...
Setting up ruby2.1 (2.1.5-4) ...
Setting up ruby (1:2.1.5.1) ...
Setting up t1utils (1.38-4) ...
Setting up xdg-utils (1.1.1-1) ...
Setting up fonts-stix (1.1.1-4) ...
Setting up ttf-adf-gillius (0.20090423-2) ...
Setting up ttf-adf-universalis (0.20090423-2) ...
Setting up ttf-adf-accanthis (0.20090423-2) ...
Setting up xsltproc (1.1.28-2+b2) ...
Processing triggers for sgml-base (1.26+nmu4) ...
Setting up docbook-xsl (1.78.1+dfsg-1) ...
Setting up libcupsfilters1:armhf (1.0.76-1) ...
Setting up dh-strip-nondeterminism (0.012-1) ...
Setting up debhelper (9.20151005) ...
Setting up libcupsimage2:armhf (2.1.0-4) ...
Setting up libgs9 (9.16~dfsg-2) ...
Setting up texlive-binaries (2015.20150524.37493-6) ...
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 (2015.20151016-1) ...
/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 (2015.20151016-1) ...
Setting up texlive-latex-base (2015.20151016-1) ...
Setting up texlive-fonts-extra (2015.20151016-1) ...
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 (2015.20151016-1) ...
Setting up texlive-pictures (2015.20151016-1) ...
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 (2015.20151016-1) ...
Processing triggers for tex-common (6.04) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Setting up sbuild-build-depends-genometools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-22) ...
Processing triggers for systemd (227-2) ...
Processing triggers for ca-certificates (20150426) ...
Updating certificates in /etc/ssl/certs...
180 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.

┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment                                                            │
└──────────────────────────────────────────────────────────────────────────────┘

Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25.1-3 dpkg-dev_1.18.3 g++-4.9_4.9.3-4 g++-5_5.2.1-21+rpi1 gcc-4.9_4.9.3-4 gcc-5_5.2.1-21+rpi1 libc6-dev_2.19-22 libstdc++-4.9-dev_4.9.3-4 libstdc++-5-dev_5.2.1-21+rpi1 libstdc++6_5.2.1-21+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.10.2 asciidoc_8.6.9-3 base-files_9.4+rpi1 base-passwd_3.5.38 bash_4.3-14 binutils_2.25.1-3 bsdmainutils_9.0.6 bsdutils_1:2.27-3 build-essential_11.7 bzip2_1.0.6-8 ca-certificates_20150426 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.2.1-4+rpi2 cpp-4.9_4.9.3-4 cpp-5_5.2.1-21+rpi1 dash_0.5.7-4 debconf_1.5.57 debfoster_2.7-2 debhelper_9.20151005 debianutils_4.5.1 dh-strip-nondeterminism_0.012-1 diffutils_1:3.3-2 dmsetup_2:1.02.104-1 docbook-xsl_1.78.1+dfsg-1 dpkg_1.18.3 dpkg-dev_1.18.3 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_4.4.2-9 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-droid_1:4.4.4r2-7 fonts-ebgaramond_0.015+git20130628-3 fonts-ebgaramond-extra_0.015+git20130628-3 fonts-font-awesome_4.4.0~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-inconsolata_001.010-5 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_1:4.4.4r2-7 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++_4:5.2.1-4+rpi2 g++-4.9_4.9.3-4 g++-5_5.2.1-21+rpi1 gcc_4:5.2.1-4+rpi2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-1 gcc-4.9_4.9.3-4 gcc-4.9-base_4.9.3-4 gcc-5_5.2.1-21+rpi1 gcc-5-base_5.2.1-21+rpi1 gettext_0.19.6-1 gettext-base_0.19.6-1 gir1.2-freedesktop_1.46.0-1 gir1.2-glib-2.0_1.46.0-1 gir1.2-pango-1.0_1.38.0-3 gnupg_1.4.19-5 gpgv_1.4.19-5 grep_2.21-2 groff-base_1.22.3-1 gzip_1.6-4 hostname_3.16 init_1.23 init-system-helpers_1.23 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-2+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.10-2 libapt-pkg4.12_1.0.9.10 libapt-pkg4.16_1.0.10.2 libarchive-zip-perl_1.53-1 libasan1_4.9.3-4 libasan2_5.2.1-21+rpi1 libatomic1_5.2.1-21+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-4 libaudit1_1:2.4.4-4 libavahi-client3_0.6.31-5 libavahi-common-data_0.6.31-5 libavahi-common3_0.6.31-5 libbam-dev_0.1.19-2 libblkid1_2.27-3 libbz2-1.0_1.0.6-8 libbz2-dev_1.0.6-8 libc-bin_2.19-22 libc-dev-bin_2.19-22 libc6_2.19-22 libc6-dev_2.19-22 libcairo-gobject2_1.14.2-2 libcairo-script-interpreter2_1.14.2-2 libcairo2_1.14.2-2 libcairo2-dev_1.14.2-2 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.2.1-21+rpi1 libcloog-isl4_0.18.3-1 libcomerr2_1.42.13-1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5 libcups2_2.1.0-4 libcupsfilters1_1.0.76-1 libcupsimage2_2.1.0-4 libdatrie1_0.2.9-3 libdb5.3_5.3.28-11 libdbus-1-3_1.10.0-3 libdebconfclient0_0.195 libdevmapper1.02.1_2:1.02.104-1 libdpkg-perl_1.18.3 libdrm2_2.4.64-1 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_2.27-3 libffi6_3.2.1-3 libfile-stripnondeterminism-perl_0.012-1 libfontconfig1_2.11.0-6.3 libfontconfig1-dev_2.11.0-6.3 libfreetype6_2.6-2 libfreetype6-dev_2.6-2 libgc1c2_1:7.4.2-7 libgcc-4.9-dev_4.9.3-4 libgcc-5-dev_5.2.1-21+rpi1 libgcc1_1:5.2.1-21+rpi1 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libgirepository-1.0-1_1.46.0-1 libglib2.0-0_2.46.0-2 libglib2.0-bin_2.46.0-2 libglib2.0-data_2.46.1-1 libglib2.0-dev_2.46.0-2 libgmp10_2:6.0.0+dfsg-7+rpi1 libgnutls-deb0-28_3.3.18-1 libgomp1_5.2.1-21+rpi1 libgpg-error0_1.20-1 libgraphite2-3_1.3.3-1 libgs9_9.16~dfsg-2 libgs9-common_9.16~dfsg-2 libgssapi-krb5-2_1.13.2+dfsg-2 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_3.1.1-4 libice-dev_2:1.0.9-1+b1 libice6_2:1.0.9-1+b1 libicu55_55.1-5 libidn11_1.32-3 libijs-0.35_0.35-11 libisl13_0.14-2 libjbig0_2.1-3.1 libjbig2dec0_0.12+20150918-1 libjpeg62-turbo_1:1.4.1-2 libk5crypto3_1.13.2+dfsg-2 libkeyutils1_1.5.9-8 libklibc_2.0.4-2+rpi1 libkmod2_21-1 libkpathsea6_2015.20150524.37493-6 libkrb5-3_1.13.2+dfsg-2 libkrb5support0_1.13.2+dfsg-2 liblcms2-2_2.6-3 libldap-2.4-2_2.4.42+dfsg-2+rpi1 liblocale-gettext-perl_1.07-1 liblua5.1-0_5.1.5-8 liblua5.1-0-dev_5.1.5-8 liblzma5_5.1.1alpha+20120614-2.1 liblzo2-2_2.08-1.2 libmagic1_1:5.25-2 libmount1_2.27-3 libmpc3_1.0.3-1 libmpfr4_3.1.3-1 libncurses5_6.0+20150810-1 libncurses5-dev_6.0+20150810-1 libncursesw5_6.0+20150810-1 libnettle6_3.1.1-4 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libopenjpeg5_1:1.5.2-3.1 libp11-kit0_0.23.1-3 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpango-1.0-0_1.38.0-3 libpango1.0-dev_1.38.0-3 libpangocairo-1.0-0_1.38.0-3 libpangoft2-1.0-0_1.38.0-3 libpangoxft-1.0-0_1.38.0-3 libpaper-utils_1.1.24+nmu4 libpaper1_1.1.24+nmu4 libpcre16-3_2:8.35-7.2 libpcre3_2:8.35-7.2 libpcre3-dev_2:8.35-7.2 libpcre32-3_2:8.35-7.2 libpcrecpp0v5_2:8.35-7.2 libpipeline1_1.4.1-1 libpixman-1-0_0.33.2-2 libpixman-1-dev_0.33.2-2 libpng12-0_1.2.50-2+b2 libpng12-dev_1.2.50-2+b2 libpoppler46_0.26.5-4 libpotrace0_1.12-1 libprocps3_2:3.3.9-9 libprocps4_2:3.3.10-2 libptexenc1_2015.20150524.37493-6 libpthread-stubs0-dev_0.3-4 libpython-stdlib_2.7.9-1 libpython2.7-minimal_2.7.10-5 libpython2.7-stdlib_2.7.10-5 libreadline-dev_6.3-8+b3 libreadline6_6.3-8+b3 libreadline6-dev_6.3-8+b3 libruby2.1_2.1.5-4 libsasl2-2_2.1.26.dfsg1-14 libsasl2-modules-db_2.1.26.dfsg1-14 libseccomp2_2.2.3-2 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-2+b1 libsm-dev_2:1.2.2-1+b1 libsm6_2:1.2.2-1+b1 libsmartcols1_2.27-3 libsqlite3-0_3.8.11.1-1 libsqlite3-dev_3.8.11.1-1 libss2_1.42.13-1 libssl1.0.0_1.0.2d-1 libstdc++-4.9-dev_4.9.3-4 libstdc++-5-dev_5.2.1-21+rpi1 libstdc++6_5.2.1-21+rpi1 libsynctex1_2015.20150524.37493-6 libsystemd0_227-2 libtasn1-6_4.7-2 libtexlua52_2015.20150524.37493-6 libtexluajit2_2015.20150524.37493-6 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7.1 libthai-data_0.1.22-2 libthai0_0.1.22-2 libtiff5_4.0.5-1 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20150810-1 libtinfo5_6.0+20150810-1 libtre-dev_0.8.0-4 libtre5_0.8.0-4 libtrio2_1.16+dfsg1-3 libubsan0_5.2.1-21+rpi1 libudev1_227-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.27-3 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_1.10-3+b1 libxcb-render0-dev_1.10-3+b1 libxcb-shm0_1.10-3+b1 libxcb-shm0-dev_1.10-3+b1 libxcb1_1.10-3+b1 libxcb1-dev_1.10-3+b1 libxdmcp-dev_1:1.1.2-1 libxdmcp6_1:1.1.2-1 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_2:1.7.5-1 libxml2_2.9.2+zdfsg1-4 libxml2-utils_2.9.2+zdfsg1-4 libxmu6_2:1.1.2-1 libxpm4_1:3.5.11-1+b1 libxrender-dev_1:0.9.8-1+b1 libxrender1_1:0.9.8-1+b1 libxslt1.1_1.1.28-2+b2 libxt6_1:1.1.4-1+b1 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 lsb-base_4.1+Debian13+rpi1+nmu1 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_4.0-8.2 makedev_2.3.1-93 man-db_2.7.4-1 mawk_1.3.3-17 mime-support_3.59 mount_2.27-3 multiarch-support_2.19-22 nano_2.4.2-1 ncurses-base_6.0+20150810-1 ncurses-bin_6.0+20150810-1 openssl_1.0.2d-1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 pkg-config_0.28-1 po-debconf_1.0.18 poppler-data_0.4.7-3 preview-latex-style_11.87-3+deb8u1 procps_2:3.3.10-2 python_2.7.9-1 python-minimal_2.7.9-1 python2.7_2.7.10-5 python2.7-minimal_2.7.10-5 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 ruby_1:2.1.5.1 ruby2.1_2.1.5-4 rubygems-integration_1.9 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_227-2 systemd-sysv_227-2 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 t1utils_1.38-4 tar_1.28-1 tex-common_6.04 texlive-base_2015.20151016-1 texlive-binaries_2015.20150524.37493-6 texlive-fonts-extra_2015.20151016-1 texlive-fonts-recommended_2015.20151016-1 texlive-latex-base_2015.20151016-1 texlive-latex-extra_2015.20151016-1 texlive-latex-recommended_2015.20151016-1 texlive-pictures_2015.20151016-1 ttf-adf-accanthis_0.20090423-2 ttf-adf-gillius_0.20090423-2 ttf-adf-universalis_0.20090423-2 tzdata_2015g-1 ucf_3.0030 udev_227-2 util-linux_2.27-3 x11-common_1:7.7+12 x11proto-core-dev_7.0.27-1 x11proto-input-dev_2.3.1-1 x11proto-kb-dev_1.0.6-2 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+b2 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 Sat Oct 10 12:30:29 2015 UTC using RSA key ID 04A3610B
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./genometools_1.5.7-2.dsc
dpkg-source: info: extracting genometools in genometools-1.5.7
dpkg-source: info: unpacking genometools_1.5.7.orig.tar.gz
dpkg-source: info: unpacking genometools_1.5.7-2.debian.tar.xz
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

Check disc space
────────────────

Sufficient free space for build

User Environment
────────────────

DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=root
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-5b2790aa-d9a9-4949-a516-82ab99da5369
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd

dpkg-buildpackage
─────────────────

dpkg-buildpackage: source package genometools
dpkg-buildpackage: source version 1.5.7-2
dpkg-buildpackage: source distribution unstable
 dpkg-source --before-build genometools-1.5.7
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 '/«PKGBUILDDIR»'
/usr/bin/make cleanup
make[2]: Entering directory '/«PKGBUILDDIR»'
rm -rf lib
find obj -name '*.o' |xargs rm -f
find: `obj': No such file or directory
rm -f obj/amalgamation.c
rm -rf testsuite/stest_testsuite testsuite/stest_stest_tests
/usr/bin/make -s -C /«PKGBUILDDIR»/doc/devguide clean
make[3]: Entering directory '/«PKGBUILDDIR»/doc/devguide'
make[3]: Leaving directory '/«PKGBUILDDIR»/doc/devguide'
/usr/bin/make -s -C /«PKGBUILDDIR»/doc/manuals clean
make[3]: Entering directory '/«PKGBUILDDIR»/doc/manuals'
make[3]: Leaving directory '/«PKGBUILDDIR»/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' | xargs rm -f
find: `obj': No such file or directory
find obj -name '*.check' | xargs rm -f
find: `obj': No such file or directory
find obj -name '*.sb' | xargs rm -f
find: `obj': No such file or directory
rm -rf bin obj
rm -rf gtpython/build
/usr/bin/make -s -C /«PKGBUILDDIR»/doc/manuals cleanup
make[3]: Entering directory '/«PKGBUILDDIR»/doc/manuals'
make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manuals'
make[2]: Leaving directory '/«PKGBUILDDIR»'
cd doc/manuals; /usr/bin/make cleanup
make[2]: Entering directory '/«PKGBUILDDIR»/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 '/«PKGBUILDDIR»/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/docs.html \
      www/genometools.org/htdocs/examples.html \
      www/genometools.org/htdocs/libgenometools.html \
      www/genometools.org/htdocs/tools/gt.html
rm -rf gtpython/build
make[1]: Leaving directory '/«PKGBUILDDIR»'
   dh_clean
 debian/rules build-arch
dh build-arch --with python2
   dh_testdir -a
   dh_auto_configure -a
   debian/rules override_dh_auto_build
make[1]: Entering directory '/«PKGBUILDDIR»'
faketime -f "`TZ=UTC date -d @1444478677 +'%Y-%m-%d %H:%M:%S'`" dh_auto_build -- useshared=yes 64bit=no errorcheck=no all docs manuals
	make -j1 useshared=yes 64bit=no errorcheck=no all docs manuals
make[2]: Entering directory '/«PKGBUILDDIR»'
[create obj/gt_config.h]
[compile str_cache.o]
[compile interval_tree.o]
[compile bitpackstringop32.o]
[compile strcmp.o]
[compile version.o]
[compile spacepeak.o]
[compile array2dim_sparse.o]
[compile checkbitpackstring32.o]
[compile complement.o]
[compile checkbitpackstring8.o]
[compile encseq_ptr.o]
[compile msort.o]
[compile ma.o]
[compile output_file.o]
[compile string_distri.o]
[compile fileutils.o]
[compile checkbitpackarray.o]
[compile range.o]
[compile timer.o]
[compile gtdatapath.o]
[compile checkbitpackstring64.o]
[compile combinatorics.o]
[compile thread.o]
[compile bitpackstringop.o]
[compile toolbox.o]
[compile qsort-ulong.o]
[compile encseq_col.o]
[compile basename.o]
[compile bioseq.o]
[compile example_a.o]
[compile fasta_reader.o]
[compile score_function.o]
[compile encseq_options.o]
[compile init.o]
[compile sequence_buffer_embl.o]
[compile readmode.o]
[compile safearith.o]
[compile seq_iterator.o]
[compile dlist.o]
[compile gc_content.o]
[compile password_entry.o]
[compile seq.o]
[compile splitter.o]
[compile encseq_metadata.o]
[compile process.o]
[compile mapspec.o]
[compile dynalloc.o]
[compile str.o]
[compile seq_iterator_sequence_buffer.o]
[compile bsearch.o]
[compile queue.o]
[compile mathsupport.o]
[compile sequence_buffer_fasta.o]
[compile codon_iterator.o]
[compile cstr_table.o]
[compile grep.o]
[compile byte_select.o]
[compile bittab.o]
[compile eansi.o]
[compile phase.o]
[compile disc_distri.o]
[compile endianess.o]
[compile symbol.o]
[compile array.o]
[compile bitpackstringop8.o]
[compile checkbitpackstring16.o]
[compile seq_col.o]
[compile encseq_access_type.o]
[compile cstr.o]
[compile seq_iterator_fastq.o]
[compile hashmap.o]
[compile md5_encoder.o]
[compile desc_buffer.o]
[compile array3dim.o]
[compile colorspace.o]
[compile xbsd.o]
[compile md5_seqid.o]
[compile io.o]
[compile tooldriver.o]
[compile checkbitpackstring-int.o]
[compile strand.o]
[compile bioseq_iterator.o]
[compile tokenizer.o]
[compile progressbar.o]
[compile fastq.o]
[compile fasta.o]
[compile class_alloc_lock.o]
[compile example.o]
[compile codon_iterator_encseq.o]
[compile countingsort.o]
[compile bitpackstringop16.o]
[compile orf.o]
[compile radix_sort.o]
[compile sequence_buffer_plain.o]
[compile bool_matrix.o]
[compile dyn_bittab.o]
[compile bitbuffer.o]
[compile encseq.o]
[compile str_array.o]
[compile class_alloc.o]
[compile md5_tab.o]
[compile fa.o]
[compile multithread.o]
[compile ezlib.o]
[compile sequence_buffer_gb.o]
[compile parseutils.o]
[compile yarandom.o]
[compile bioseq_col.o]
[compile trans_table.o]
[compile md5_fingerprint.o]
[compile qsort_r.o]
[compile showtime.o]
[compile xansi.o]
[compile compact_ulong_store.o]
[compile fasta_reader_fsm.o]
[compile dual-pivot-qsort.o]
[compile error.o]
[compile log.o]
[compile translator.o]
[compile xzlib.o]
[compile bitpackstringop64.o]
[compile sig.o]
[compile logger.o]
[compile warning.o]
[compile seq_info_cache.o]
[compile option.o]
[compile sequence_buffer_fastq.o]
[compile compat.o]
[compile example_b.o]
[compile tool_iterator.o]
[compile alphabet.o]
[compile score_matrix.o]
[compile file.o]
[compile fasta_reader_seqit.o]
[compile tool.o]
[compile versionfunc.o]
[compile ebzlib.o]
[compile array2dim.o]
[compile xbzlib.o]
[compile hashtable.o]
[compile codon_iterator_simple.o]
[compile sequence_buffer.o]
[compile checkbitpackstring.o]
[compile quality.o]
[compile xposix.o]
[compile unit_testing.o]
[compile byte_popcount.o]
[compile fasta_reader_rec.o]
[compile cstr_array.o]
[compile extract_feature_visitor.o]
[compile hmm.o]
[compile sequence_node_out_stream.o]
[compile splicedseq.o]
[compile seqid2file.o]
[compile regioncov_visitor.o]
[compile sequence_node_add_stream.o]
[compile feature_node_observer.o]
[compile eof_node.o]
[compile orf_finder_visitor.o]
[compile node_visitor.o]
[compile sequence_node.o]
[compile consensus_sa.o]
[compile md5_to_id_visitor.o]
[compile dot_out_stream.o]
[compile sspliced_alignment_parsing.o]
[compile ranked_list.o]
[compile hcr.o]
[compile xrf_abbr_parse_tree.o]
[compile io_function_pointers.o]
[compile add_ids_stream.o]
[compile transcript_exons.o]
[compile samfile_iterator.o]
[compile intset_32.o]
[compile feature_node_iterator.o]
[compile spec_visitor.o]
[compile swalign.o]
[compile snp_annotator_visitor.o]
[compile anno_db_schema.o]
[compile hpol_processor.o]
[compile array_in_stream.o]
[compile script_filter.o]
[compile id_to_md5_stream.o]
[compile transcript_evaluators.o]
[compile priority_queue.o]
[compile region_node_builder.o]
[compile inter_feature_stream.o]
[compile regular_seqid.o]
[compile gff3_in_stream_plain.o]
[compile dice_hmm.o]
[compile splice_site_info_stream.o]
[compile cds_visitor.o]
[compile gff3_out_stream.o]
[compile union_find.o]
[compile reverse.o]
[compile select_visitor.o]
[compile uint64hashtable.o]
[compile permute_words.o]
[compile safe_popen.o]
[compile cds_check_stream.o]
[compile mutate.o]
[compile aligned_segments_pile.o]
[compile array_out_stream.o]
[compile feature_out_stream.o]
[compile genome_node.o]
[compile extract_feature_sequence.o]
[compile merge_feature_stream.o]
[compile xrfcheck_info.o]
[compile inter_feature_visitor.o]
[compile script_wrapper_stream.o]
[compile match_iterator.o]
[compile intset_8.o]
[compile fasta_header_iterator.o]
[compile golomb.o]
[compile wtree_encseq.o]
[compile sequence_node_out_visitor.o]
[compile md5set.o]
[compile script_wrapper_visitor.o]
[compile rdb_sqlite.o]
[compile match_iterator_last.o]
[compile cds_check_visitor.o]
[compile encdesc_header_io.o]
[compile match.o]
[compile shredder.o]
[compile feature_node.o]
[compile gff3_numsorted_out_stream.o]
[compile add_introns_stream.o]
[compile luaserialize.o]
[compile cstr_iterator.o]
[compile gff3_output.o]
[compile check_boundaries_visitor.o]
[compile extract_feature_stream.o]
[compile huffcode.o]
[compile csa_visitor.o]
[compile splice_site_info_visitor.o]
[compile transcript_used_exons.o]
[compile match_iterator_open.o]
[compile type_checker_obo.o]
[compile spec_results.o]
[compile tidy_region_node_stream.o]
[compile orphanage.o]
[compile gff3_escaping.o]
[compile gff3_linesorted_out_stream.o]
[compile feature_stream.o]
[compile stat_stream.o]
[compile gap_str.o]
[compile id_to_md5_visitor.o]
[compile rcr.o]
[compile gtf_in_stream.o]
[compile obo_parse_tree.o]
[compile type_node.o]
[compile editscript.o]
[compile popcount_tab.o]
[compile typecheck_info.o]
[compile elias_gamma.o]
[compile alignment.o]
[compile compressed_bitsequence.o]
[compile match_sw.o]
[compile multi_sanitizer_visitor.o]
[compile globalchaining.o]
[compile aligned_segment.o]
[compile encdesc.o]
[compile type_graph.o]
[compile md5_to_id_stream.o]
[compile affinealign.o]
[compile gtf_visitor.o]
[compile add_ids_visitor.o]
[compile node_stream.o]
[compile gff3_parser.o]
[compile coin_hmm.o]
[compile rdb.o]
[compile clustered_set.o]
[compile set_source_visitor.o]
[compile match_last.o]
[compile rbtree.o]
[compile visitor_stream.o]
[compile kmer_database.o]
[compile feature_index.o]
[compile csa_splice_form.o]
[compile transcript_counts.o]
[compile maxcoordvalue.o]
[compile seqpos_classifier.o]
[compile condenseq_search_arguments.o]
[compile seqid2seqnum_mapping.o]
[compile luahelper.o]
[compile multieoplist.o]
[compile evaluator.o]
[compile buffer_stream.o]
[compile sampling.o]
[compile cds_stream.o]
[compile csa_variable_strands.o]
[compile stream_evaluator.o]
[compile meta_node.o]
[compile dot_visitor.o]
[compile xrf_abbr_entry.o]
[compile region_node.o]
[compile select_stream.o]
[compile dup_feature_visitor.o]
[compile intset_16.o]
[compile tir_stream.o]
[compile wtree.o]
[compile chseqids_stream.o]
[compile mapping.o]
[compile intset.o]
[compile linearalign.o]
[compile comment_node.o]
[compile targetbest_select_stream.o]
[compile intset_combined.o]
[compile feature_index_memory.o]
[compile samfile_encseq_mapping.o]
[compile sort_stream.o]
[compile collect_ids_visitor.o]
[compile reconstructalignment.o]
[compile uniq_stream.o]
[compile snp_annotator_stream.o]
[compile sam_query_name_iterator.o]
[compile gff3_visitor.o]
[compile sspliced_alignment.o]
[compile csa_stream.o]
[compile feature_info.o]
[compile match_visitor.o]
[compile merge_stream.o]
[compile gtf_out_stream.o]
[compile anno_db_gfflike.o]
[compile string_matching.o]
[compile assembly_stats_calculator.o]
[compile bed_in_stream.o]
[compile orf_iterator.o]
[compile type_checker.o]
[compile linearalign_affinegapcost.o]
[compile blast_process_call.o]
[compile feature_visitor.o]
[compile stat_visitor.o]
[compile transcript_bittabs.o]
[compile xrf_checker.o]
[compile gff3_in_stream.o]
[compile tag_value_map.o]
[compile match_iterator_sw.o]
[compile region_mapping.o]
[compile match_iterator_blast.o]
[compile match_open.o]
[compile bitoutstream.o]
[compile sam_alignment.o]
[compile csa_gene.o]
[compile match_blast.o]
[compile feature_in_stream.o]
[compile bitinstream.o]
[compile type_checker_builtin.o]
[compile rmq.o]
[compile rdb_visitor.o]
[compile bed_parser.o]
[compile gtdatahelp.o]
[compile condenseq_creator.o]
[compile condenseq.o]
[compile tidy_region_node_visitor.o]
[compile orf_finder_stream.o]
[compile load_stream.o]
[compile dup_feature_stream.o]
[compile merge_feature_visitor.o]
[compile chain.o]
[compile clustered_set_uf.o]
[compile obo_stanza.o]
[compile gtf_parser.o]
[compile bittab_lua.o]
[compile canvas_lua.o]
[compile gtext_lua.o]
[compile encseq_lua.o]
[compile genome_stream_lua.o]
[compile feature_stream_lua.o]
[compile annotationsketch_lua.o]
[compile feature_index_lua.o]
[compile gtcore_lua.o]
[compile layout_lua.o]
[compile feature_visitor_lua.o]
[compile csa_stream_lua.o]
[compile image_info_lua.o]
[compile diagram_lua.o]
[compile translate_lua.o]
[compile feature_node_iterator_lua.o]
[compile genome_node_lua.o]
[compile region_mapping_lua.o]
[compile genome_visitor_lua.o]
[compile cds_stream_lua.o]
[compile alphabet_lua.o]
[compile score_matrix_lua.o]
[compile gt_lua.o]
[compile stream_evaluator_lua.o]
[compile mathsupport_lua.o]
[compile range_lua.o]
[compile sfx-bentsedg.o]
[compile greedyedist.o]
[compile revcompl.o]
[compile rdj-contigs-writer.o]
[compile sfx-mappedstr.o]
[compile eis-bwtseq-extinfo.o]
[compile sfx-suffixer.o]
[compile esa-dfs.o]
[compile idxlocali.o]
[compile echoseq.o]
[compile spaced-seeds.o]
[compile pckbucket.o]
[compile seqnumrelpos.o]
[compile querymatch-align.o]
[compile esa-mmsearch.o]
[compile chain2dim.o]
[compile eis-blockcomp-param.o]
[compile shu_unitfile.o]
[compile eis-bwtseq-param.o]
[compile rdj-errfind.o]
[compile eis-voiditf.o]
[compile shu-dfs.o]
[compile apmeoveridx.o]
[compile rdj-spmproc.o]
[compile encseq2offset.o]
[compile sfx-outprj.o]
[compile ft-trimstat.o]
[compile test-mappedstr.o]
[compile enum-patt.o]
[compile tyr-mkindex.o]
[compile fmi-keyval.o]
[compile rdj-contigs-graph.o]
[compile nullcols.o]
[compile rdj-contigpaths.o]
[compile eis-bwtseq-context.o]
[compile twobits2kmers.o]
[compile rdj-pairwise.o]
[compile xdrop.o]
[compile randomcodes-sfx-partssuf.o]
[compile esa-maxpairs.o]
[compile asqg_writer.o]
[compile pckdfs.o]
[compile merger-trie.o]
[compile greedyfwdmat.o]
[compile rdj-strgraph.o]
[compile firstcodes-scan.o]
[compile fmi-mkindex.o]
[compile tyr-search.o]
[compile fmi-mapspec.o]
[compile randomcodes-tab.o]
[compile seqabstract.o]
[compile randomcodes-correct.o]
[compile spmsuftab.o]
[compile rdj-version.o]
[compile sfx-shortreadsort.o]
[compile rdj-contfind-bottomup.o]
[compile pck-count-nodes.o]
[compile optionargmode.o]
[compile chainofin.o]
[compile fmi-locate.o]
[compile squarededist.o]
[compile test-pairwise.o]
[compile fmi-fwduni.o]
[compile radixsort_str.o]
[compile bcktab.o]
[compile eis-bwtseq-sass.o]
[compile esa-map.o]
[compile idxlocalidp.o]
[compile tyr-occratio.o]
[compile prsqualint.o]
[compile shu-encseq-gc.o]
[compile firstcodes.o]
[compile eis-mrangealphabet.o]
[compile querymatch.o]
[compile esa_spmitvs_visitor.o]
[compile initeqsvec.o]
[compile esa-splititv.o]
[compile ft-front-prune.o]
[compile esa-scanprj.o]
[compile sfx-opt.o]
[compile sfx-suffixgetset.o]
[compile randomcodes-insert.o]
[compile rdj-ovlfind-dp.o]
[compile mssufpat.o]
[compile rdj-ovlfind-bf.o]
[compile eis-bwtseq-context-param.o]
[compile reads_libraries_table.o]
[compile shu-genomediff.o]
[compile sfx-copysort.o]
[compile sfx-radixsort.o]
[compile rdj-cntlist.o]
[compile bare-encseq.o]
[compile sfx-lcpvalues.o]
[compile firstcodes-tab.o]
[compile sfx-sain.o]
[compile sfx-apfxlen.o]
[compile firstcodes-cache.o]
[compile eis-suffixerator-interface.o]
[compile randomcodes-hpcorrect.o]
[compile sfx-bltrie.o]
[compile randomcodes.o]
[compile eis-encidxseq-construct.o]
[compile sfx-suftaborder.o]
[compile dist-short.o]
[compile lua_tools.o]
[compile sfx-run.o]
[compile tyr-mersplit.o]
[compile randomcodes-find-seldom.o]
[compile sfx-lwcheck.o]
[compile shu-divergence.o]
[compile seed-extend.o]
[compile eis-suffixarray-interface.o]
[compile idxlocalisw.o]
[compile firstcodes-psbuf.o]
[compile esa-lcpintervals.o]
[compile idx-limdfs.o]
[compile cgr_spacedseed.o]
[compile rdj-ovlfind-gusfield.o]
[compile giextract.o]
[compile myersapm.o]
[compile eis-seqranges.o]
[compile eis-sequencemultiread.o]
[compile iter-window.o]
[compile sfx-diffcov.o]
[compile esa-seqread.o]
[compile sfx-enumcodes.o]
[compile firstcodes-accum.o]
[compile cutendpfx.o]
[compile rdj-spmlist.o]
[compile reads2twobit.o]
[compile test-mergeesa.o]
[compile esa_visitor.o]
[compile fmi-sufbwtstream.o]
[compile esa-minunique.o]
[compile esa-splititv-simple.o]
[compile rdj-contfinder.o]
[compile test-mtrieins.o]
[compile sfx-maprange.o]
[compile sfx-partssuf.o]
[compile turnwheels.o]
[compile test-maxpairs.o]
[compile eis-seqblocktranslate.o]
[compile esa-spmsk.o]
[compile fmi-save.o]
[compile eis-encidxseq.o]
[compile eis-encidxseq-param.o]
[compile index_options.o]
[compile fmi-map.o]
[compile eis-blockcomp.o]
[compile ft-polish.o]
[compile specialrank.o]
[compile eis-bwtseq.o]
[compile rdj-ovlfind-kmp.o]
[compile kmer2string.o]
[compile eis-specialsrank.o]
[compile esa-spmitvs.o]
[compile eis-bwtseq-construct.o]
[compile hlk-version.o]
[compile esa-merge.o]
[compile firstcodes-insert.o]
[compile tyr-map.o]
[compile pssm.o]
[compile esa_lcpintervals_visitor.o]
[compile firstcodes-spacelog.o]
[compile rdj-twobitenc-editor.o]
[compile sfx-linlcp.o]
[compile esa-bottomup.o]
[compile hashfirstcodes.o]
[compile eis-sa-common.o]
[compile ft-front-generation.o]
[compile marksubstring.o]
[compile esa-shulen.o]
[compile hplstore.o]
[compile substriter.o]
[compile tagerator.o]
[compile rdj-spmfind.o]
[compile initbasepower.o]
[compile xml_pgl_visitor.o]
[compile gthmatch.o]
[compile gt_gthbssmrmsd.o]
[compile gthsadistri.o]
[compile gt_gthconsensus.o]
[compile backtrace_path.o]
[compile gthcutoffsstrict.o]
[compile sa.o]
[compile editoperation.o]
[compile compute_scores.o]
[compile gthverbosefunc.o]
[compile indent.o]
[compile time.o]
[compile chaining.o]
[compile pgl_visitor.o]
[compile input.o]
[compile pgl_collection.o]
[compile sa_collection.o]
[compile gt_gthbssmprint.o]
[compile txt_pgl_visitor.o]
[compile gthorf.o]
[compile gthcutoffsminimal.o]
[compile dp_scores_protein.o]
[compile gff3_sa_visitor.o]
[compile chain_collection.o]
[compile gt_gthbssmfileinfo.o]
[compile gt_gthmkbssmfiles.o]
[compile gthverbosefuncvm.o]
[compile splice_site_model.o]
[compile spliced_seq.o]
[compile seq_con.o]
[compile intermediate.o]
[compile region_factory.o]
[compile gthchain.o]
[compile dp_options_postpro.o]
[compile dp_options_est.o]
[compile sa_filter.o]
[compile proc_sa_collection.o]
[compile txt_sa_visitor.o]
[compile gthxml.o]
[compile gt_gthsplit.o]
[compile gthoutput.o]
[compile bssm_param_rmsd.o]
[compile gt_gth.o]
[compile gt_gthbssmbuild.o]
[compile xml_inter_sa_visitor.o]
[compile path_walker.o]
[compile gthtravalign.o]
[compile bssm_param.o]
[compile bssm_train_stream.o]
[compile align_dna.o]
[compile sa_cmp.o]
[compile bssm_train_visitor.o]
[compile call_info.o]
[compile pgl.o]
[compile gthalignment.o]
[compile bssm_seq_processor.o]
[compile sa_visitor.o]
[compile dp_options_core.o]
[compile ags_build.o]
[compile bssm_helper.o]
[compile gt_gthfilestat.o]
[compile run_header.o]
[compile xml_final_sa_visitor.o]
[compile gthsortags.o]
[compile gt_gthbssmtrain.o]
[compile path_matrix.o]
[compile gthsplicesitescr.o]
[compile gff3_pgl_visitor.o]
[compile parse_options.o]
[compile gthcluster.o]
[compile stat.o]
[compile similarity_filter.o]
[compile md5_cache.o]
[compile gthtrans.o]
[compile align_protein.o]
[compile dp_param.o]
[compile desc_cache.o]
[compile gthcutoffsrelaxed.o]
[compile ags.o]
[compile ltrharvest_fasta_out_visitor.o]
[compile ltr_input_check_visitor.o]
[compile pdom_model_set.o]
[compile ltrdigest_pdom_visitor.o]
[compile ltr_four_char_motif.o]
[compile ltrharvest_stream.o]
[compile ltrdigest_ppt_visitor.o]
[compile gt_ltrclustering.o]
[compile ltr_refseq_match_stream.o]
[compile gt_ltrharvest.o]
[compile ltrdigest_pbs_visitor.o]
[compile ltrharvest_tabout_visitor.o]
[compile ltrdigest_file_out_stream.o]
[compile ltrharvest_fasta_out_stream.o]
[compile gt_ltrdigest.o]
[compile ltrdigest_strand_assign_visitor.o]
[compile ltr_cluster_prepare_seq_visitor.o]
[compile ltr_cluster_stream.o]
[compile ltr_classify_stream.o]
[compile ltrharvest_tabout_stream.o]
[compile ltr_orf_annotator_stream.o]
[compile mg_compute_gene_prediction.o]
[compile metagenomethreader.o]
[compile mg_outputwriter.o]
[compile mg_combinedscore.o]
[compile mg_codon.o]
[compile mg_xmlparser.o]
[compile mg_reverse.o]
[compile mg_computepath.o]
[compile style.o]
[compile image_info.o]
[compile luastyle.o]
[compile custom_track_example.o]
[compile canvas_cairo.o]
[compile line_breaker_bases.o]
[compile custom_track_script_wrapper.o]
[compile element.o]
[compile coords.o]
[compile block.o]
[compile text_width_calculator_cairo.o]
[compile canvas_cairo_context.o]
[compile gt_sketch_page.o]
[compile custom_track.o]
[compile line_breaker.o]
[compile layout.o]
[compile canvas_cairo_file.o]
[compile track.o]
[compile custom_track_gc_content.o]
[compile diagram.o]
[compile line_breaker_captions.o]
[compile graphics_cairo.o]
[compile text_width_calculator.o]
[compile graphics.o]
[compile line.o]
[compile gt_sketch.o]
[compile color.o]
[compile canvas.o]
[compile drawing_range.o]
[compile rec_map.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_packedindex_mkctxmap.o]
[compile gt_convertseq.o]
[compile gt_compreads_refcompress.o]
[compile gt_matstat.o]
[compile gt_orffinder.o]
[compile gt_fastq_sample.o]
[compile gt_readjoiner_asqg.o]
[compile gt_speck.o]
[compile gt_condenseq_hmmsearch.o]
[compile gt_mkfeatureindex.o]
[compile gt_compressedbits.o]
[compile gt_kmer_database.o]
[compile gt_seqmutate.o]
[compile gt_packedindex_chk_search.o]
[compile gt_dupfeat.o]
[compile gt_shredder.o]
[compile gt_shulen.o]
[compile gt_mgth.o]
[compile gt_packedindex.o]
[compile gt_extractfeat.o]
[compile gt_condenseq_info.o]
[compile gt_packedindex_trsuftab.o]
[compile gt_gff3_to_gtf.o]
[compile gt_readreads.o]
[compile gt_readjoiner_prefilter.o]
[compile gt_suffixerator.o]
[compile gt_packedindex_chk_integrity.o]
[compile gt_sortbench.o]
[compile gt_encseq_encode.o]
[compile gt_seqtransform.o]
[compile gt_trieins.o]
[compile gt_featureindex.o]
[compile gt_readjoiner_graph.o]
[compile gt_cds.o]
[compile gt_fingerprint.o]
[compile gt_congruence.o]
[compile gt_encseq_bitextract.o]
[compile gt_wtree_bench.o]
[compile gt_select.o]
[compile gt_patternmatch.o]
[compile gt_magicmatch.o]
[compile gt_splitfasta.o]
[compile gt_extracttarget.o]
[compile gt_compreads_decompress.o]
[compile gt_seq.o]
[compile gt_consensus_sa.o]
[compile gt_skproto.o]
[compile gt_chseqids.o]
[compile gt_genomediff.o]
[compile gt_inlineseq_split.o]
[compile gt_guessprot.o]
[compile gt_uniq.o]
[compile gt_readjoiner_correct.o]
[compile gt_seqstat.o]
[compile gt_encseq_decode.o]
[compile gt_gff3.o]
[compile gt_bed_to_gff3.o]
[compile gt_readjoiner.o]
[compile gt_sain.o]
[compile gt_readjoiner_cnttest.o]
[compile gt_seqids.o]
[compile gt_md5_to_id.o]
[compile gt_mergeesa.o]
[compile gt_encseq_bench.o]
[compile gt_tagerator.o]
[compile gt_loccheck.o]
[compile gt_encseq_check.o]
[compile gt_prebwt.o]
[compile gt_dev.o]
[compile gt_template.o]
[compile gt_mmapandread.o]
[compile gt_chain2dim.o]
[compile gt_tir.o]
[compile gt_encseq.o]
[compile gt_compreads_refdecompress.o]
[compile gt_sam_interface.o]
[compile gt_compreads_compress.o]
[compile gt_stat.o]
[compile gt_condenseq_blast.o]
[compile gt_script_filter.o]
[compile gt_hop.o]
[compile gt_regioncov.o]
[compile gt_eval.o]
[compile gt_snpper.o]
[compile gt_linspace_align.o]
[compile gt_seqorder.o]
[compile gt_compreads.o]
[compile gt_encseq_sample.o]
[compile gt_readjoiner_assembly.o]
[compile gt_encseq2spm.o]
[compile gt_parsexrf.o]
[compile gt_readjoiner_cgraph.o]
[compile gt_clean.o]
[compile gt_id_to_md5.o]
[compile gt_condenseq_extract.o]
[compile gt_tallymer.o]
[compile gt_readjoiner_overlap.o]
[compile gt_seqfilter.o]
[compile gt_condenseq_search.o]
[compile gt_paircmp.o]
[compile gt_mkfmindex.o]
[compile gt_condenseq_compress.o]
[compile gt_extractseq.o]
[compile gt_merge.o]
[compile gt_encseq_info.o]
[compile gt_interfeat.o]
[compile gt_matchtool.o]
[compile gt_gdiffcalc.o]
[compile gt_repfind.o]
[compile gt_mergefeat.o]
[compile gt_readjoiner_spmtest.o]
[compile gt_inlineseq_add.o]
[compile gt_csa.o]
[compile gt_sfxmap.o]
[compile gt_seqlensort.o]
[compile gt_simreads.o]
[compile gt_encseq_md5.o]
[compile gt_dot.o]
[compile gt_condenseq.o]
[compile gt_gtf_to_gff3.o]
[compile gt_idxlocali.o]
[compile gt_splicesiteinfo.o]
[compile gt_sequniq.o]
[compile gt_seqcorrect.o]
[compile gt_wtree.o]
[compile gt_gff3validator.o]
[compile gt_seqtranslate.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]
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bin/gt gtscripts/gtdoc.lua -html /«PKGBUILDDIR» \
        > www/genometools.org/htdocs/libgenometools.html
bin/gt gtscripts/gtdoc.lua -lua -html /«PKGBUILDDIR» \
        > www/genometools.org/htdocs/docs.html
bin/examples/sketch_parsed gtdata/sketch/default.style \
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bin/examples/sketch_constructed gtdata/sketch/default.style \
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sed -nf scripts/incl.sed \
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  www/genometools.org/htdocs/examples_tmpl.html > \
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bin/gt gtscripts/gtdoc.lua -tex /«PKGBUILDDIR» \
> doc/manuals/api_reference.tex
bin/gt gtscripts/gtdoc.lua -lua -tex /«PKGBUILDDIR» \
> doc/manuals/gtscript_reference.tex
make -C /«PKGBUILDDIR»/doc/devguide
make[3]: Entering directory '/«PKGBUILDDIR»/doc/devguide'
while (pdflatex --shell-escape devguide ; \
grep -q "Rerun to get cross" devguide.log ) do true ; \
done
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chapter 2.

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e 89.


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e 123.


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e 199.


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e 205.


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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]gfflike[]get[]all[]features([]GtF
eatureIndex *gfi, GtArray

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]dup[]feature[]stream[]new([]GtNodeStrea
m*, const char

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[]\OT1/cmtt/m/n/10.95 GtAlphabet* gt[]alphabet[]new[]from[]file[]no[]suffix([]c
onst char *filename,

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[]\OT1/cmtt/m/n/10.95 GtAlphabet* gt[]alphabet[]new[]from[]string([]const char 
*alphadef, GtUword

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[]\OT1/cmtt/m/n/10.95 GtAlphabet* gt[]alphabet[]new[]from[]sequence([]const GtS
trArray *filenametab,

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[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]add[]mapping([]GtAlphabet *alphabet, c
onst char

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[]\OT1/cmtt/m/n/10.95 int gt[]alphabet[]to[]file([]const GtAlphabet *alphabet, 
const char

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[]\OT1/cmtt/m/n/10.95 GtUchar gt[]alphabet[]pretty[]symbol([]const GtAlphabet *
alphabet, unsigned

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[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]echo[]pretty[]symbol([]const GtAlphabe
t *alphabet, FILE

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[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]encode[]seq([]const GtAlphabet *alphab
et, GtUchar *out,

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[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]decode[]seq[]to[]fp([]const GtAlphabet
 *alphabet, FILE *fpout,

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[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]decode[]seq[]to[]cstr([]const GtAlphab
et *alphabet, char

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[]\OT1/cmtt/m/n/10.95 GtStr* gt[]alphabet[]decode[]seq[]to[]str([]const GtAlpha
bet *alphabet, const

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[]\OT1/cmtt/m/n/10.95 GtFeatureIndex* gt[]anno[]db[]schema[]get[]feature[]index
([]GtAnnoDBSchema

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[]\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

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[]\OT1/cmtt/m/n/10.95 void gt[]array[]sort[]with[]data([]GtArray *array, GtComp
areWithData compar,

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[]\OT1/cmtt/m/n/10.95 void gt[]array[]sort[]stable[]with[]data([]GtArray *array
, GtCompareWithData

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\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]in[]stream[]new([]GtArray *nodes
, GtUword *progress,

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]out[]stream[]new([]GtNodeStream 
*in[]stream, GtArray

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]out[]stream[]all[]new([]GtNodeSt
ream *in[]stream, GtArray

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[]\OT1/cmtt/m/n/10.95 void gt[]bed[]in[]stream[]set[]feature[]type([]GtBEDInStr
eam *bed[]in[]stream, const

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[]\OT1/cmtt/m/n/10.95 void gt[]bed[]in[]stream[]set[]thick[]feature[]type([]GtB
EDInStream *bed[]in[]stream,

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[]\OT1/cmtt/m/n/10.95 void gt[]bed[]in[]stream[]set[]block[]type([]GtBEDInStrea
m *bed[]in[]stream, const

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[]\OT1/cmtt/m/n/10.95 void gt[]bittab[]and([]GtBittab *bittab[]a, const GtBitta
b *bittab[]b, const

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[]\OT1/cmtt/m/n/10.95 void gt[]bittab[]or([]GtBittab *bittab[]a, const GtBittab
 *bittab[]b, const

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[]\OT1/cmtt/m/n/10.95 void gt[]bittab[]nand([]GtBittab *bittab[]a, const GtBitt
ab *bittab[]b, const

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]cds[]stream[]new([]GtNodeStream *in[]st
ream, GtRegionMapping

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\OT1/cmtt/m/n/10.95 *region[]mapping, unsigned int minorflen, const char *sourc
e, bool

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]csa[]stream[]new([]GtNodeStream *in[]st
ream, GtUword

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[]\OT1/cmtt/m/n/10.95 GtCanvas* gt[]canvas[]cairo[]context[]new([]GtStyle *styl
e, cairo[]t *context,

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\OT1/cmtt/m/n/10.95 double offsetpos, GtUword width, GtUword height, GtImageInf
o *image[]info,

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[]\OT1/cmtt/m/n/10.95 GtCanvas* gt[]canvas[]cairo[]file[]new([]GtStyle *style, 
GtGraphicsOutType

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\OT1/cmtt/m/n/10.95 output[]type, GtUword width, GtUword height, GtImageInfo *i
mage[]info,

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[]\OT1/cmtt/m/n/10.95 int gt[]canvas[]cairo[]file[]to[]file([]GtCanvasCairoFile
 *canvas, const char

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[]\OT1/cmtt/m/n/10.95 int gt[]canvas[]cairo[]file[]to[]stream([]GtCanvasCairoFi
le *canvas, GtStr

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[]\OT1/cmtt/m/n/10.95 GtUword gt[]codon[]iterator[]current[]position([]GtCodonI
terator

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[]\OT1/cmtt/m/n/10.95 GtCodonIteratorStatus gt[]codon[]iterator[]next([]GtCodon
Iterator

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\OT1/cmtt/m/n/10.95 *codon[]iterator, char *n1, char *n2, char *n3, unsigned in
t *frame,

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[]\OT1/cmtt/m/n/10.95 GtCodonIterator* gt[]codon[]iterator[]encseq[]new([]GtEnc
seq *encseq, GtUword

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[]\OT1/cmtt/m/n/10.95 GtCodonIterator* gt[]codon[]iterator[]encseq[]new[]with[]
readmode([]GtEncseq

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\OT1/cmtt/m/n/10.95 *encseq, GtUword startpos, GtUword length, GtReadmode readm
ode, GtError

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[]\OT1/cmtt/m/n/10.95 GtCodonIterator* gt[]codon[]iterator[]simple[]new([]const
 char *seq, GtUword

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[]\OT1/cmtt/m/n/10.95 GtColor* gt[]color[]new([]double red, double green, doubl
e blue, double

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[]\OT1/cmtt/m/n/10.95 void gt[]color[]set([]GtColor *color, double red, double 
green, double blue,

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[]\OT1/cmtt/m/n/10.95 GtCustomTrack* gt[]custom[]track[]gc[]content[]new([]cons
t char *seq, GtUword

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[]\OT1/cmtt/m/n/10.95 GtCustomTrack* gt[]custom[]track[]script[]wrapper[]new([]
GtCtScriptRenderFunc

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\OT1/cmtt/m/n/10.95 render[]func, GtCtScriptGetHeightFunc get[]height[]func,

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[]\OT1/cmtt/m/n/10.95 GtDiagram* gt[]diagram[]new([]GtFeatureIndex *feature[]in
dex, const char

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[]\OT1/cmtt/m/n/10.95 GtDiagram* gt[]diagram[]new[]from[]array([]GtArray *featu
res, const GtRange

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[]\OT1/cmtt/m/n/10.95 void gt[]diagram[]set[]track[]selector[]func([]GtDiagram*
, GtTrackSelectorFunc,

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[]\OT1/cmtt/m/n/10.95 void gt[]disc[]distri[]add[]multi([]GtDiscDistri *d, GtUw
ord key, GtUint64

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[]\OT1/cmtt/m/n/10.95 void gt[]disc[]distri[]foreach([]const GtDiscDistri *d, G
tDiscDistriIterFunc

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[]\OT1/cmtt/m/n/10.95 void gt[]disc[]distri[]foreach[]in[]reverse[]order([]cons
t GtDiscDistri *d,

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[]\OT1/cmtt/m/n/10.95 GtUchar gt[]encseq[]get[]encoded[]char([]const GtEncseq *
encseq, GtUword pos,

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[]\OT1/cmtt/m/n/10.95 char gt[]encseq[]get[]decoded[]char([]const GtEncseq *enc
seq, GtUword pos,

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[]\OT1/cmtt/m/n/10.95 bool gt[]encseq[]position[]is[]separator([]const GtEncseq
 *encseq, GtUword pos,

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[]\OT1/cmtt/m/n/10.95 bool gt[]encseq[]position[]is[]wildcard([]const GtEncseq 
*encseq, GtUword pos,

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[]\OT1/cmtt/m/n/10.95 GtEncseqReader* gt[]encseq[]create[]reader[]with[]readmod
e([]const GtEncseq

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]extract[]encoded([]const GtEncseq *encse
q, GtUchar *buffer,

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]extract[]decoded([]const GtEncseq *encse
q, char *buffer,

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[]\OT1/cmtt/m/n/10.95 const char* gt[]encseq[]description([]const GtEncseq *enc
seq, GtUword

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[]\OT1/cmtt/m/n/10.95 GtUint64 gt[]encseq[]effective[]filelength([]const GtEncs
eq *encseq, GtUword

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[]\OT1/cmtt/m/n/10.95 GtUword gt[]encseq[]filenum[]first[]seqnum([]const GtEncs
eq *encseq, GtUword

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]cstr([]GtEncseqBuilder *eb
, const char *str,

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]str([]GtEncseqBuilder *eb,
 GtStr *str, const

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]encoded([]GtEncseqBuilder 
*eb, const GtUchar

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]encoded[]own([]GtEncseqBui
lder *eb, const GtUchar

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]multiple[]encoded([]GtEncs
eqBuilder *eb, const

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[]\OT1/cmtt/m/n/10.95 int gt[]encseq[]encoder[]use[]representation([]GtEncseqEn
coder *ee, const char

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[]\OT1/cmtt/m/n/10.95 int gt[]encseq[]encoder[]use[]symbolmap[]file([]GtEncseqE
ncoder *ee, const char

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[]\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

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\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-

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\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

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[]\OT1/cmtt/m/n/10.95 int gt[]encseq[]encoder[]encode([]GtEncseqEncoder *ee, Gt
StrArray *seqfiles,

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[]\OT1/cmtt/m/n/10.95 GtEncseq* gt[]encseq[]loader[]load([]GtEncseqLoader *el, 
const char

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[60] [61] [62]
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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]reader[]reinit[]with[]readmode([]GtEncse
qReader *esr, const

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]extract[]feature[]stream[]new([]GtNodeS
tream *in[]stream,

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\OT1/cmtt/m/n/10.95 GtRegionMapping *region[]Mapping, const char *type, bool jo
in, bool

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]add[]region[]node([]GtFeatureInde
x *feature[]index,

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]add[]feature[]node([]GtFeatureInd
ex *feature[]index,

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]remove[]node([]GtFeatureIndex *fe
ature[]index,

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]add[]gff3file([]GtFeatureIndex *f
eature[]index, const

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[]\OT1/cmtt/m/n/10.95 GtArray* gt[]feature[]index[]get[]features[]for[]seqid([]
GtFeatureIndex*, const

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]get[]features[]for[]range([]GtFea
tureIndex *feature[]index,

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[]\OT1/cmtt/m/n/10.95 char* gt[]feature[]index[]get[]first[]seqid([]const GtFea
tureIndex

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[]\OT1/cmtt/m/n/10.95 GtStrArray* gt[]feature[]index[]get[]seqids([]const GtFea
tureIndex

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]get[]range[]for[]seqid([]GtFeatur
eIndex *feature[]index,

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]get[]orig[]range[]for[]seqid([]Gt
FeatureIndex

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]has[]seqid([]const GtFeatureIndex
 *feature[]index, bool

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[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]index[]memory[]get[]node[]by[
]ptr([]GtFeatureIndexMemory*,

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\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()

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[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]feature[]node[]new([]GtStr *seqid, cons
t char *type, GtUword

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[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]feature[]node[]new[]pseudo([]GtStr *seq
id, GtUword start,

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[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]feature[]node[]new[]pseudo[]template([]
GtFeatureNode

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]add[]child([]GtFeatureNode *paren
t, GtFeatureNode

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]source([]GtFeatureNode *feat
ure[]node, GtStr

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]type([]GtFeatureNode *featur
e[]node, const char

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[]\OT1/cmtt/m/n/10.95 bool gt[]feature[]node[]has[]type([]GtFeatureNode *featur
e[]node, const char

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[]\OT1/cmtt/m/n/10.95 GtUword gt[]feature[]node[]number[]of[]children([]const G
tFeatureNode

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[]\OT1/cmtt/m/n/10.95 GtUword gt[]feature[]node[]number[]of[]children[]of[]type
([]const GtFeatureNode

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]strand([]GtFeatureNode *feat
ure[]node, GtStrand

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[]\OT1/cmtt/m/n/10.95 const char* gt[]feature[]node[]get[]attribute([]const GtF
eatureNode

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[]\OT1/cmtt/m/n/10.95 GtStrArray* gt[]feature[]node[]get[]attribute[]list([]con
st GtFeatureNode

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]add[]attribute([]GtFeatureNode *f
eature[]node, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]attribute([]GtFeatureNode* f
eature[]node, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]remove[]attribute([]GtFeatureNode
* feature[]node, const

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[]\OT1/cmtt/m/n/10.95 void GtFeatureNodeAttributeIterFunc([]const char *attr[]n
ame, const char

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[]\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-

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\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

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]foreach[]attribute([]GtFeatureNod
e *feature[]node,

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]make[]multi[]representative([]GtF
eatureNode

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]multi[]representative([]GtFe
atureNode *feature[]node,

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[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]node[]get[]multi[]representat
ive([]GtFeatureNode

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[]\OT1/cmtt/m/n/10.95 bool gt[]feature[]node[]is[]similar([]const GtFeatureNode
 *feature[]node[]a, const

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]remove[]leaf([]GtFeatureNode *tre
e, GtFeatureNode

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[67] [68] [69] [70]
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[]\OT1/cmtt/m/n/10.95 GtFeatureNodeIterator* gt[]feature[]node[]iterator[]new([
]const GtFeatureNode

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[]\OT1/cmtt/m/n/10.95 GtFeatureNodeIterator* gt[]feature[]node[]iterator[]new[]
direct([]const

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[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]node[]iterator[]next([]GtFeat
ureNodeIterator

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]iterator[]delete([]GtFeatureNodeI
terator

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[71]
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]feature[]out[]stream[]new([]GtNodeStrea
m*, GtFeatureIndex

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\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]gff3[]in[]stream[]new[]unsorted([]int n
um[]of[]files, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]in[]stream[]set[]type[]checker([]GtNodeStr
eam *gff3[]in[]stream,

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]gff3[]out[]stream[]new([]GtNodeStream *
in[]stream, GtFile

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]out[]stream[]set[]fasta[]width([]GtGFF3Out
Stream *gff3[]out[]stream,

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]out[]stream[]retain[]id[]attributes([]GtGF
F3OutStream

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[74]
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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]parser[]do[]not[]check[]region[]boundaries
([]GtGFF3Parser

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]parser[]set[]type[]checker([]GtGFF3Parser 
*gff3[]parser,

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]parser[]set[]xrf[]checker([]GtGFF3Parser *
gff3[]parser,

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[]\OT1/cmtt/m/n/10.95 int gt[]gff3[]parser[]parse[]genome[]nodes([]GtGFF3Parser
 *gff3[]parser, int

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\OT1/cmtt/m/n/10.95 *status[]code, GtQueue *genome[]nodes, GtCstrTable *used[]t
ypes, GtStr

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]visitor[]set[]fasta[]width([]GtGFF3Visitor
 *gff3[]visitor, GtUword

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]gtf[]out[]stream[]new([]GtNodeStream *i
n[]stream, GtFile

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[]\OT1/cmtt/m/n/10.95 void gt[]genome[]node[]set[]range([]GtGenomeNode *genome[
]node, const GtRange

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[]\OT1/cmtt/m/n/10.95 void gt[]genome[]node[]add[]user[]data([]GtGenomeNode *ge
nome[]node, const char

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[]\OT1/cmtt/m/n/10.95 void* gt[]genome[]node[]get[]user[]data([]const GtGenomeN
ode *genome[]node, const

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[]\OT1/cmtt/m/n/10.95 void gt[]genome[]node[]release[]user[]data([]GtGenomeNode
 *genome[]node, const

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[]\OT1/cmtt/m/n/10.95 int gt[]genome[]node[]cmp([]GtGenomeNode *genome[]node[]a
, GtGenomeNode

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[]\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

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[]\OT1/cmtt/m/n/10.95 int gt[]genome[]node[]accept([]GtGenomeNode *genome[]node
, GtNodeVisitor

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[77] [78]
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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]text[]clip([]GtGraphics*, double
 x, double y, const

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]text[]centered([]GtGraphics*, do
uble x, double y,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]text[]right([]GtGraphics*, doubl
e x, double y, const

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]colored[]text([]GtGraphics*, dou
ble x, double y,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]set[]font([]GtGraphics *g, const char 
*family, FontSlant

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]set[]margins([]GtGraphics*, double mar
gin[]x, double

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]horizontal[]line([]GtGraphics *g
, double x, double y,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]vertical[]line([]GtGraphics *g, 
double x, double y,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]line([]GtGraphics *g, double x, 
double y, double xto,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]box([]GtGraphics*, double x, dou
ble y, double width,

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\OT1/cmtt/m/n/10.95 double height, GtColor fill[]color, ArrowStatus arrow[]stat
us, double

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]dashes([]GtGraphics*, double x, 
double y, double

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\OT1/cmtt/m/n/10.95 width, double height, ArrowStatus arrow[]status, double arr
ow[]width,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]caret([]GtGraphics*, double x, d
ouble y, double

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\OT1/cmtt/m/n/10.95 width, double height, ArrowStatus arrow[]status, double arr
ow[]width,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]rectangle([]GtGraphics*, double 
x, double y, bool

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\OT1/cmtt/m/n/10.95 filled, GtColor fill[]color, bool stroked, GtColor stroke[]
color, double

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]arrowhead([]GtGraphics*, double 
x, double y, GtColor,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]curve[]data([]GtGraphics *g, dou
ble x, double y,

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\OT1/cmtt/m/n/10.95 GtColor color, double data[], GtUword ndata, GtRange valran
ge, GtUword

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[]\OT1/cmtt/m/n/10.95 int gt[]graphics[]save[]to[]file([]const GtGraphics*, con
st char *filename,

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[79] [80] [81]
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[]\OT1/cmtt/m/n/10.95 GtGraphics* gt[]graphics[]cairo[]new([]GtGraphicsOutType 
type, unsigned int

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[]\OT1/cmtt/m/n/10.95 GtGraphics* gt[]graphics[]cairo[]new[]from[]context([]cai
ro[]t *context, unsigned

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]cairo[]draw[]curve[]data([]GtGraphics 
*gg, double x, double y,

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\OT1/cmtt/m/n/10.95 GtColor color, double data[], GtUword ndata, GtRange valran
ge, GtUword

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[]\OT1/cmtt/m/n/10.95 GtHashmap* gt[]hashmap[]new([]GtHashType keyhashtype, GtF
ree keyfree, GtFree

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[]\OT1/cmtt/m/n/10.95 int gt[]hashmap[]foreach[]ordered([]GtHashmap *hashmap, G
tHashmapVisitFunc

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[]\OT1/cmtt/m/n/10.95 int gt[]hashmap[]foreach([]GtHashmap *hashmap, GtHashmapV
isitFunc func, void

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[]\OT1/cmtt/m/n/10.95 int gt[]hashmap[]foreach[]in[]key[]order([]GtHashmap *has
hmap, GtHashmapVisitFunc

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[]\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-

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\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]id[]to[]md5[]stream[]new([]GtNodeStream
 *in[]stream,

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[]\OT1/cmtt/m/n/10.95 const GtRecMap* gt[]image[]info[]get[]rec[]map([]GtImageI
nfo *image[]info, GtUword

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\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]inter[]feature[]stream[]new([]GtNodeStr
eam *in[]stream, const

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[]\OT1/cmtt/m/n/10.95 GtIntervalTreeNode* gt[]interval[]tree[]find[]first[]over
lapping([]GtIntervalTree*,

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[]\OT1/cmtt/m/n/10.95 void gt[]interval[]tree[]insert([]GtIntervalTree *tree, G
tIntervalTreeNode

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[]\OT1/cmtt/m/n/10.95 void gt[]interval[]tree[]find[]all[]overlapping([]GtInter
valTree*, GtUword start,

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[]\OT1/cmtt/m/n/10.95 void gt[]interval[]tree[]iterate[]overlapping([]GtInterva
lTree *it,

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[]\OT1/cmtt/m/n/10.95 int gt[]interval[]tree[]traverse([]GtIntervalTree*, GtInt
ervalTreeIteratorFunc

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[]\OT1/cmtt/m/n/10.95 GtIntervalTreeNode* gt[]interval[]tree[]node[]new([]void 
*data, GtUword low,

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[]\OT1/cmtt/m/n/10.95 GtLayout* gt[]layout[]new([]GtDiagram *diagram, unsigned 
int width, GtStyle*,

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[]\OT1/cmtt/m/n/10.95 GtLayout* gt[]layout[]new[]with[]twc([]GtDiagram*, unsign
ed int width,

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[]\OT1/cmtt/m/n/10.95 void gt[]layout[]set[]track[]ordering[]func([]GtLayout *l
ayout,

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[]\OT1/cmtt/m/n/10.95 void gt[]md5[]encoder[]add[]block([]GtMD5Encoder *enc, co
nst char *message,

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[]\OT1/cmtt/m/n/10.95 void gt[]md5[]encoder[]finish([]GtMD5Encoder *enc, unsign
ed char *output, char

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]md5[]to[]id[]stream[]new([]GtNodeStream
 *in[]stream,

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[]\OT1/cmtt/m/n/10.95 void gt[]match[]set[]seqid1[]nt([]GtMatch *match, const c
har *seqid, GtUword

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[]\OT1/cmtt/m/n/10.95 void gt[]match[]set[]seqid2[]nt([]GtMatch *match, const c
har *seqid, GtUword

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[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]blast[]new([]char *seqid1, char *seqi
d2, GtUword

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\OT1/cmtt/m/n/10.95 start[]seq1, GtUword start[]seq2, GtUword end[]seq1, GtUwor
d end[]seq2,

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\OT1/cmtt/m/n/10.95 double evalue, float bitscore, GtUword ali[]l, double simil
arity,

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[]\OT1/cmtt/m/n/10.95 GtMatchIteratorStatus gt[]match[]iterator[]next([]GtMatch
Iterator *mp, GtMatch

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[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]last[]new([]const char *seqid1, const
 char *seqid2,

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\OT1/cmtt/m/n/10.95 GtUword score, GtUword seqno1, GtUword seqno2, GtUword star
t[]seq1,

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\OT1/cmtt/m/n/10.95 GtUword start[]seq2, GtUword end[]seq1, GtUword end[]seq2, 
GtMatchDirection

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[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]open[]new([]char *seqid1, char *seqid
2, GtUword

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\OT1/cmtt/m/n/10.95 start[]seq1, GtUword start[]seq2, GtUword end[]seq1, GtUwor
d end[]seq2,

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[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]sw[]new([]const char *seqid1, const c
har *seqid2,

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\OT1/cmtt/m/n/10.95 GtUword seqno1, GtUword seqno2, GtUword length, GtUword edi
st, GtUword

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\OT1/cmtt/m/n/10.95 start[]seq1, GtUword start[]seq2, GtUword end[]seq1, GtUwor
d end[]seq2,

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[]\OT1/cmtt/m/n/10.95 int gt[]match[]visitor[]visit[]match[]blast([]GtMatchVisi
tor *match[]visitor,

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[]\OT1/cmtt/m/n/10.95 int gt[]match[]visitor[]visit[]match[]open([]GtMatchVisit
or *match[]visitor,

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[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]meta[]node[]new([]const char *meta[]dir
ective, const char

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[]\OT1/cmtt/m/n/10.95 int gt[]node[]stream[]next([]GtNodeStream *node[]stream, 
GtGenomeNode

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\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

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\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

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\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

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\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]node[]stream[]create([]const GtNodeStre
amClass

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[]\OT1/cmtt/m/n/10.95 void* gt[]node[]stream[]cast([]const GtNodeStreamClass *n
ode[]stream[]class,

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[]\OT1/cmtt/m/n/10.95 const GtNodeStreamClass* gt[]node[]stream[]class[]new([]s
ize[]t size,

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[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]comment[]node([]GtNodeVisit
or *node[]visitor,

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[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]feature[]node([]GtNodeVisit
or *node[]visitor,

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[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]meta[]node([]GtNodeVisitor 
*node[]visitor,

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[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]region[]node([]GtNodeVisito
r *node[]visitor,

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[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]sequence[]node([]GtNodeVisi
tor *node[]visitor,

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[]\OT1/cmtt/m/n/10.95 GtORFIterator* gt[]orf[]iterator[]new([]GtCodonIterator *
ci, GtTranslator

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[]\OT1/cmtt/m/n/10.95 GtORFIteratorStatus gt[]orf[]iterator[]next([]GtORFIterat
or *orf[]iterator,

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[97]
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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]bool([]const char *option[]str
ing, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]double([]const char *option[]s
tring, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]double[]min([]const char *opti
on[]string, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]double[]min[]max([]const char 
*option[]string,

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\OT1/cmtt/m/n/10.95 const char *description, double *value, double default[]val
ue, double

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]probability([]const char *opti
on[]string, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int([]const char *option[]stri
ng, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int[]min([]const char *option[
]string, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int[]max([]const char *option[
]string, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int[]min[]max([]const char *op
tion[]string, const char

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\OT1/cmtt/m/n/10.95 *description, int *value, int default[]value, int minimum[]
value, int

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint([]const char *option[]str
ing, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint[]min([]const char *option
[]string, const char

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\OT1/cmtt/m/n/10.95 *description, unsigned int *value, unsigned int default[]va
lue, unsigned

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint[]max([]const char *option
[]string, const char

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\OT1/cmtt/m/n/10.95 *description, unsigned int *value, unsigned int default[]va
lue, unsigned

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint[]min[]max([]const char *o
ption[]string, const char

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\OT1/cmtt/m/n/10.95 *description, unsigned int *value, unsigned int default[]va
lue, unsigned

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]word([]const char *option[]str
ing, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uword([]const char *option[]st
ring, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uword[]min([]const char *optio
n[]string, const

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\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uword[]min[]max([]const char *
option[]string, const

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\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]long([]const char *option[]str
ing, const char

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]ulong([]const char *option[]st
ring, const char

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]ulong[]min([]const char *optio
n[]string, const

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\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]ulong[]min[]max([]const char *
option[]string, const

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\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]range([]const char *option[]st
ring, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]range[]min[]max([]const char *
option[]string, const

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\OT1/cmtt/m/n/10.95 char *description, GtRange *value, GtRange *default[]value,
 GtUword

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]string([]const char *option[]s
tring, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]string[]array([]const char *op
tion[]string, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]choice([]const char *option[]s
tring, const char

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\OT1/cmtt/m/n/10.95 *description, GtStr *value, const char *default[]value, con
st char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]filename([]const char *option[
]string, const char

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]filename[]array([]const char *
option[]string, const

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[]\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

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]is[]mandatory[]either([]GtOption *option
[]a, const GtOption

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]is[]mandatory[]either[]3([]GtOption *opt
ion[]a, const GtOption

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]is[]mandatory[]either[]4([]GtOption *opt
ion[]a, const GtOption

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]imply[]either[]2([]GtOption *option[]a, 
const GtOption

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]imply[]either[]3([]GtOption *option[]a, 
const GtOption

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[]\OT1/cmtt/m/n/10.95 int gt[]option[]parse[]spacespec([]GtUword *maximumspace,
 const char *optname,

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[98] [99] [100] [101] [102]
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[]\OT1/cmtt/m/n/10.95 GtOptionParser* gt[]option[]parser[]new([]const char *syn
opsis, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]add[]option([]GtOptionParser *op
tion[]parser, GtOption

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]parser[]get[]option([]GtOptionParse
r *option[]parser, const

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[]\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

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]comment[]func([]GtOptionPar
ser *option[]parser,

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]version[]func([]GtOptionPar
ser *option[]parser,

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]mail[]address([]GtOptionPar
ser*, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]register[]hook([]GtOptionParser 
*option[]parser,

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]min[]args([]GtOptionParser 
*option[]parser, unsigned

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]max[]args([]GtOptionParser 
*option[]parser, unsigned

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]min[]max[]args([]GtOptionPa
rser *option[]parser,

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOPrval gt[]option[]parser[]parse([]GtOptionParser *opti
on[]parser,

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\OT1/cmtt/m/n/10.95 int *parsed[]args, int argc, const char **argv, GtShowVersi
onFunc

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[103] [104]
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[]\OT1/cmtt/m/n/10.95 void gt[]output[]file[]info[]register[]options([]GtOutput
FileInfo

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[105]
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[106]
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[]\OT1/cmtt/m/n/10.95 GtRDB* gt[]rdb[]mysql[]new([]const char *server, unsigned
 int port, const char

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[]\OT1/cmtt/m/n/10.95 int gt[]rdb[]visitor[]visit[]sqlite([]GtRDBVisitor *rdbv,
 GtRDBSqlite *rdbs,

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[]\OT1/cmtt/m/n/10.95 int gt[]rdb[]visitor[]visit[]mysql([]GtRDBVisitor *rdbv, 
GtRDBMySQL *rdbm,

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[107]
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[]\OT1/cmtt/m/n/10.95 int gt[]range[]compare[]with[]delta([]const GtRange *rang
e[]a, const GtRange

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[]\OT1/cmtt/m/n/10.95 bool gt[]range[]overlap[]delta([]const GtRange *range[]a,
 const GtRange

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[108]
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\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 ,

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtRecMap* gt[]rec[]map[]new([]double nw[]x, double nw[]y,
 double se[]x, double

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[109]
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[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]mapping([]GtSt
r *mapping[]filename,

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]seqfiles([]GtS
trArray

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[]\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

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\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

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[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]encseq([]GtEnc
seq *encseq, bool

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[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]rawseq([]const
 char *rawseq, GtUword

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[]\OT1/cmtt/m/n/10.95 int gt[]region[]mapping[]get[]sequence([]GtRegionMapping 
*region[]mapping, char

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[]\OT1/cmtt/m/n/10.95 int gt[]region[]mapping[]get[]sequence[]length([]GtRegion
Mapping *region[]mapping,

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[]\OT1/cmtt/m/n/10.95 int gt[]region[]mapping[]get[]description([]GtRegionMappi
ng *region[]mapping,

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[]\OT1/cmtt/m/n/10.95 const char* gt[]region[]mapping[]get[]md5[]fingerprint([]
GtRegionMapping

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\OT1/cmtt/m/n/10.95 *region[]mapping, GtStr *seqid, const GtRange *range, GtUwo
rd *offset,

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[110]
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\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

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[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]region[]node[]new([]GtStr *seqid, GtUwo
rd start, GtUword

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[111]
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]script[]wrapper[]stream[]new([]GtScript
WrapperStreamNextFunc,

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[]\OT1/cmtt/m/n/10.95 GtNodeVisitor* gt[]script[]wrapper[]visitor[]new([]GtScri
ptWrapperVisitorCommentNodeFunc,

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\OT1/cmtt/m/n/10.95 GtScriptWrapperVisitorFeatureNodeFunc, GtScriptWrapperVisit
orRegionNodeFunc,

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\OT1/cmtt/m/n/10.95 GtScriptWrapperVisitorSequenceNodeFunc, GtScriptWrapperVisi
torMetaNodeFunc,

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[112]
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]select[]stream[]new([]GtNodeStream *in[
]stream, GtStr

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\OT1/cmtt/m/n/10.95 *seqid, GtStr *source, const GtRange *contain[]range, const
 GtRange

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\OT1/cmtt/m/n/10.95 *overlap[]range, GtStrand strand, GtStrand targetstrand, bo
ol has[]CDS,

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\OT1/cmtt/m/n/10.95 GtUword max[]gene[]length, GtUword max[]gene[]num, double m
in[]gene[]score,

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\OT1/cmtt/m/n/10.95 double max[]gene[]score, double min[]average[]splice[]site[
]prob, GtUword

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[]\OT1/cmtt/m/n/10.95 void gt[]select[]stream[]set[]drophandler([]GtSelectStrea
m *sstr,

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[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]set[]symbolmap([]GtSeqIterator*, 
const GtUchar

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[]\OT1/cmtt/m/n/10.95 int gt[]seq[]iterator[]next([]GtSeqIterator *seqit, const
 GtUchar **sequence,

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[]\OT1/cmtt/m/n/10.95 const GtUint64* gt[]seq[]iterator[]getcurrentcounter([]Gt
SeqIterator*,

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[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]set[]quality[]buffer([]GtSeqItera
tor *seqit, const

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[113]
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[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]fastq[]new([]const GtSt
rArray *filenametab,

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[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]fastq[]new[]colorspace(
[]const GtStrArray

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[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]fastq[]relax[]check[]of[]quality[
]description([]GtSeqIteratorFastQ

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[114]
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[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]sequence[]buffer[]new([
]const GtStrArray

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[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]sequence[]node[]new([]const char *descr
iption, GtStr

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[]\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

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[]\OT1/cmtt/m/n/10.95 const char* gt[]sequence[]node[]get[]description([]const 
GtSequenceNode

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[]\OT1/cmtt/m/n/10.95 const char* gt[]sequence[]node[]get[]sequence([]const GtS
equenceNode

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[]\OT1/cmtt/m/n/10.95 GtUword gt[]sequence[]node[]get[]sequence[]length([]const
 GtSequenceNode

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[115]
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\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

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[]\OT1/cmtt/m/n/10.95 void gt[]splitter[]split([]GtSplitter *splitter, char *st
ring, GtUword

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[]\OT1/cmtt/m/n/10.95 void gt[]splitter[]split[]non[]empty([]GtSplitter *s, cha
r *string, GtUword

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[116]
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\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]stat[]stream[]new([]GtNodeStream *in[]s
tream, bool

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\OT1/cmtt/m/n/10.95 gene[]length[]distribution, bool gene[]score[]distribution,
 bool

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\OT1/cmtt/m/n/10.95 exon[]length[]distribution, bool exon[]number[]distribution
, bool

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\OT1/cmtt/m/n/10.95 intron[]length[]distribution, bool cds[]length[]distributio
n, bool

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\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 ,

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\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 ,

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[117]
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[]\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

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[118]
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[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]add[]cstr[]nt([]GtStrArray *str[]arr
ay, const char *cstr,

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[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]set[]cstr([]GtStrArray *str[]array, 
GtUword strnum, const

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[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]set([]GtStrArray *str[]array, GtUwor
d strnum, const GtStr

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[]\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

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[119]
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\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 ,

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[]\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

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[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]color([]GtStyle*, const char *sectio
n, const char *key,

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]color([]const GtStyle 
*style, const char

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\OT1/cmtt/m/n/10.95 *section, const char *key, GtColor *result, GtFeatureNode *
fn, GtError

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]color[]with[]track([]c
onst GtStyle *style,

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\OT1/cmtt/m/n/10.95 const char *section, const char *key, GtColor *result, GtFe
atureNode

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[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]str([]GtStyle*, const char *section,
 const char *key,

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]str([]const GtStyle *s
tyle, const char

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\OT1/cmtt/m/n/10.95 *section, const char *key, GtStr *result, GtFeatureNode *fn
, GtError

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]str[]with[]track([]con
st GtStyle *style, const

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\OT1/cmtt/m/n/10.95 char *section, const char *key, GtStr *result, GtFeatureNod
e *fn, const

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[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]num([]GtStyle*, const char *section,
 const char *key,

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]num([]const GtStyle *s
tyle, const char

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\OT1/cmtt/m/n/10.95 *section, const char *key, double *result, GtFeatureNode *f
n, GtError

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]num[]with[]track([]con
st GtStyle *style, const

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\OT1/cmtt/m/n/10.95 char *section, const char *key, double *result, GtFeatureNo
de *fn, const

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[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]bool([]GtStyle*, const char *section
, const char *key,

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]bool([]const GtStyle *
style, const char

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\OT1/cmtt/m/n/10.95 *section, const char *key, bool *result, GtFeatureNode *fn,
 GtError

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]bool[]with[]track([]co
nst GtStyle *style,

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\OT1/cmtt/m/n/10.95 const char *section, const char *key, bool *result, GtFeatu
reNode *fn,

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[120] [121] [122] [123]
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[]\OT1/cmtt/m/n/10.95 void GtTagValueMapIteratorFunc([]const char *tag, const c
har *value, void

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[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]add([]GtTagValueMap *tag[]value
[]map, const char *tag,

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[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]set([]GtTagValueMap *tag[]value
[]map, const char *tag,

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[]\OT1/cmtt/m/n/10.95 const char* gt[]tag[]value[]map[]get([]const GtTagValueMa
p tag[]value[]map, const

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[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]remove([]GtTagValueMap *tag[]va
lue[]map, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]foreach([]const GtTagValueMap t
ag[]value[]map,

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[124]
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[]\OT1/cmtt/m/n/10.95 GtTextWidthCalculator* gt[]text[]width[]calculator[]ref([
]GtTextWidthCalculator*[]) 

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[]\OT1/cmtt/m/n/10.95 double gt[]text[]width[]calculator[]get[]text[]width([]Gt
TextWidthCalculator*,

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\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

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[]\OT1/cmtt/m/n/10.95 GtTextWidthCalculator* gt[]text[]width[]calculator[]cairo
[]new([]cairo[]t*,

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[]\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

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[]\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

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\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

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[]\OT1/cmtt/m/n/10.95 void gt[]timer[]show[]progress[]formatted([]GtTimer *time
r, FILE *fp, const

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[]\OT1/cmtt/m/n/10.95 void gt[]timer[]show[]progress[]va([]GtTimer *timer, FILE
 *fp, const char

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[]\OT1/cmtt/m/n/10.95 int GtToolArgumentsCheck([]int rest[]argc, void *tool[]ar
guments, GtError

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[]\OT1/cmtt/m/n/10.95 int GtToolRunner([]int argc, const char **argv, int parse
d[]args, void

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[]\OT1/cmtt/m/n/10.95 GtTool* gt[]tool[]new([]GtToolArgumentsNew tool[]argument
s[]new,

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\OT1/cmtt/m/n/10.95 GtToolArgumentsDelete tool[]arguments[]delete, GtToolOption
ParserNew

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\OT1/cmtt/m/n/10.95 tool[]option[]parser[]new, GtToolArgumentsCheck tool[]argum
ents[]check,

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[]\OT1/cmtt/m/n/10.95 void gt[]toolbox[]add[]tool([]GtToolbox *toolbox, const c
har *toolname, GtTool

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[]\OT1/cmtt/m/n/10.95 void gt[]toolbox[]add[]hidden[]tool([]GtToolbox *toolbox,
 const char *toolname,

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[]\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

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[]\OT1/cmtt/m/n/10.95 int gt[]trans[]table[]translate[]codon([]const GtTransTab
le *tt, char c1, char

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[]\OT1/cmtt/m/n/10.95 GtTranslator* gt[]translator[]new[]with[]table([]GtTransT
able *tt,

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[]\OT1/cmtt/m/n/10.95 void gt[]translator[]set[]codon[]iterator([]GtTranslator 
*translator,

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[]\OT1/cmtt/m/n/10.95 void gt[]translator[]set[]translation[]table([]GtTranslat
or *translator,

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[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]next([]GtTranslator *t
ranslator, char

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[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]find[]startcodon([]GtT
ranslator

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[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]find[]stopcodon([]GtTr
anslator *translator,

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[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]find[]codon([]GtTransl
ator *translator,

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[]\OT1/cmtt/m/n/10.95 bool gt[]type[]checker[]is[]valid([]GtTypeChecker *type[]
checker, const char

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[]\OT1/cmtt/m/n/10.95 bool gt[]type[]checker[]is[]partof([]GtTypeChecker *type[
]checker, const char

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[]\OT1/cmtt/m/n/10.95 bool gt[]type[]checker[]is[]a([]GtTypeChecker *type[]chec
ker, const char

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[]\OT1/cmtt/m/n/10.95 GtTypeChecker* gt[]type[]checker[]obo[]new([]const char *
obo[]file[]path, GtError

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]visitor[]stream[]new([]GtNodeStream *in
[]stream,

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[]\OT1/cmtt/m/n/10.95 bool gt[]xrf[]checker[]is[]valid([]GtXRFChecker *xrf[]che
cker, const char *value,

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[]\OT1/cmtt/m/n/10.95 void* gt[]bsearch[]data([]const void *key, const void *ba
se, size[]t nmemb,

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[]\OT1/cmtt/m/n/10.95 void gt[]bsearch[]all([]GtArray *members, const void *key
, const void *base,

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[]\OT1/cmtt/m/n/10.95 void gt[]bsearch[]all[]mark([]GtArray *members, const voi
d *key, const

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\OT1/cmtt/m/n/10.95 void *base, size[]t nmemb, size[]t size, GtCompareWithData,
 void *data,

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[]\OT1/cmtt/m/n/10.95 void gt[]countingsort([]void *out, const void *in, size[]
t elem[]size, GtUword

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[]\OT1/cmtt/m/n/10.95 GtUword gt[]countingsort[]get[]max([]const void *in, size
[]t elem[]size, GtUword

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[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry([]const char *description, co
nst char *sequence,

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[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry[]nt([]const char *description
, GtUword

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\OT1/cmtt/m/n/10.95 description[]length, const char *sequence, GtUword sequence
[]length,

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[]\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

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[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry[]str([]const char *descriptio
n, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry[]nt[]str([]const char *descri
ption, GtUword

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\OT1/cmtt/m/n/10.95 description[]length, const char *sequence, GtUword sequence
[]length,

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[]\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

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[]\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. 

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[]\OT1/cmtt/m/n/10.95 int gt[]file[]find[]in[]env([]GtStr *path, const char *fi
le, const char *env,

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[]\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-

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\OT1/ptm/m/n/10.95 dows ';'-separated) spec-i-fied in en-vi-ron-ment vari-able

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[]\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 . 

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[]\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

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[]\OT1/cmtt/m/n/10.95 int gt[]files[]guess[]if[]protein[]sequences([]const GtSt
rArray *filenames,

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[]\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. 

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[]\OT1/cmtt/m/n/10.95 int gt[]grep[]nt([]bool *match, const char *pattern, cons
t char *line, size[]t

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[]\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-

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\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

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[]\OT1/cmtt/m/n/10.95 void gt[]msort[]r([]void *base, size[]t nmemb, size[]t si
ze, void *comparinfo,

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[]\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-

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\OT1/ptm/m/n/10.95 ca-tions in http://www.unix-systems.org/onlinepubs/7908799/x
sh/basename.html and
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[]\OT1/cmtt/m/n/10.95 int gt[]parse[]range([]GtRange *rng, const char *start, c
onst char *end,

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[]\OT1/cmtt/m/n/10.95 int gt[]parse[]range[]tidy([]GtRange *rng, const char *st
art, const char *end,

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[]\OT1/cmtt/m/n/10.95 void gt[]qsort[]r([]void *a, size[]t n, size[]t es, void 
*data,

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[]\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

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[]\OT1/cmtt/m/n/10.95 const char* gt[]version[]check([]unsigned int required[]m
ajor, unsigned int

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[]\OT1/cmtt/m/n/10.95 void gt[]warning[]default[]handler([]void *data, const ch
ar *format, va[]list

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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
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chapter 1.

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[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]decode[]seq[]to[]cstr([]const GtAlphab
et *alphabet, char

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[]\OT1/cmtt/m/n/10.95 GtStr* gt[]alphabet[]decode[]seq[]to[]str([]const GtAlpha
bet *alphabet, const

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[]\OT1/cmtt/m/n/10.95 GtFeatureIndex* gt[]anno[]db[]schema[]get[]feature[]index
([]GtAnnoDBSchema

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[]\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

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[]\OT1/cmtt/m/n/10.95 void gt[]array[]sort[]with[]data([]GtArray *array, GtComp
areWithData compar,

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[]\OT1/cmtt/m/n/10.95 void gt[]array[]sort[]stable[]with[]data([]GtArray *array
, GtCompareWithData

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\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]in[]stream[]new([]GtArray *nodes
, GtUword *progress,

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]out[]stream[]new([]GtNodeStream 
*in[]stream, GtArray

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]out[]stream[]all[]new([]GtNodeSt
ream *in[]stream, GtArray

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[]\OT1/cmtt/m/n/10.95 void gt[]bed[]in[]stream[]set[]feature[]type([]GtBEDInStr
eam *bed[]in[]stream, const

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[]\OT1/cmtt/m/n/10.95 void gt[]bed[]in[]stream[]set[]thick[]feature[]type([]GtB
EDInStream *bed[]in[]stream,

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[]\OT1/cmtt/m/n/10.95 void gt[]bed[]in[]stream[]set[]block[]type([]GtBEDInStrea
m *bed[]in[]stream, const

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[]\OT1/cmtt/m/n/10.95 void gt[]bittab[]and([]GtBittab *bittab[]a, const GtBitta
b *bittab[]b, const

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[]\OT1/cmtt/m/n/10.95 void gt[]bittab[]or([]GtBittab *bittab[]a, const GtBittab
 *bittab[]b, const

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[]\OT1/cmtt/m/n/10.95 void gt[]bittab[]nand([]GtBittab *bittab[]a, const GtBitt
ab *bittab[]b, const

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]cds[]stream[]new([]GtNodeStream *in[]st
ream, GtRegionMapping

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\OT1/cmtt/m/n/10.95 *region[]mapping, unsigned int minorflen, const char *sourc
e, bool

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]csa[]stream[]new([]GtNodeStream *in[]st
ream, GtUword

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[]\OT1/cmtt/m/n/10.95 GtCanvas* gt[]canvas[]cairo[]context[]new([]GtStyle *styl
e, cairo[]t *context,

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\OT1/cmtt/m/n/10.95 double offsetpos, GtUword width, GtUword height, GtImageInf
o *image[]info,

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[]\OT1/cmtt/m/n/10.95 GtCanvas* gt[]canvas[]cairo[]file[]new([]GtStyle *style, 
GtGraphicsOutType

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\OT1/cmtt/m/n/10.95 output[]type, GtUword width, GtUword height, GtImageInfo *i
mage[]info,

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[]\OT1/cmtt/m/n/10.95 int gt[]canvas[]cairo[]file[]to[]file([]GtCanvasCairoFile
 *canvas, const char

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[]\OT1/cmtt/m/n/10.95 int gt[]canvas[]cairo[]file[]to[]stream([]GtCanvasCairoFi
le *canvas, GtStr

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[]\OT1/cmtt/m/n/10.95 GtUword gt[]codon[]iterator[]current[]position([]GtCodonI
terator

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[]\OT1/cmtt/m/n/10.95 GtCodonIteratorStatus gt[]codon[]iterator[]next([]GtCodon
Iterator

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\OT1/cmtt/m/n/10.95 *codon[]iterator, char *n1, char *n2, char *n3, unsigned in
t *frame,

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[]\OT1/cmtt/m/n/10.95 GtCodonIterator* gt[]codon[]iterator[]encseq[]new([]GtEnc
seq *encseq, GtUword

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[]\OT1/cmtt/m/n/10.95 GtCodonIterator* gt[]codon[]iterator[]encseq[]new[]with[]
readmode([]GtEncseq

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\OT1/cmtt/m/n/10.95 *encseq, GtUword startpos, GtUword length, GtReadmode readm
ode, GtError

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[]\OT1/cmtt/m/n/10.95 GtCodonIterator* gt[]codon[]iterator[]simple[]new([]const
 char *seq, GtUword

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[]\OT1/cmtt/m/n/10.95 GtColor* gt[]color[]new([]double red, double green, doubl
e blue, double

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[]\OT1/cmtt/m/n/10.95 void gt[]color[]set([]GtColor *color, double red, double 
green, double blue,

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[]\OT1/cmtt/m/n/10.95 GtCustomTrack* gt[]custom[]track[]gc[]content[]new([]cons
t char *seq, GtUword

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[]\OT1/cmtt/m/n/10.95 GtCustomTrack* gt[]custom[]track[]script[]wrapper[]new([]
GtCtScriptRenderFunc

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\OT1/cmtt/m/n/10.95 render[]func, GtCtScriptGetHeightFunc get[]height[]func,

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[]\OT1/cmtt/m/n/10.95 GtDiagram* gt[]diagram[]new([]GtFeatureIndex *feature[]in
dex, const char

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[]\OT1/cmtt/m/n/10.95 GtDiagram* gt[]diagram[]new[]from[]array([]GtArray *featu
res, const GtRange

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[]\OT1/cmtt/m/n/10.95 void gt[]diagram[]set[]track[]selector[]func([]GtDiagram*
, GtTrackSelectorFunc,

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[]\OT1/cmtt/m/n/10.95 void gt[]disc[]distri[]add[]multi([]GtDiscDistri *d, GtUw
ord key, GtUint64

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[]\OT1/cmtt/m/n/10.95 void gt[]disc[]distri[]foreach([]const GtDiscDistri *d, G
tDiscDistriIterFunc

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[]\OT1/cmtt/m/n/10.95 void gt[]disc[]distri[]foreach[]in[]reverse[]order([]cons
t GtDiscDistri *d,

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[]\OT1/cmtt/m/n/10.95 GtUchar gt[]encseq[]get[]encoded[]char([]const GtEncseq *
encseq, GtUword pos,

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[]\OT1/cmtt/m/n/10.95 char gt[]encseq[]get[]decoded[]char([]const GtEncseq *enc
seq, GtUword pos,

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[]\OT1/cmtt/m/n/10.95 bool gt[]encseq[]position[]is[]separator([]const GtEncseq
 *encseq, GtUword pos,

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[]\OT1/cmtt/m/n/10.95 bool gt[]encseq[]position[]is[]wildcard([]const GtEncseq 
*encseq, GtUword pos,

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[]\OT1/cmtt/m/n/10.95 GtEncseqReader* gt[]encseq[]create[]reader[]with[]readmod
e([]const GtEncseq

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]extract[]encoded([]const GtEncseq *encse
q, GtUchar *buffer,

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]extract[]decoded([]const GtEncseq *encse
q, char *buffer,

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[]\OT1/cmtt/m/n/10.95 const char* gt[]encseq[]description([]const GtEncseq *enc
seq, GtUword

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[]\OT1/cmtt/m/n/10.95 GtUint64 gt[]encseq[]effective[]filelength([]const GtEncs
eq *encseq, GtUword

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[]\OT1/cmtt/m/n/10.95 GtUword gt[]encseq[]filenum[]first[]seqnum([]const GtEncs
eq *encseq, GtUword

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]cstr([]GtEncseqBuilder *eb
, const char *str,

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]str([]GtEncseqBuilder *eb,
 GtStr *str, const

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]encoded([]GtEncseqBuilder 
*eb, const GtUchar

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]encoded[]own([]GtEncseqBui
lder *eb, const GtUchar

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]multiple[]encoded([]GtEncs
eqBuilder *eb, const

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[]\OT1/cmtt/m/n/10.95 int gt[]encseq[]encoder[]use[]representation([]GtEncseqEn
coder *ee, const char

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[]\OT1/cmtt/m/n/10.95 int gt[]encseq[]encoder[]use[]symbolmap[]file([]GtEncseqE
ncoder *ee, const char

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[]\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

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\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-

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\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

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[]\OT1/cmtt/m/n/10.95 int gt[]encseq[]encoder[]encode([]GtEncseqEncoder *ee, Gt
StrArray *seqfiles,

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[]\OT1/cmtt/m/n/10.95 GtEncseq* gt[]encseq[]loader[]load([]GtEncseqLoader *el, 
const char

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[64] [65] [66]
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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]reader[]reinit[]with[]readmode([]GtEncse
qReader *esr, const

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]extract[]feature[]stream[]new([]GtNodeS
tream *in[]stream,

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\OT1/cmtt/m/n/10.95 GtRegionMapping *region[]Mapping, const char *type, bool jo
in, bool

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]add[]region[]node([]GtFeatureInde
x *feature[]index,

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]add[]feature[]node([]GtFeatureInd
ex *feature[]index,

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]remove[]node([]GtFeatureIndex *fe
ature[]index,

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]add[]gff3file([]GtFeatureIndex *f
eature[]index, const

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[]\OT1/cmtt/m/n/10.95 GtArray* gt[]feature[]index[]get[]features[]for[]seqid([]
GtFeatureIndex*, const

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]get[]features[]for[]range([]GtFea
tureIndex *feature[]index,

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[]\OT1/cmtt/m/n/10.95 char* gt[]feature[]index[]get[]first[]seqid([]const GtFea
tureIndex

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[]\OT1/cmtt/m/n/10.95 GtStrArray* gt[]feature[]index[]get[]seqids([]const GtFea
tureIndex

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]get[]range[]for[]seqid([]GtFeatur
eIndex *feature[]index,

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]get[]orig[]range[]for[]seqid([]Gt
FeatureIndex

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]has[]seqid([]const GtFeatureIndex
 *feature[]index, bool

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[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]index[]memory[]get[]node[]by[
]ptr([]GtFeatureIndexMemory*,

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\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()

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[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]feature[]node[]new([]GtStr *seqid, cons
t char *type, GtUword

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[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]feature[]node[]new[]pseudo([]GtStr *seq
id, GtUword start,

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[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]feature[]node[]new[]pseudo[]template([]
GtFeatureNode

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]add[]child([]GtFeatureNode *paren
t, GtFeatureNode

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]source([]GtFeatureNode *feat
ure[]node, GtStr

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]type([]GtFeatureNode *featur
e[]node, const char

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[]\OT1/cmtt/m/n/10.95 bool gt[]feature[]node[]has[]type([]GtFeatureNode *featur
e[]node, const char

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[]\OT1/cmtt/m/n/10.95 GtUword gt[]feature[]node[]number[]of[]children([]const G
tFeatureNode

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[]\OT1/cmtt/m/n/10.95 GtUword gt[]feature[]node[]number[]of[]children[]of[]type
([]const GtFeatureNode

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]strand([]GtFeatureNode *feat
ure[]node, GtStrand

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[]\OT1/cmtt/m/n/10.95 const char* gt[]feature[]node[]get[]attribute([]const GtF
eatureNode

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[]\OT1/cmtt/m/n/10.95 GtStrArray* gt[]feature[]node[]get[]attribute[]list([]con
st GtFeatureNode

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]add[]attribute([]GtFeatureNode *f
eature[]node, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]attribute([]GtFeatureNode* f
eature[]node, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]remove[]attribute([]GtFeatureNode
* feature[]node, const

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[]\OT1/cmtt/m/n/10.95 void GtFeatureNodeAttributeIterFunc([]const char *attr[]n
ame, const char

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[]\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-

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\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

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]foreach[]attribute([]GtFeatureNod
e *feature[]node,

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]make[]multi[]representative([]GtF
eatureNode

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]multi[]representative([]GtFe
atureNode *feature[]node,

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[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]node[]get[]multi[]representat
ive([]GtFeatureNode

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[]\OT1/cmtt/m/n/10.95 bool gt[]feature[]node[]is[]similar([]const GtFeatureNode
 *feature[]node[]a, const

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]remove[]leaf([]GtFeatureNode *tre
e, GtFeatureNode

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[71] [72] [73] [74]
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[]\OT1/cmtt/m/n/10.95 GtFeatureNodeIterator* gt[]feature[]node[]iterator[]new([
]const GtFeatureNode

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[]\OT1/cmtt/m/n/10.95 GtFeatureNodeIterator* gt[]feature[]node[]iterator[]new[]
direct([]const

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[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]node[]iterator[]next([]GtFeat
ureNodeIterator

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]iterator[]delete([]GtFeatureNodeI
terator

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[75]
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]feature[]out[]stream[]new([]GtNodeStrea
m*, GtFeatureIndex

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\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]gff3[]in[]stream[]new[]unsorted([]int n
um[]of[]files, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]in[]stream[]set[]type[]checker([]GtNodeStr
eam *gff3[]in[]stream,

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]gff3[]out[]stream[]new([]GtNodeStream *
in[]stream, GtFile

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]out[]stream[]set[]fasta[]width([]GtGFF3Out
Stream *gff3[]out[]stream,

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]out[]stream[]retain[]id[]attributes([]GtGF
F3OutStream

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]parser[]do[]not[]check[]region[]boundaries
([]GtGFF3Parser

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]parser[]set[]type[]checker([]GtGFF3Parser 
*gff3[]parser,

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]parser[]set[]xrf[]checker([]GtGFF3Parser *
gff3[]parser,

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[]\OT1/cmtt/m/n/10.95 int gt[]gff3[]parser[]parse[]genome[]nodes([]GtGFF3Parser
 *gff3[]parser, int

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\OT1/cmtt/m/n/10.95 *status[]code, GtQueue *genome[]nodes, GtCstrTable *used[]t
ypes, GtStr

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]visitor[]set[]fasta[]width([]GtGFF3Visitor
 *gff3[]visitor, GtUword

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]gtf[]out[]stream[]new([]GtNodeStream *i
n[]stream, GtFile

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[]\OT1/cmtt/m/n/10.95 void gt[]genome[]node[]set[]range([]GtGenomeNode *genome[
]node, const GtRange

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[]\OT1/cmtt/m/n/10.95 void gt[]genome[]node[]add[]user[]data([]GtGenomeNode *ge
nome[]node, const char

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[]\OT1/cmtt/m/n/10.95 void* gt[]genome[]node[]get[]user[]data([]const GtGenomeN
ode *genome[]node, const

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[]\OT1/cmtt/m/n/10.95 void gt[]genome[]node[]release[]user[]data([]GtGenomeNode
 *genome[]node, const

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[]\OT1/cmtt/m/n/10.95 int gt[]genome[]node[]cmp([]GtGenomeNode *genome[]node[]a
, GtGenomeNode

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[]\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

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[]\OT1/cmtt/m/n/10.95 int gt[]genome[]node[]accept([]GtGenomeNode *genome[]node
, GtNodeVisitor

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]text[]clip([]GtGraphics*, double
 x, double y, const

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]text[]centered([]GtGraphics*, do
uble x, double y,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]text[]right([]GtGraphics*, doubl
e x, double y, const

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]colored[]text([]GtGraphics*, dou
ble x, double y,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]set[]font([]GtGraphics *g, const char 
*family, FontSlant

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]set[]margins([]GtGraphics*, double mar
gin[]x, double

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]horizontal[]line([]GtGraphics *g
, double x, double y,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]vertical[]line([]GtGraphics *g, 
double x, double y,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]line([]GtGraphics *g, double x, 
double y, double xto,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]box([]GtGraphics*, double x, dou
ble y, double width,

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\OT1/cmtt/m/n/10.95 double height, GtColor fill[]color, ArrowStatus arrow[]stat
us, double

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]dashes([]GtGraphics*, double x, 
double y, double

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\OT1/cmtt/m/n/10.95 width, double height, ArrowStatus arrow[]status, double arr
ow[]width,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]caret([]GtGraphics*, double x, d
ouble y, double

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\OT1/cmtt/m/n/10.95 width, double height, ArrowStatus arrow[]status, double arr
ow[]width,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]rectangle([]GtGraphics*, double 
x, double y, bool

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\OT1/cmtt/m/n/10.95 filled, GtColor fill[]color, bool stroked, GtColor stroke[]
color, double

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]arrowhead([]GtGraphics*, double 
x, double y, GtColor,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]curve[]data([]GtGraphics *g, dou
ble x, double y,

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\OT1/cmtt/m/n/10.95 GtColor color, double data[], GtUword ndata, GtRange valran
ge, GtUword

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[]\OT1/cmtt/m/n/10.95 int gt[]graphics[]save[]to[]file([]const GtGraphics*, con
st char *filename,

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[]\OT1/cmtt/m/n/10.95 GtGraphics* gt[]graphics[]cairo[]new([]GtGraphicsOutType 
type, unsigned int

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[]\OT1/cmtt/m/n/10.95 GtGraphics* gt[]graphics[]cairo[]new[]from[]context([]cai
ro[]t *context, unsigned

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]cairo[]draw[]curve[]data([]GtGraphics 
*gg, double x, double y,

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\OT1/cmtt/m/n/10.95 GtColor color, double data[], GtUword ndata, GtRange valran
ge, GtUword

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[86]
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[]\OT1/cmtt/m/n/10.95 GtHashmap* gt[]hashmap[]new([]GtHashType keyhashtype, GtF
ree keyfree, GtFree

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[]\OT1/cmtt/m/n/10.95 int gt[]hashmap[]foreach[]ordered([]GtHashmap *hashmap, G
tHashmapVisitFunc

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[]\OT1/cmtt/m/n/10.95 int gt[]hashmap[]foreach([]GtHashmap *hashmap, GtHashmapV
isitFunc func, void

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[]\OT1/cmtt/m/n/10.95 int gt[]hashmap[]foreach[]in[]key[]order([]GtHashmap *has
hmap, GtHashmapVisitFunc

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[]\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-

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\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]id[]to[]md5[]stream[]new([]GtNodeStream
 *in[]stream,

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[]\OT1/cmtt/m/n/10.95 const GtRecMap* gt[]image[]info[]get[]rec[]map([]GtImageI
nfo *image[]info, GtUword

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\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]inter[]feature[]stream[]new([]GtNodeStr
eam *in[]stream, const

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[]\OT1/cmtt/m/n/10.95 GtIntervalTreeNode* gt[]interval[]tree[]find[]first[]over
lapping([]GtIntervalTree*,

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[]\OT1/cmtt/m/n/10.95 void gt[]interval[]tree[]insert([]GtIntervalTree *tree, G
tIntervalTreeNode

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[]\OT1/cmtt/m/n/10.95 void gt[]interval[]tree[]find[]all[]overlapping([]GtInter
valTree*, GtUword start,

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[]\OT1/cmtt/m/n/10.95 void gt[]interval[]tree[]iterate[]overlapping([]GtInterva
lTree *it,

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[]\OT1/cmtt/m/n/10.95 int gt[]interval[]tree[]traverse([]GtIntervalTree*, GtInt
ervalTreeIteratorFunc

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[]\OT1/cmtt/m/n/10.95 GtIntervalTreeNode* gt[]interval[]tree[]node[]new([]void 
*data, GtUword low,

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[]\OT1/cmtt/m/n/10.95 GtLayout* gt[]layout[]new([]GtDiagram *diagram, unsigned 
int width, GtStyle*,

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[]\OT1/cmtt/m/n/10.95 GtLayout* gt[]layout[]new[]with[]twc([]GtDiagram*, unsign
ed int width,

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[]\OT1/cmtt/m/n/10.95 void gt[]layout[]set[]track[]ordering[]func([]GtLayout *l
ayout,

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[]\OT1/cmtt/m/n/10.95 void gt[]md5[]encoder[]add[]block([]GtMD5Encoder *enc, co
nst char *message,

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[]\OT1/cmtt/m/n/10.95 void gt[]md5[]encoder[]finish([]GtMD5Encoder *enc, unsign
ed char *output, char

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]md5[]to[]id[]stream[]new([]GtNodeStream
 *in[]stream,

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[]\OT1/cmtt/m/n/10.95 void gt[]match[]set[]seqid1[]nt([]GtMatch *match, const c
har *seqid, GtUword

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[]\OT1/cmtt/m/n/10.95 void gt[]match[]set[]seqid2[]nt([]GtMatch *match, const c
har *seqid, GtUword

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[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]blast[]new([]char *seqid1, char *seqi
d2, GtUword

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\OT1/cmtt/m/n/10.95 start[]seq1, GtUword start[]seq2, GtUword end[]seq1, GtUwor
d end[]seq2,

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\OT1/cmtt/m/n/10.95 double evalue, float bitscore, GtUword ali[]l, double simil
arity,

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[]\OT1/cmtt/m/n/10.95 GtMatchIteratorStatus gt[]match[]iterator[]next([]GtMatch
Iterator *mp, GtMatch

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[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]last[]new([]const char *seqid1, const
 char *seqid2,

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\OT1/cmtt/m/n/10.95 GtUword score, GtUword seqno1, GtUword seqno2, GtUword star
t[]seq1,

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\OT1/cmtt/m/n/10.95 GtUword start[]seq2, GtUword end[]seq1, GtUword end[]seq2, 
GtMatchDirection

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[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]open[]new([]char *seqid1, char *seqid
2, GtUword

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\OT1/cmtt/m/n/10.95 start[]seq1, GtUword start[]seq2, GtUword end[]seq1, GtUwor
d end[]seq2,

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[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]sw[]new([]const char *seqid1, const c
har *seqid2,

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\OT1/cmtt/m/n/10.95 GtUword seqno1, GtUword seqno2, GtUword length, GtUword edi
st, GtUword

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\OT1/cmtt/m/n/10.95 start[]seq1, GtUword start[]seq2, GtUword end[]seq1, GtUwor
d end[]seq2,

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[]\OT1/cmtt/m/n/10.95 int gt[]match[]visitor[]visit[]match[]blast([]GtMatchVisi
tor *match[]visitor,

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[]\OT1/cmtt/m/n/10.95 int gt[]match[]visitor[]visit[]match[]open([]GtMatchVisit
or *match[]visitor,

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[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]meta[]node[]new([]const char *meta[]dir
ective, const char

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[]\OT1/cmtt/m/n/10.95 int gt[]node[]stream[]next([]GtNodeStream *node[]stream, 
GtGenomeNode

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\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

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\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

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\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

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\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]node[]stream[]create([]const GtNodeStre
amClass

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[]\OT1/cmtt/m/n/10.95 void* gt[]node[]stream[]cast([]const GtNodeStreamClass *n
ode[]stream[]class,

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[99]
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[]\OT1/cmtt/m/n/10.95 const GtNodeStreamClass* gt[]node[]stream[]class[]new([]s
ize[]t size,

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[100]
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[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]comment[]node([]GtNodeVisit
or *node[]visitor,

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[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]feature[]node([]GtNodeVisit
or *node[]visitor,

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[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]meta[]node([]GtNodeVisitor 
*node[]visitor,

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[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]region[]node([]GtNodeVisito
r *node[]visitor,

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[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]sequence[]node([]GtNodeVisi
tor *node[]visitor,

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[]\OT1/cmtt/m/n/10.95 GtORFIterator* gt[]orf[]iterator[]new([]GtCodonIterator *
ci, GtTranslator

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[]\OT1/cmtt/m/n/10.95 GtORFIteratorStatus gt[]orf[]iterator[]next([]GtORFIterat
or *orf[]iterator,

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[101]
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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]bool([]const char *option[]str
ing, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]double([]const char *option[]s
tring, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]double[]min([]const char *opti
on[]string, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]double[]min[]max([]const char 
*option[]string,

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\OT1/cmtt/m/n/10.95 const char *description, double *value, double default[]val
ue, double

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]probability([]const char *opti
on[]string, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int([]const char *option[]stri
ng, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int[]min([]const char *option[
]string, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int[]max([]const char *option[
]string, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int[]min[]max([]const char *op
tion[]string, const char

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\OT1/cmtt/m/n/10.95 *description, int *value, int default[]value, int minimum[]
value, int

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint([]const char *option[]str
ing, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint[]min([]const char *option
[]string, const char

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\OT1/cmtt/m/n/10.95 *description, unsigned int *value, unsigned int default[]va
lue, unsigned

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint[]max([]const char *option
[]string, const char

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\OT1/cmtt/m/n/10.95 *description, unsigned int *value, unsigned int default[]va
lue, unsigned

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint[]min[]max([]const char *o
ption[]string, const char

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\OT1/cmtt/m/n/10.95 *description, unsigned int *value, unsigned int default[]va
lue, unsigned

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]word([]const char *option[]str
ing, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uword([]const char *option[]st
ring, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uword[]min([]const char *optio
n[]string, const

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\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uword[]min[]max([]const char *
option[]string, const

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\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]long([]const char *option[]str
ing, const char

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]ulong([]const char *option[]st
ring, const char

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]ulong[]min([]const char *optio
n[]string, const

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\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]ulong[]min[]max([]const char *
option[]string, const

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\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]range([]const char *option[]st
ring, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]range[]min[]max([]const char *
option[]string, const

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\OT1/cmtt/m/n/10.95 char *description, GtRange *value, GtRange *default[]value,
 GtUword

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]string([]const char *option[]s
tring, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]string[]array([]const char *op
tion[]string, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]choice([]const char *option[]s
tring, const char

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\OT1/cmtt/m/n/10.95 *description, GtStr *value, const char *default[]value, con
st char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]filename([]const char *option[
]string, const char

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]filename[]array([]const char *
option[]string, const

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[]\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

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]is[]mandatory[]either([]GtOption *option
[]a, const GtOption

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]is[]mandatory[]either[]3([]GtOption *opt
ion[]a, const GtOption

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]is[]mandatory[]either[]4([]GtOption *opt
ion[]a, const GtOption

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]imply[]either[]2([]GtOption *option[]a, 
const GtOption

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]imply[]either[]3([]GtOption *option[]a, 
const GtOption

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[]\OT1/cmtt/m/n/10.95 int gt[]option[]parse[]spacespec([]GtUword *maximumspace,
 const char *optname,

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[]\OT1/cmtt/m/n/10.95 GtOptionParser* gt[]option[]parser[]new([]const char *syn
opsis, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]add[]option([]GtOptionParser *op
tion[]parser, GtOption

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]parser[]get[]option([]GtOptionParse
r *option[]parser, const

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[]\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

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]comment[]func([]GtOptionPar
ser *option[]parser,

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]version[]func([]GtOptionPar
ser *option[]parser,

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]mail[]address([]GtOptionPar
ser*, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]register[]hook([]GtOptionParser 
*option[]parser,

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]min[]args([]GtOptionParser 
*option[]parser, unsigned

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]max[]args([]GtOptionParser 
*option[]parser, unsigned

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]min[]max[]args([]GtOptionPa
rser *option[]parser,

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOPrval gt[]option[]parser[]parse([]GtOptionParser *opti
on[]parser,

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\OT1/cmtt/m/n/10.95 int *parsed[]args, int argc, const char **argv, GtShowVersi
onFunc

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[]\OT1/cmtt/m/n/10.95 void gt[]output[]file[]info[]register[]options([]GtOutput
FileInfo

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[110]
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[]\OT1/cmtt/m/n/10.95 GtRDB* gt[]rdb[]mysql[]new([]const char *server, unsigned
 int port, const char

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[]\OT1/cmtt/m/n/10.95 int gt[]rdb[]visitor[]visit[]sqlite([]GtRDBVisitor *rdbv,
 GtRDBSqlite *rdbs,

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[]\OT1/cmtt/m/n/10.95 int gt[]rdb[]visitor[]visit[]mysql([]GtRDBVisitor *rdbv, 
GtRDBMySQL *rdbm,

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[]\OT1/cmtt/m/n/10.95 int gt[]range[]compare[]with[]delta([]const GtRange *rang
e[]a, const GtRange

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[]\OT1/cmtt/m/n/10.95 bool gt[]range[]overlap[]delta([]const GtRange *range[]a,
 const GtRange

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[112]
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\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 ,

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtRecMap* gt[]rec[]map[]new([]double nw[]x, double nw[]y,
 double se[]x, double

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[113]
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[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]mapping([]GtSt
r *mapping[]filename,

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]seqfiles([]GtS
trArray

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[]\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

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\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

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[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]encseq([]GtEnc
seq *encseq, bool

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[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]rawseq([]const
 char *rawseq, GtUword

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[]\OT1/cmtt/m/n/10.95 int gt[]region[]mapping[]get[]sequence([]GtRegionMapping 
*region[]mapping, char

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[]\OT1/cmtt/m/n/10.95 int gt[]region[]mapping[]get[]sequence[]length([]GtRegion
Mapping *region[]mapping,

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[]\OT1/cmtt/m/n/10.95 int gt[]region[]mapping[]get[]description([]GtRegionMappi
ng *region[]mapping,

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[]\OT1/cmtt/m/n/10.95 const char* gt[]region[]mapping[]get[]md5[]fingerprint([]
GtRegionMapping

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\OT1/cmtt/m/n/10.95 *region[]mapping, GtStr *seqid, const GtRange *range, GtUwo
rd *offset,

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[114]
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\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

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[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]region[]node[]new([]GtStr *seqid, GtUwo
rd start, GtUword

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]script[]wrapper[]stream[]new([]GtScript
WrapperStreamNextFunc,

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[]\OT1/cmtt/m/n/10.95 GtNodeVisitor* gt[]script[]wrapper[]visitor[]new([]GtScri
ptWrapperVisitorCommentNodeFunc,

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\OT1/cmtt/m/n/10.95 GtScriptWrapperVisitorFeatureNodeFunc, GtScriptWrapperVisit
orRegionNodeFunc,

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\OT1/cmtt/m/n/10.95 GtScriptWrapperVisitorSequenceNodeFunc, GtScriptWrapperVisi
torMetaNodeFunc,

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]select[]stream[]new([]GtNodeStream *in[
]stream, GtStr

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\OT1/cmtt/m/n/10.95 *seqid, GtStr *source, const GtRange *contain[]range, const
 GtRange

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\OT1/cmtt/m/n/10.95 *overlap[]range, GtStrand strand, GtStrand targetstrand, bo
ol has[]CDS,

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\OT1/cmtt/m/n/10.95 GtUword max[]gene[]length, GtUword max[]gene[]num, double m
in[]gene[]score,

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\OT1/cmtt/m/n/10.95 double max[]gene[]score, double min[]average[]splice[]site[
]prob, GtUword

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[]\OT1/cmtt/m/n/10.95 void gt[]select[]stream[]set[]drophandler([]GtSelectStrea
m *sstr,

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[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]set[]symbolmap([]GtSeqIterator*, 
const GtUchar

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[]\OT1/cmtt/m/n/10.95 int gt[]seq[]iterator[]next([]GtSeqIterator *seqit, const
 GtUchar **sequence,

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[]\OT1/cmtt/m/n/10.95 const GtUint64* gt[]seq[]iterator[]getcurrentcounter([]Gt
SeqIterator*,

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[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]set[]quality[]buffer([]GtSeqItera
tor *seqit, const

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[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]fastq[]new([]const GtSt
rArray *filenametab,

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[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]fastq[]new[]colorspace(
[]const GtStrArray

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[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]fastq[]relax[]check[]of[]quality[
]description([]GtSeqIteratorFastQ

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[118]
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[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]sequence[]buffer[]new([
]const GtStrArray

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[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]sequence[]node[]new([]const char *descr
iption, GtStr

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[]\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

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[]\OT1/cmtt/m/n/10.95 const char* gt[]sequence[]node[]get[]description([]const 
GtSequenceNode

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[]\OT1/cmtt/m/n/10.95 const char* gt[]sequence[]node[]get[]sequence([]const GtS
equenceNode

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[]\OT1/cmtt/m/n/10.95 GtUword gt[]sequence[]node[]get[]sequence[]length([]const
 GtSequenceNode

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[119]
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\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

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[]\OT1/cmtt/m/n/10.95 void gt[]splitter[]split([]GtSplitter *splitter, char *st
ring, GtUword

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[]\OT1/cmtt/m/n/10.95 void gt[]splitter[]split[]non[]empty([]GtSplitter *s, cha
r *string, GtUword

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[120]
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\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]stat[]stream[]new([]GtNodeStream *in[]s
tream, bool

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\OT1/cmtt/m/n/10.95 gene[]length[]distribution, bool gene[]score[]distribution,
 bool

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\OT1/cmtt/m/n/10.95 exon[]length[]distribution, bool exon[]number[]distribution
, bool

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\OT1/cmtt/m/n/10.95 intron[]length[]distribution, bool cds[]length[]distributio
n, bool

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\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 ,

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\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 ,

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[]\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

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[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]add[]cstr[]nt([]GtStrArray *str[]arr
ay, const char *cstr,

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[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]set[]cstr([]GtStrArray *str[]array, 
GtUword strnum, const

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[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]set([]GtStrArray *str[]array, GtUwor
d strnum, const GtStr

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[]\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

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\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 ,

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[]\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

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[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]color([]GtStyle*, const char *sectio
n, const char *key,

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]color([]const GtStyle 
*style, const char

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\OT1/cmtt/m/n/10.95 *section, const char *key, GtColor *result, GtFeatureNode *
fn, GtError

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]color[]with[]track([]c
onst GtStyle *style,

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\OT1/cmtt/m/n/10.95 const char *section, const char *key, GtColor *result, GtFe
atureNode

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[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]str([]GtStyle*, const char *section,
 const char *key,

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]str([]const GtStyle *s
tyle, const char

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\OT1/cmtt/m/n/10.95 *section, const char *key, GtStr *result, GtFeatureNode *fn
, GtError

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]str[]with[]track([]con
st GtStyle *style, const

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\OT1/cmtt/m/n/10.95 char *section, const char *key, GtStr *result, GtFeatureNod
e *fn, const

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[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]num([]GtStyle*, const char *section,
 const char *key,

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]num([]const GtStyle *s
tyle, const char

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\OT1/cmtt/m/n/10.95 *section, const char *key, double *result, GtFeatureNode *f
n, GtError

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]num[]with[]track([]con
st GtStyle *style, const

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\OT1/cmtt/m/n/10.95 char *section, const char *key, double *result, GtFeatureNo
de *fn, const

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[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]bool([]GtStyle*, const char *section
, const char *key,

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]bool([]const GtStyle *
style, const char

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\OT1/cmtt/m/n/10.95 *section, const char *key, bool *result, GtFeatureNode *fn,
 GtError

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]bool[]with[]track([]co
nst GtStyle *style,

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\OT1/cmtt/m/n/10.95 const char *section, const char *key, bool *result, GtFeatu
reNode *fn,

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[]\OT1/cmtt/m/n/10.95 void GtTagValueMapIteratorFunc([]const char *tag, const c
har *value, void

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[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]add([]GtTagValueMap *tag[]value
[]map, const char *tag,

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[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]set([]GtTagValueMap *tag[]value
[]map, const char *tag,

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[]\OT1/cmtt/m/n/10.95 const char* gt[]tag[]value[]map[]get([]const GtTagValueMa
p tag[]value[]map, const

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[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]remove([]GtTagValueMap *tag[]va
lue[]map, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]foreach([]const GtTagValueMap t
ag[]value[]map,

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[]\OT1/cmtt/m/n/10.95 GtTextWidthCalculator* gt[]text[]width[]calculator[]ref([
]GtTextWidthCalculator*[]) 

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[]\OT1/cmtt/m/n/10.95 double gt[]text[]width[]calculator[]get[]text[]width([]Gt
TextWidthCalculator*,

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\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

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[]\OT1/cmtt/m/n/10.95 GtTextWidthCalculator* gt[]text[]width[]calculator[]cairo
[]new([]cairo[]t*,

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[]\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

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[]\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

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\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

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[]\OT1/cmtt/m/n/10.95 void gt[]timer[]show[]progress[]formatted([]GtTimer *time
r, FILE *fp, const

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[]\OT1/cmtt/m/n/10.95 void gt[]timer[]show[]progress[]va([]GtTimer *timer, FILE
 *fp, const char

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[]\OT1/cmtt/m/n/10.95 int GtToolArgumentsCheck([]int rest[]argc, void *tool[]ar
guments, GtError

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[]\OT1/cmtt/m/n/10.95 int GtToolRunner([]int argc, const char **argv, int parse
d[]args, void

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[]\OT1/cmtt/m/n/10.95 GtTool* gt[]tool[]new([]GtToolArgumentsNew tool[]argument
s[]new,

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\OT1/cmtt/m/n/10.95 GtToolArgumentsDelete tool[]arguments[]delete, GtToolOption
ParserNew

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\OT1/cmtt/m/n/10.95 tool[]option[]parser[]new, GtToolArgumentsCheck tool[]argum
ents[]check,

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[]\OT1/cmtt/m/n/10.95 void gt[]toolbox[]add[]tool([]GtToolbox *toolbox, const c
har *toolname, GtTool

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[]\OT1/cmtt/m/n/10.95 void gt[]toolbox[]add[]hidden[]tool([]GtToolbox *toolbox,
 const char *toolname,

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[]\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

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[]\OT1/cmtt/m/n/10.95 int gt[]trans[]table[]translate[]codon([]const GtTransTab
le *tt, char c1, char

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[]\OT1/cmtt/m/n/10.95 GtTranslator* gt[]translator[]new[]with[]table([]GtTransT
able *tt,

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[]\OT1/cmtt/m/n/10.95 void gt[]translator[]set[]codon[]iterator([]GtTranslator 
*translator,

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[]\OT1/cmtt/m/n/10.95 void gt[]translator[]set[]translation[]table([]GtTranslat
or *translator,

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[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]next([]GtTranslator *t
ranslator, char

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[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]find[]startcodon([]GtT
ranslator

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[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]find[]stopcodon([]GtTr
anslator *translator,

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[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]find[]codon([]GtTransl
ator *translator,

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[]\OT1/cmtt/m/n/10.95 bool gt[]type[]checker[]is[]valid([]GtTypeChecker *type[]
checker, const char

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[]\OT1/cmtt/m/n/10.95 bool gt[]type[]checker[]is[]partof([]GtTypeChecker *type[
]checker, const char

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[]\OT1/cmtt/m/n/10.95 bool gt[]type[]checker[]is[]a([]GtTypeChecker *type[]chec
ker, const char

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[]\OT1/cmtt/m/n/10.95 GtTypeChecker* gt[]type[]checker[]obo[]new([]const char *
obo[]file[]path, GtError

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]visitor[]stream[]new([]GtNodeStream *in
[]stream,

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[]\OT1/cmtt/m/n/10.95 bool gt[]xrf[]checker[]is[]valid([]GtXRFChecker *xrf[]che
cker, const char *value,

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[]\OT1/cmtt/m/n/10.95 void* gt[]bsearch[]data([]const void *key, const void *ba
se, size[]t nmemb,

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[]\OT1/cmtt/m/n/10.95 void gt[]bsearch[]all([]GtArray *members, const void *key
, const void *base,

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[]\OT1/cmtt/m/n/10.95 void gt[]bsearch[]all[]mark([]GtArray *members, const voi
d *key, const

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\OT1/cmtt/m/n/10.95 void *base, size[]t nmemb, size[]t size, GtCompareWithData,
 void *data,

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[]\OT1/cmtt/m/n/10.95 void gt[]countingsort([]void *out, const void *in, size[]
t elem[]size, GtUword

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[]\OT1/cmtt/m/n/10.95 GtUword gt[]countingsort[]get[]max([]const void *in, size
[]t elem[]size, GtUword

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[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry([]const char *description, co
nst char *sequence,

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[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry[]nt([]const char *description
, GtUword

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\OT1/cmtt/m/n/10.95 description[]length, const char *sequence, GtUword sequence
[]length,

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[]\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

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[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry[]str([]const char *descriptio
n, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry[]nt[]str([]const char *descri
ption, GtUword

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\OT1/cmtt/m/n/10.95 description[]length, const char *sequence, GtUword sequence
[]length,

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[]\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
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[]\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
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[]\OT1/cmtt/m/n/10.95 void gt[]msort[]r([]void *base, size[]t nmemb, size[]t si
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[]\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-

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[]\OT1/cmtt/m/n/10.95 void gt[]qsort[]r([]void *a, size[]t n, size[]t es, void 
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[]\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
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[]\OT1/cmtt/m/n/10.95 const char* gt[]version[]check([]unsigned int required[]m
ajor, unsigned int

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\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]
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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]gfflike[]get[]all[]features([]GtF
eatureIndex *gfi, GtArray

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]dup[]feature[]stream[]new([]GtNodeStrea
m*, const char

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[35]
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[]\OT1/cmtt/m/n/10.95 GtAlphabet* gt[]alphabet[]new[]from[]file[]no[]suffix([]c
onst char *filename,

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[]\OT1/cmtt/m/n/10.95 GtAlphabet* gt[]alphabet[]new[]from[]string([]const char 
*alphadef, GtUword

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[]\OT1/cmtt/m/n/10.95 GtAlphabet* gt[]alphabet[]new[]from[]sequence([]const GtS
trArray *filenametab,

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[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]add[]mapping([]GtAlphabet *alphabet, c
onst char

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[]\OT1/cmtt/m/n/10.95 int gt[]alphabet[]to[]file([]const GtAlphabet *alphabet, 
const char

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[]\OT1/cmtt/m/n/10.95 GtUchar gt[]alphabet[]pretty[]symbol([]const GtAlphabet *
alphabet, unsigned

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[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]echo[]pretty[]symbol([]const GtAlphabe
t *alphabet, FILE

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[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]encode[]seq([]const GtAlphabet *alphab
et, GtUchar *out,

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[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]decode[]seq[]to[]fp([]const GtAlphabet
 *alphabet, FILE *fpout,

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[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]decode[]seq[]to[]cstr([]const GtAlphab
et *alphabet, char

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[]\OT1/cmtt/m/n/10.95 GtStr* gt[]alphabet[]decode[]seq[]to[]str([]const GtAlpha
bet *alphabet, const

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[36] [37] [38]
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[]\OT1/cmtt/m/n/10.95 GtFeatureIndex* gt[]anno[]db[]schema[]get[]feature[]index
([]GtAnnoDBSchema

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[]\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

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[]\OT1/cmtt/m/n/10.95 void gt[]array[]sort[]with[]data([]GtArray *array, GtComp
areWithData compar,

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[]\OT1/cmtt/m/n/10.95 void gt[]array[]sort[]stable[]with[]data([]GtArray *array
, GtCompareWithData

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[40] [41]
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\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]in[]stream[]new([]GtArray *nodes
, GtUword *progress,

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]out[]stream[]new([]GtNodeStream 
*in[]stream, GtArray

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]out[]stream[]all[]new([]GtNodeSt
ream *in[]stream, GtArray

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[42]
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[]\OT1/cmtt/m/n/10.95 void gt[]bed[]in[]stream[]set[]feature[]type([]GtBEDInStr
eam *bed[]in[]stream, const

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[]\OT1/cmtt/m/n/10.95 void gt[]bed[]in[]stream[]set[]thick[]feature[]type([]GtB
EDInStream *bed[]in[]stream,

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[]\OT1/cmtt/m/n/10.95 void gt[]bed[]in[]stream[]set[]block[]type([]GtBEDInStrea
m *bed[]in[]stream, const

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[]\OT1/cmtt/m/n/10.95 void gt[]bittab[]and([]GtBittab *bittab[]a, const GtBitta
b *bittab[]b, const

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[]\OT1/cmtt/m/n/10.95 void gt[]bittab[]or([]GtBittab *bittab[]a, const GtBittab
 *bittab[]b, const

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[]\OT1/cmtt/m/n/10.95 void gt[]bittab[]nand([]GtBittab *bittab[]a, const GtBitt
ab *bittab[]b, const

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[45]
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]cds[]stream[]new([]GtNodeStream *in[]st
ream, GtRegionMapping

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\OT1/cmtt/m/n/10.95 *region[]mapping, unsigned int minorflen, const char *sourc
e, bool

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[46]
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]csa[]stream[]new([]GtNodeStream *in[]st
ream, GtUword

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[]\OT1/cmtt/m/n/10.95 GtCanvas* gt[]canvas[]cairo[]context[]new([]GtStyle *styl
e, cairo[]t *context,

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\OT1/cmtt/m/n/10.95 double offsetpos, GtUword width, GtUword height, GtImageInf
o *image[]info,

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[47]
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[]\OT1/cmtt/m/n/10.95 GtCanvas* gt[]canvas[]cairo[]file[]new([]GtStyle *style, 
GtGraphicsOutType

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\OT1/cmtt/m/n/10.95 output[]type, GtUword width, GtUword height, GtImageInfo *i
mage[]info,

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[]\OT1/cmtt/m/n/10.95 int gt[]canvas[]cairo[]file[]to[]file([]GtCanvasCairoFile
 *canvas, const char

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[]\OT1/cmtt/m/n/10.95 int gt[]canvas[]cairo[]file[]to[]stream([]GtCanvasCairoFi
le *canvas, GtStr

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[]\OT1/cmtt/m/n/10.95 GtUword gt[]codon[]iterator[]current[]position([]GtCodonI
terator

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[]\OT1/cmtt/m/n/10.95 GtCodonIteratorStatus gt[]codon[]iterator[]next([]GtCodon
Iterator

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\OT1/cmtt/m/n/10.95 *codon[]iterator, char *n1, char *n2, char *n3, unsigned in
t *frame,

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[48]
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[]\OT1/cmtt/m/n/10.95 GtCodonIterator* gt[]codon[]iterator[]encseq[]new([]GtEnc
seq *encseq, GtUword

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[]\OT1/cmtt/m/n/10.95 GtCodonIterator* gt[]codon[]iterator[]encseq[]new[]with[]
readmode([]GtEncseq

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\OT1/cmtt/m/n/10.95 *encseq, GtUword startpos, GtUword length, GtReadmode readm
ode, GtError

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[]\OT1/cmtt/m/n/10.95 GtCodonIterator* gt[]codon[]iterator[]simple[]new([]const
 char *seq, GtUword

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[49]
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[]\OT1/cmtt/m/n/10.95 GtColor* gt[]color[]new([]double red, double green, doubl
e blue, double

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[]\OT1/cmtt/m/n/10.95 void gt[]color[]set([]GtColor *color, double red, double 
green, double blue,

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[51]
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[]\OT1/cmtt/m/n/10.95 GtCustomTrack* gt[]custom[]track[]gc[]content[]new([]cons
t char *seq, GtUword

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[]\OT1/cmtt/m/n/10.95 GtCustomTrack* gt[]custom[]track[]script[]wrapper[]new([]
GtCtScriptRenderFunc

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\OT1/cmtt/m/n/10.95 render[]func, GtCtScriptGetHeightFunc get[]height[]func,

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[]\OT1/cmtt/m/n/10.95 GtDiagram* gt[]diagram[]new([]GtFeatureIndex *feature[]in
dex, const char

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[]\OT1/cmtt/m/n/10.95 GtDiagram* gt[]diagram[]new[]from[]array([]GtArray *featu
res, const GtRange

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[]\OT1/cmtt/m/n/10.95 void gt[]diagram[]set[]track[]selector[]func([]GtDiagram*
, GtTrackSelectorFunc,

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[]\OT1/cmtt/m/n/10.95 void gt[]disc[]distri[]add[]multi([]GtDiscDistri *d, GtUw
ord key, GtUint64

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[]\OT1/cmtt/m/n/10.95 void gt[]disc[]distri[]foreach([]const GtDiscDistri *d, G
tDiscDistriIterFunc

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[]\OT1/cmtt/m/n/10.95 void gt[]disc[]distri[]foreach[]in[]reverse[]order([]cons
t GtDiscDistri *d,

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[53]
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[]\OT1/cmtt/m/n/10.95 GtUchar gt[]encseq[]get[]encoded[]char([]const GtEncseq *
encseq, GtUword pos,

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[]\OT1/cmtt/m/n/10.95 char gt[]encseq[]get[]decoded[]char([]const GtEncseq *enc
seq, GtUword pos,

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[]\OT1/cmtt/m/n/10.95 bool gt[]encseq[]position[]is[]separator([]const GtEncseq
 *encseq, GtUword pos,

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[]\OT1/cmtt/m/n/10.95 bool gt[]encseq[]position[]is[]wildcard([]const GtEncseq 
*encseq, GtUword pos,

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[]\OT1/cmtt/m/n/10.95 GtEncseqReader* gt[]encseq[]create[]reader[]with[]readmod
e([]const GtEncseq

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]extract[]encoded([]const GtEncseq *encse
q, GtUchar *buffer,

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]extract[]decoded([]const GtEncseq *encse
q, char *buffer,

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[]\OT1/cmtt/m/n/10.95 const char* gt[]encseq[]description([]const GtEncseq *enc
seq, GtUword

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[]\OT1/cmtt/m/n/10.95 GtUint64 gt[]encseq[]effective[]filelength([]const GtEncs
eq *encseq, GtUword

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[]\OT1/cmtt/m/n/10.95 GtUword gt[]encseq[]filenum[]first[]seqnum([]const GtEncs
eq *encseq, GtUword

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]cstr([]GtEncseqBuilder *eb
, const char *str,

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]str([]GtEncseqBuilder *eb,
 GtStr *str, const

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]encoded([]GtEncseqBuilder 
*eb, const GtUchar

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]encoded[]own([]GtEncseqBui
lder *eb, const GtUchar

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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]builder[]add[]multiple[]encoded([]GtEncs
eqBuilder *eb, const

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[]\OT1/cmtt/m/n/10.95 int gt[]encseq[]encoder[]use[]representation([]GtEncseqEn
coder *ee, const char

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[]\OT1/cmtt/m/n/10.95 int gt[]encseq[]encoder[]use[]symbolmap[]file([]GtEncseqE
ncoder *ee, const char

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[]\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

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\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-

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\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

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[]\OT1/cmtt/m/n/10.95 int gt[]encseq[]encoder[]encode([]GtEncseqEncoder *ee, Gt
StrArray *seqfiles,

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[]\OT1/cmtt/m/n/10.95 GtEncseq* gt[]encseq[]loader[]load([]GtEncseqLoader *el, 
const char

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[64] [65] [66]
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[]\OT1/cmtt/m/n/10.95 void gt[]encseq[]reader[]reinit[]with[]readmode([]GtEncse
qReader *esr, const

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]extract[]feature[]stream[]new([]GtNodeS
tream *in[]stream,

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\OT1/cmtt/m/n/10.95 GtRegionMapping *region[]Mapping, const char *type, bool jo
in, bool

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]add[]region[]node([]GtFeatureInde
x *feature[]index,

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]add[]feature[]node([]GtFeatureInd
ex *feature[]index,

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]remove[]node([]GtFeatureIndex *fe
ature[]index,

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]add[]gff3file([]GtFeatureIndex *f
eature[]index, const

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[]\OT1/cmtt/m/n/10.95 GtArray* gt[]feature[]index[]get[]features[]for[]seqid([]
GtFeatureIndex*, const

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]get[]features[]for[]range([]GtFea
tureIndex *feature[]index,

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[]\OT1/cmtt/m/n/10.95 char* gt[]feature[]index[]get[]first[]seqid([]const GtFea
tureIndex

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[]\OT1/cmtt/m/n/10.95 GtStrArray* gt[]feature[]index[]get[]seqids([]const GtFea
tureIndex

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]get[]range[]for[]seqid([]GtFeatur
eIndex *feature[]index,

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]get[]orig[]range[]for[]seqid([]Gt
FeatureIndex

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[]\OT1/cmtt/m/n/10.95 int gt[]feature[]index[]has[]seqid([]const GtFeatureIndex
 *feature[]index, bool

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[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]index[]memory[]get[]node[]by[
]ptr([]GtFeatureIndexMemory*,

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\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()

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[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]feature[]node[]new([]GtStr *seqid, cons
t char *type, GtUword

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[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]feature[]node[]new[]pseudo([]GtStr *seq
id, GtUword start,

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[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]feature[]node[]new[]pseudo[]template([]
GtFeatureNode

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]add[]child([]GtFeatureNode *paren
t, GtFeatureNode

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]source([]GtFeatureNode *feat
ure[]node, GtStr

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]type([]GtFeatureNode *featur
e[]node, const char

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[]\OT1/cmtt/m/n/10.95 bool gt[]feature[]node[]has[]type([]GtFeatureNode *featur
e[]node, const char

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[]\OT1/cmtt/m/n/10.95 GtUword gt[]feature[]node[]number[]of[]children([]const G
tFeatureNode

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[]\OT1/cmtt/m/n/10.95 GtUword gt[]feature[]node[]number[]of[]children[]of[]type
([]const GtFeatureNode

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]strand([]GtFeatureNode *feat
ure[]node, GtStrand

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[]\OT1/cmtt/m/n/10.95 const char* gt[]feature[]node[]get[]attribute([]const GtF
eatureNode

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[]\OT1/cmtt/m/n/10.95 GtStrArray* gt[]feature[]node[]get[]attribute[]list([]con
st GtFeatureNode

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]add[]attribute([]GtFeatureNode *f
eature[]node, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]attribute([]GtFeatureNode* f
eature[]node, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]remove[]attribute([]GtFeatureNode
* feature[]node, const

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[]\OT1/cmtt/m/n/10.95 void GtFeatureNodeAttributeIterFunc([]const char *attr[]n
ame, const char

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[]\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-

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\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

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]foreach[]attribute([]GtFeatureNod
e *feature[]node,

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]make[]multi[]representative([]GtF
eatureNode

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]set[]multi[]representative([]GtFe
atureNode *feature[]node,

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[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]node[]get[]multi[]representat
ive([]GtFeatureNode

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[]\OT1/cmtt/m/n/10.95 bool gt[]feature[]node[]is[]similar([]const GtFeatureNode
 *feature[]node[]a, const

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]remove[]leaf([]GtFeatureNode *tre
e, GtFeatureNode

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[71] [72] [73] [74]
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[]\OT1/cmtt/m/n/10.95 GtFeatureNodeIterator* gt[]feature[]node[]iterator[]new([
]const GtFeatureNode

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[]\OT1/cmtt/m/n/10.95 GtFeatureNodeIterator* gt[]feature[]node[]iterator[]new[]
direct([]const

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[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]node[]iterator[]next([]GtFeat
ureNodeIterator

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[]\OT1/cmtt/m/n/10.95 void gt[]feature[]node[]iterator[]delete([]GtFeatureNodeI
terator

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[75]
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]feature[]out[]stream[]new([]GtNodeStrea
m*, GtFeatureIndex

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\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]gff3[]in[]stream[]new[]unsorted([]int n
um[]of[]files, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]in[]stream[]set[]type[]checker([]GtNodeStr
eam *gff3[]in[]stream,

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]gff3[]out[]stream[]new([]GtNodeStream *
in[]stream, GtFile

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]out[]stream[]set[]fasta[]width([]GtGFF3Out
Stream *gff3[]out[]stream,

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]out[]stream[]retain[]id[]attributes([]GtGF
F3OutStream

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]parser[]do[]not[]check[]region[]boundaries
([]GtGFF3Parser

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]parser[]set[]type[]checker([]GtGFF3Parser 
*gff3[]parser,

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]parser[]set[]xrf[]checker([]GtGFF3Parser *
gff3[]parser,

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[]\OT1/cmtt/m/n/10.95 int gt[]gff3[]parser[]parse[]genome[]nodes([]GtGFF3Parser
 *gff3[]parser, int

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\OT1/cmtt/m/n/10.95 *status[]code, GtQueue *genome[]nodes, GtCstrTable *used[]t
ypes, GtStr

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[]\OT1/cmtt/m/n/10.95 void gt[]gff3[]visitor[]set[]fasta[]width([]GtGFF3Visitor
 *gff3[]visitor, GtUword

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]gtf[]out[]stream[]new([]GtNodeStream *i
n[]stream, GtFile

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[]\OT1/cmtt/m/n/10.95 void gt[]genome[]node[]set[]range([]GtGenomeNode *genome[
]node, const GtRange

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[]\OT1/cmtt/m/n/10.95 void gt[]genome[]node[]add[]user[]data([]GtGenomeNode *ge
nome[]node, const char

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[]\OT1/cmtt/m/n/10.95 void* gt[]genome[]node[]get[]user[]data([]const GtGenomeN
ode *genome[]node, const

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[]\OT1/cmtt/m/n/10.95 void gt[]genome[]node[]release[]user[]data([]GtGenomeNode
 *genome[]node, const

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[]\OT1/cmtt/m/n/10.95 int gt[]genome[]node[]cmp([]GtGenomeNode *genome[]node[]a
, GtGenomeNode

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[]\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

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[]\OT1/cmtt/m/n/10.95 int gt[]genome[]node[]accept([]GtGenomeNode *genome[]node
, GtNodeVisitor

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]text[]clip([]GtGraphics*, double
 x, double y, const

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]text[]centered([]GtGraphics*, do
uble x, double y,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]text[]right([]GtGraphics*, doubl
e x, double y, const

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]colored[]text([]GtGraphics*, dou
ble x, double y,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]set[]font([]GtGraphics *g, const char 
*family, FontSlant

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]set[]margins([]GtGraphics*, double mar
gin[]x, double

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]horizontal[]line([]GtGraphics *g
, double x, double y,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]vertical[]line([]GtGraphics *g, 
double x, double y,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]line([]GtGraphics *g, double x, 
double y, double xto,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]box([]GtGraphics*, double x, dou
ble y, double width,

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\OT1/cmtt/m/n/10.95 double height, GtColor fill[]color, ArrowStatus arrow[]stat
us, double

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]dashes([]GtGraphics*, double x, 
double y, double

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\OT1/cmtt/m/n/10.95 width, double height, ArrowStatus arrow[]status, double arr
ow[]width,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]caret([]GtGraphics*, double x, d
ouble y, double

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\OT1/cmtt/m/n/10.95 width, double height, ArrowStatus arrow[]status, double arr
ow[]width,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]rectangle([]GtGraphics*, double 
x, double y, bool

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\OT1/cmtt/m/n/10.95 filled, GtColor fill[]color, bool stroked, GtColor stroke[]
color, double

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]arrowhead([]GtGraphics*, double 
x, double y, GtColor,

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]draw[]curve[]data([]GtGraphics *g, dou
ble x, double y,

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\OT1/cmtt/m/n/10.95 GtColor color, double data[], GtUword ndata, GtRange valran
ge, GtUword

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[]\OT1/cmtt/m/n/10.95 int gt[]graphics[]save[]to[]file([]const GtGraphics*, con
st char *filename,

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[]\OT1/cmtt/m/n/10.95 GtGraphics* gt[]graphics[]cairo[]new([]GtGraphicsOutType 
type, unsigned int

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[]\OT1/cmtt/m/n/10.95 GtGraphics* gt[]graphics[]cairo[]new[]from[]context([]cai
ro[]t *context, unsigned

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[]\OT1/cmtt/m/n/10.95 void gt[]graphics[]cairo[]draw[]curve[]data([]GtGraphics 
*gg, double x, double y,

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\OT1/cmtt/m/n/10.95 GtColor color, double data[], GtUword ndata, GtRange valran
ge, GtUword

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[]\OT1/cmtt/m/n/10.95 GtHashmap* gt[]hashmap[]new([]GtHashType keyhashtype, GtF
ree keyfree, GtFree

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[]\OT1/cmtt/m/n/10.95 int gt[]hashmap[]foreach[]ordered([]GtHashmap *hashmap, G
tHashmapVisitFunc

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[]\OT1/cmtt/m/n/10.95 int gt[]hashmap[]foreach([]GtHashmap *hashmap, GtHashmapV
isitFunc func, void

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[]\OT1/cmtt/m/n/10.95 int gt[]hashmap[]foreach[]in[]key[]order([]GtHashmap *has
hmap, GtHashmapVisitFunc

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[]\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-

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\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]id[]to[]md5[]stream[]new([]GtNodeStream
 *in[]stream,

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[]\OT1/cmtt/m/n/10.95 const GtRecMap* gt[]image[]info[]get[]rec[]map([]GtImageI
nfo *image[]info, GtUword

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\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]inter[]feature[]stream[]new([]GtNodeStr
eam *in[]stream, const

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[]\OT1/cmtt/m/n/10.95 GtIntervalTreeNode* gt[]interval[]tree[]find[]first[]over
lapping([]GtIntervalTree*,

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[]\OT1/cmtt/m/n/10.95 void gt[]interval[]tree[]insert([]GtIntervalTree *tree, G
tIntervalTreeNode

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[]\OT1/cmtt/m/n/10.95 void gt[]interval[]tree[]find[]all[]overlapping([]GtInter
valTree*, GtUword start,

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[]\OT1/cmtt/m/n/10.95 void gt[]interval[]tree[]iterate[]overlapping([]GtInterva
lTree *it,

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[]\OT1/cmtt/m/n/10.95 int gt[]interval[]tree[]traverse([]GtIntervalTree*, GtInt
ervalTreeIteratorFunc

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[]\OT1/cmtt/m/n/10.95 GtIntervalTreeNode* gt[]interval[]tree[]node[]new([]void 
*data, GtUword low,

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[]\OT1/cmtt/m/n/10.95 GtLayout* gt[]layout[]new([]GtDiagram *diagram, unsigned 
int width, GtStyle*,

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[]\OT1/cmtt/m/n/10.95 GtLayout* gt[]layout[]new[]with[]twc([]GtDiagram*, unsign
ed int width,

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[]\OT1/cmtt/m/n/10.95 void gt[]layout[]set[]track[]ordering[]func([]GtLayout *l
ayout,

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[]\OT1/cmtt/m/n/10.95 void gt[]md5[]encoder[]add[]block([]GtMD5Encoder *enc, co
nst char *message,

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[]\OT1/cmtt/m/n/10.95 void gt[]md5[]encoder[]finish([]GtMD5Encoder *enc, unsign
ed char *output, char

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]md5[]to[]id[]stream[]new([]GtNodeStream
 *in[]stream,

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[]\OT1/cmtt/m/n/10.95 void gt[]match[]set[]seqid1[]nt([]GtMatch *match, const c
har *seqid, GtUword

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[]\OT1/cmtt/m/n/10.95 void gt[]match[]set[]seqid2[]nt([]GtMatch *match, const c
har *seqid, GtUword

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[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]blast[]new([]char *seqid1, char *seqi
d2, GtUword

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\OT1/cmtt/m/n/10.95 start[]seq1, GtUword start[]seq2, GtUword end[]seq1, GtUwor
d end[]seq2,

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\OT1/cmtt/m/n/10.95 double evalue, float bitscore, GtUword ali[]l, double simil
arity,

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[]\OT1/cmtt/m/n/10.95 GtMatchIteratorStatus gt[]match[]iterator[]next([]GtMatch
Iterator *mp, GtMatch

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[95]
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[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]last[]new([]const char *seqid1, const
 char *seqid2,

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\OT1/cmtt/m/n/10.95 GtUword score, GtUword seqno1, GtUword seqno2, GtUword star
t[]seq1,

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\OT1/cmtt/m/n/10.95 GtUword start[]seq2, GtUword end[]seq1, GtUword end[]seq2, 
GtMatchDirection

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[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]open[]new([]char *seqid1, char *seqid
2, GtUword

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\OT1/cmtt/m/n/10.95 start[]seq1, GtUword start[]seq2, GtUword end[]seq1, GtUwor
d end[]seq2,

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[]\OT1/cmtt/m/n/10.95 GtMatch* gt[]match[]sw[]new([]const char *seqid1, const c
har *seqid2,

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\OT1/cmtt/m/n/10.95 GtUword seqno1, GtUword seqno2, GtUword length, GtUword edi
st, GtUword

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\OT1/cmtt/m/n/10.95 start[]seq1, GtUword start[]seq2, GtUword end[]seq1, GtUwor
d end[]seq2,

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[]\OT1/cmtt/m/n/10.95 int gt[]match[]visitor[]visit[]match[]blast([]GtMatchVisi
tor *match[]visitor,

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[]\OT1/cmtt/m/n/10.95 int gt[]match[]visitor[]visit[]match[]open([]GtMatchVisit
or *match[]visitor,

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[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]meta[]node[]new([]const char *meta[]dir
ective, const char

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[]\OT1/cmtt/m/n/10.95 int gt[]node[]stream[]next([]GtNodeStream *node[]stream, 
GtGenomeNode

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\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

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\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

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\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

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\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]node[]stream[]create([]const GtNodeStre
amClass

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[]\OT1/cmtt/m/n/10.95 void* gt[]node[]stream[]cast([]const GtNodeStreamClass *n
ode[]stream[]class,

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[99]
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[]\OT1/cmtt/m/n/10.95 const GtNodeStreamClass* gt[]node[]stream[]class[]new([]s
ize[]t size,

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[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]comment[]node([]GtNodeVisit
or *node[]visitor,

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[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]feature[]node([]GtNodeVisit
or *node[]visitor,

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[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]meta[]node([]GtNodeVisitor 
*node[]visitor,

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[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]region[]node([]GtNodeVisito
r *node[]visitor,

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[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]sequence[]node([]GtNodeVisi
tor *node[]visitor,

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[]\OT1/cmtt/m/n/10.95 GtORFIterator* gt[]orf[]iterator[]new([]GtCodonIterator *
ci, GtTranslator

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[]\OT1/cmtt/m/n/10.95 GtORFIteratorStatus gt[]orf[]iterator[]next([]GtORFIterat
or *orf[]iterator,

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[101]
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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]bool([]const char *option[]str
ing, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]double([]const char *option[]s
tring, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]double[]min([]const char *opti
on[]string, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]double[]min[]max([]const char 
*option[]string,

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\OT1/cmtt/m/n/10.95 const char *description, double *value, double default[]val
ue, double

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]probability([]const char *opti
on[]string, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int([]const char *option[]stri
ng, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int[]min([]const char *option[
]string, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int[]max([]const char *option[
]string, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]int[]min[]max([]const char *op
tion[]string, const char

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\OT1/cmtt/m/n/10.95 *description, int *value, int default[]value, int minimum[]
value, int

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint([]const char *option[]str
ing, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint[]min([]const char *option
[]string, const char

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\OT1/cmtt/m/n/10.95 *description, unsigned int *value, unsigned int default[]va
lue, unsigned

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint[]max([]const char *option
[]string, const char

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\OT1/cmtt/m/n/10.95 *description, unsigned int *value, unsigned int default[]va
lue, unsigned

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uint[]min[]max([]const char *o
ption[]string, const char

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\OT1/cmtt/m/n/10.95 *description, unsigned int *value, unsigned int default[]va
lue, unsigned

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]word([]const char *option[]str
ing, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uword([]const char *option[]st
ring, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uword[]min([]const char *optio
n[]string, const

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\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]uword[]min[]max([]const char *
option[]string, const

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\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]long([]const char *option[]str
ing, const char

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]ulong([]const char *option[]st
ring, const char

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]ulong[]min([]const char *optio
n[]string, const

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\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]ulong[]min[]max([]const char *
option[]string, const

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\OT1/cmtt/m/n/10.95 char *description, GtUword *value, GtUword default[]value, 
GtUword

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]range([]const char *option[]st
ring, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]range[]min[]max([]const char *
option[]string, const

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\OT1/cmtt/m/n/10.95 char *description, GtRange *value, GtRange *default[]value,
 GtUword

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]string([]const char *option[]s
tring, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]string[]array([]const char *op
tion[]string, const char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]choice([]const char *option[]s
tring, const char

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\OT1/cmtt/m/n/10.95 *description, GtStr *value, const char *default[]value, con
st char

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]filename([]const char *option[
]string, const char

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]new[]filename[]array([]const char *
option[]string, const

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[]\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

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]is[]mandatory[]either([]GtOption *option
[]a, const GtOption

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]is[]mandatory[]either[]3([]GtOption *opt
ion[]a, const GtOption

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]is[]mandatory[]either[]4([]GtOption *opt
ion[]a, const GtOption

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]imply[]either[]2([]GtOption *option[]a, 
const GtOption

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]imply[]either[]3([]GtOption *option[]a, 
const GtOption

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[]\OT1/cmtt/m/n/10.95 int gt[]option[]parse[]spacespec([]GtUword *maximumspace,
 const char *optname,

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[102] [103] [104] [105] [106]
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[]\OT1/cmtt/m/n/10.95 GtOptionParser* gt[]option[]parser[]new([]const char *syn
opsis, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]add[]option([]GtOptionParser *op
tion[]parser, GtOption

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[]\OT1/cmtt/m/n/10.95 GtOption* gt[]option[]parser[]get[]option([]GtOptionParse
r *option[]parser, const

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[]\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

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]comment[]func([]GtOptionPar
ser *option[]parser,

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]version[]func([]GtOptionPar
ser *option[]parser,

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]mail[]address([]GtOptionPar
ser*, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]register[]hook([]GtOptionParser 
*option[]parser,

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]min[]args([]GtOptionParser 
*option[]parser, unsigned

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]max[]args([]GtOptionParser 
*option[]parser, unsigned

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[]\OT1/cmtt/m/n/10.95 void gt[]option[]parser[]set[]min[]max[]args([]GtOptionPa
rser *option[]parser,

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtOPrval gt[]option[]parser[]parse([]GtOptionParser *opti
on[]parser,

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\OT1/cmtt/m/n/10.95 int *parsed[]args, int argc, const char **argv, GtShowVersi
onFunc

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[107] [108]
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[]\OT1/cmtt/m/n/10.95 void gt[]output[]file[]info[]register[]options([]GtOutput
FileInfo

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[109]
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[110]
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[]\OT1/cmtt/m/n/10.95 GtRDB* gt[]rdb[]mysql[]new([]const char *server, unsigned
 int port, const char

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[]\OT1/cmtt/m/n/10.95 int gt[]rdb[]visitor[]visit[]sqlite([]GtRDBVisitor *rdbv,
 GtRDBSqlite *rdbs,

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[]\OT1/cmtt/m/n/10.95 int gt[]rdb[]visitor[]visit[]mysql([]GtRDBVisitor *rdbv, 
GtRDBMySQL *rdbm,

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[111]
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[]\OT1/cmtt/m/n/10.95 int gt[]range[]compare[]with[]delta([]const GtRange *rang
e[]a, const GtRange

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[]\OT1/cmtt/m/n/10.95 bool gt[]range[]overlap[]delta([]const GtRange *range[]a,
 const GtRange

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[112]
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\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 ,

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtRecMap* gt[]rec[]map[]new([]double nw[]x, double nw[]y,
 double se[]x, double

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[113]
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[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]mapping([]GtSt
r *mapping[]filename,

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[]\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

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[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]seqfiles([]GtS
trArray

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[]\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

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\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

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[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]encseq([]GtEnc
seq *encseq, bool

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[]\OT1/cmtt/m/n/10.95 GtRegionMapping* gt[]region[]mapping[]new[]rawseq([]const
 char *rawseq, GtUword

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[]\OT1/cmtt/m/n/10.95 int gt[]region[]mapping[]get[]sequence([]GtRegionMapping 
*region[]mapping, char

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[]\OT1/cmtt/m/n/10.95 int gt[]region[]mapping[]get[]sequence[]length([]GtRegion
Mapping *region[]mapping,

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[]\OT1/cmtt/m/n/10.95 int gt[]region[]mapping[]get[]description([]GtRegionMappi
ng *region[]mapping,

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[]\OT1/cmtt/m/n/10.95 const char* gt[]region[]mapping[]get[]md5[]fingerprint([]
GtRegionMapping

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\OT1/cmtt/m/n/10.95 *region[]mapping, GtStr *seqid, const GtRange *range, GtUwo
rd *offset,

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[114]
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\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

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[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]region[]node[]new([]GtStr *seqid, GtUwo
rd start, GtUword

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[115]
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]script[]wrapper[]stream[]new([]GtScript
WrapperStreamNextFunc,

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[]\OT1/cmtt/m/n/10.95 GtNodeVisitor* gt[]script[]wrapper[]visitor[]new([]GtScri
ptWrapperVisitorCommentNodeFunc,

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\OT1/cmtt/m/n/10.95 GtScriptWrapperVisitorFeatureNodeFunc, GtScriptWrapperVisit
orRegionNodeFunc,

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\OT1/cmtt/m/n/10.95 GtScriptWrapperVisitorSequenceNodeFunc, GtScriptWrapperVisi
torMetaNodeFunc,

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[116]
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]select[]stream[]new([]GtNodeStream *in[
]stream, GtStr

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\OT1/cmtt/m/n/10.95 *seqid, GtStr *source, const GtRange *contain[]range, const
 GtRange

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\OT1/cmtt/m/n/10.95 *overlap[]range, GtStrand strand, GtStrand targetstrand, bo
ol has[]CDS,

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\OT1/cmtt/m/n/10.95 GtUword max[]gene[]length, GtUword max[]gene[]num, double m
in[]gene[]score,

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\OT1/cmtt/m/n/10.95 double max[]gene[]score, double min[]average[]splice[]site[
]prob, GtUword

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[]\OT1/cmtt/m/n/10.95 void gt[]select[]stream[]set[]drophandler([]GtSelectStrea
m *sstr,

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[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]set[]symbolmap([]GtSeqIterator*, 
const GtUchar

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[]\OT1/cmtt/m/n/10.95 int gt[]seq[]iterator[]next([]GtSeqIterator *seqit, const
 GtUchar **sequence,

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[]\OT1/cmtt/m/n/10.95 const GtUint64* gt[]seq[]iterator[]getcurrentcounter([]Gt
SeqIterator*,

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[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]set[]quality[]buffer([]GtSeqItera
tor *seqit, const

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[117]
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[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]fastq[]new([]const GtSt
rArray *filenametab,

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[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]fastq[]new[]colorspace(
[]const GtStrArray

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[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]fastq[]relax[]check[]of[]quality[
]description([]GtSeqIteratorFastQ

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[118]
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[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]sequence[]buffer[]new([
]const GtStrArray

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[]\OT1/cmtt/m/n/10.95 GtGenomeNode* gt[]sequence[]node[]new([]const char *descr
iption, GtStr

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[]\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

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[]\OT1/cmtt/m/n/10.95 const char* gt[]sequence[]node[]get[]description([]const 
GtSequenceNode

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[]\OT1/cmtt/m/n/10.95 const char* gt[]sequence[]node[]get[]sequence([]const GtS
equenceNode

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[]\OT1/cmtt/m/n/10.95 GtUword gt[]sequence[]node[]get[]sequence[]length([]const
 GtSequenceNode

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[119]
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\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

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[]\OT1/cmtt/m/n/10.95 void gt[]splitter[]split([]GtSplitter *splitter, char *st
ring, GtUword

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[]\OT1/cmtt/m/n/10.95 void gt[]splitter[]split[]non[]empty([]GtSplitter *s, cha
r *string, GtUword

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\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

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]stat[]stream[]new([]GtNodeStream *in[]s
tream, bool

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\OT1/cmtt/m/n/10.95 gene[]length[]distribution, bool gene[]score[]distribution,
 bool

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\OT1/cmtt/m/n/10.95 exon[]length[]distribution, bool exon[]number[]distribution
, bool

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\OT1/cmtt/m/n/10.95 intron[]length[]distribution, bool cds[]length[]distributio
n, bool

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\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 ,

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\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 ,

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[]\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

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[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]add[]cstr[]nt([]GtStrArray *str[]arr
ay, const char *cstr,

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[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]set[]cstr([]GtStrArray *str[]array, 
GtUword strnum, const

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[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]set([]GtStrArray *str[]array, GtUwor
d strnum, const GtStr

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[]\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

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\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 ,

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[]\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

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[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]color([]GtStyle*, const char *sectio
n, const char *key,

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]color([]const GtStyle 
*style, const char

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\OT1/cmtt/m/n/10.95 *section, const char *key, GtColor *result, GtFeatureNode *
fn, GtError

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]color[]with[]track([]c
onst GtStyle *style,

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\OT1/cmtt/m/n/10.95 const char *section, const char *key, GtColor *result, GtFe
atureNode

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[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]str([]GtStyle*, const char *section,
 const char *key,

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]str([]const GtStyle *s
tyle, const char

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\OT1/cmtt/m/n/10.95 *section, const char *key, GtStr *result, GtFeatureNode *fn
, GtError

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]str[]with[]track([]con
st GtStyle *style, const

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\OT1/cmtt/m/n/10.95 char *section, const char *key, GtStr *result, GtFeatureNod
e *fn, const

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[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]num([]GtStyle*, const char *section,
 const char *key,

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]num([]const GtStyle *s
tyle, const char

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\OT1/cmtt/m/n/10.95 *section, const char *key, double *result, GtFeatureNode *f
n, GtError

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]num[]with[]track([]con
st GtStyle *style, const

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\OT1/cmtt/m/n/10.95 char *section, const char *key, double *result, GtFeatureNo
de *fn, const

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[]\OT1/cmtt/m/n/10.95 void gt[]style[]set[]bool([]GtStyle*, const char *section
, const char *key,

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]bool([]const GtStyle *
style, const char

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\OT1/cmtt/m/n/10.95 *section, const char *key, bool *result, GtFeatureNode *fn,
 GtError

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[]\OT1/cmtt/m/n/10.95 GtStyleQueryStatus gt[]style[]get[]bool[]with[]track([]co
nst GtStyle *style,

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\OT1/cmtt/m/n/10.95 const char *section, const char *key, bool *result, GtFeatu
reNode *fn,

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[]\OT1/cmtt/m/n/10.95 void GtTagValueMapIteratorFunc([]const char *tag, const c
har *value, void

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[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]add([]GtTagValueMap *tag[]value
[]map, const char *tag,

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[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]set([]GtTagValueMap *tag[]value
[]map, const char *tag,

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[]\OT1/cmtt/m/n/10.95 const char* gt[]tag[]value[]map[]get([]const GtTagValueMa
p tag[]value[]map, const

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[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]remove([]GtTagValueMap *tag[]va
lue[]map, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]tag[]value[]map[]foreach([]const GtTagValueMap t
ag[]value[]map,

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[]\OT1/cmtt/m/n/10.95 GtTextWidthCalculator* gt[]text[]width[]calculator[]ref([
]GtTextWidthCalculator*[]) 

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[]\OT1/cmtt/m/n/10.95 double gt[]text[]width[]calculator[]get[]text[]width([]Gt
TextWidthCalculator*,

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\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

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[]\OT1/cmtt/m/n/10.95 GtTextWidthCalculator* gt[]text[]width[]calculator[]cairo
[]new([]cairo[]t*,

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[]\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

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[]\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

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\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

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[]\OT1/cmtt/m/n/10.95 void gt[]timer[]show[]progress[]formatted([]GtTimer *time
r, FILE *fp, const

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[]\OT1/cmtt/m/n/10.95 void gt[]timer[]show[]progress[]va([]GtTimer *timer, FILE
 *fp, const char

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[]\OT1/cmtt/m/n/10.95 int GtToolArgumentsCheck([]int rest[]argc, void *tool[]ar
guments, GtError

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[]\OT1/cmtt/m/n/10.95 int GtToolRunner([]int argc, const char **argv, int parse
d[]args, void

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[]\OT1/cmtt/m/n/10.95 GtTool* gt[]tool[]new([]GtToolArgumentsNew tool[]argument
s[]new,

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\OT1/cmtt/m/n/10.95 GtToolArgumentsDelete tool[]arguments[]delete, GtToolOption
ParserNew

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\OT1/cmtt/m/n/10.95 tool[]option[]parser[]new, GtToolArgumentsCheck tool[]argum
ents[]check,

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[]\OT1/cmtt/m/n/10.95 void gt[]toolbox[]add[]tool([]GtToolbox *toolbox, const c
har *toolname, GtTool

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[]\OT1/cmtt/m/n/10.95 void gt[]toolbox[]add[]hidden[]tool([]GtToolbox *toolbox,
 const char *toolname,

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[]\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

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[]\OT1/cmtt/m/n/10.95 int gt[]trans[]table[]translate[]codon([]const GtTransTab
le *tt, char c1, char

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[]\OT1/cmtt/m/n/10.95 GtTranslator* gt[]translator[]new[]with[]table([]GtTransT
able *tt,

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[]\OT1/cmtt/m/n/10.95 void gt[]translator[]set[]codon[]iterator([]GtTranslator 
*translator,

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[]\OT1/cmtt/m/n/10.95 void gt[]translator[]set[]translation[]table([]GtTranslat
or *translator,

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[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]next([]GtTranslator *t
ranslator, char

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[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]find[]startcodon([]GtT
ranslator

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[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]find[]stopcodon([]GtTr
anslator *translator,

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[]\OT1/cmtt/m/n/10.95 GtTranslatorStatus gt[]translator[]find[]codon([]GtTransl
ator *translator,

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[]\OT1/cmtt/m/n/10.95 bool gt[]type[]checker[]is[]valid([]GtTypeChecker *type[]
checker, const char

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[]\OT1/cmtt/m/n/10.95 bool gt[]type[]checker[]is[]partof([]GtTypeChecker *type[
]checker, const char

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[]\OT1/cmtt/m/n/10.95 bool gt[]type[]checker[]is[]a([]GtTypeChecker *type[]chec
ker, const char

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[]\OT1/cmtt/m/n/10.95 GtTypeChecker* gt[]type[]checker[]obo[]new([]const char *
obo[]file[]path, GtError

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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]visitor[]stream[]new([]GtNodeStream *in
[]stream,

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[]\OT1/cmtt/m/n/10.95 bool gt[]xrf[]checker[]is[]valid([]GtXRFChecker *xrf[]che
cker, const char *value,

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[]\OT1/cmtt/m/n/10.95 void* gt[]bsearch[]data([]const void *key, const void *ba
se, size[]t nmemb,

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[]\OT1/cmtt/m/n/10.95 void gt[]bsearch[]all([]GtArray *members, const void *key
, const void *base,

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[]\OT1/cmtt/m/n/10.95 void gt[]bsearch[]all[]mark([]GtArray *members, const voi
d *key, const

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\OT1/cmtt/m/n/10.95 void *base, size[]t nmemb, size[]t size, GtCompareWithData,
 void *data,

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[]\OT1/cmtt/m/n/10.95 void gt[]countingsort([]void *out, const void *in, size[]
t elem[]size, GtUword

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[]\OT1/cmtt/m/n/10.95 GtUword gt[]countingsort[]get[]max([]const void *in, size
[]t elem[]size, GtUword

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[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry([]const char *description, co
nst char *sequence,

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[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry[]nt([]const char *description
, GtUword

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\OT1/cmtt/m/n/10.95 description[]length, const char *sequence, GtUword sequence
[]length,

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[]\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

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n, const char

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[]\OT1/cmtt/m/n/10.95 void gt[]fasta[]show[]entry[]nt[]str([]const char *descri
ption, GtUword

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[]length,

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[]\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

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[]\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. 

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[]\OT1/cmtt/m/n/10.95 int gt[]file[]find[]in[]env([]GtStr *path, const char *fi
le, const char *env,

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[]\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-

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[]\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 . 

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[]\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

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[]\OT1/cmtt/m/n/10.95 int gt[]files[]guess[]if[]protein[]sequences([]const GtSt
rArray *filenames,

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[]\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. 

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[]\OT1/cmtt/m/n/10.95 int gt[]grep[]nt([]bool *match, const char *pattern, cons
t char *line, size[]t

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[]\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-

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\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

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[]\OT1/cmtt/m/n/10.95 void gt[]msort[]r([]void *base, size[]t nmemb, size[]t si
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[]\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-

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\OT1/ptm/m/n/10.95 ca-tions in http://www.unix-systems.org/onlinepubs/7908799/x
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[]\OT1/cmtt/m/n/10.95 int gt[]parse[]range([]GtRange *rng, const char *start, c
onst char *end,

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[]\OT1/cmtt/m/n/10.95 int gt[]parse[]range[]tidy([]GtRange *rng, const char *st
art, const char *end,

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[145]
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[]\OT1/cmtt/m/n/10.95 void gt[]qsort[]r([]void *a, size[]t n, size[]t es, void 
*data,

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[]\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

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[]\OT1/cmtt/m/n/10.95 const char* gt[]version[]check([]unsigned int required[]m
ajor, unsigned int

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[]\OT1/cmtt/m/n/10.95 void gt[]warning[]default[]handler([]void *data, const ch
ar *format, va[]list

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[148] [149]) [150] (./annotationsketch.aux)

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c/amsfonts/cm/cmtt8.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/ut
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mv annotationsketch.aux annotationsketch-pdf.aux
test -e annotationsketch.bbl && mv annotationsketch.bbl annotationsketch-pdf.bbl
make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manuals'
make -C /«PKGBUILDDIR»/doc/manuals
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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)
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[]\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 ,
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[]\OT1/ptm/m/n/12 a single-end li-brary plus an in-ter-leaved
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[5] [6] [7] (./readjoiner.aux)

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(see the transcript file for additional information){/usr/share/texlive/texmf-d
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</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
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bibtex readjoiner
This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
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This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
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entering extended mode
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(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
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(./readjoiner.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
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[] 

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[]\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 ,
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[]\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
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</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, 108822 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 <2015/10/01> patch level 1
Babel <3.9m> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
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[] 

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[]\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 ,
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[]\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
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t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
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Output written on readjoiner.pdf (8 pages, 108822 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
make[3]: [hop-pdf.aux] Error 1 (ignored)
Makefile:39: recipe for target 'hop-pdf.aux' failed
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 <2015/10/01> patch level 1
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(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (./optionman.sty)
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*geometry* driver: auto-detecting
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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]
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[]\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

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[]\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)
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\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)
make[3]: [hop-pdf.bbl] Error 2 (ignored)
Makefile:32: recipe for target 'hop-pdf.bbl' failed
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 <2015/10/01> patch level 1
Babel <3.9m> 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
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(/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
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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

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[]\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)
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\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 <2015/10/01> patch level 1
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(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
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[]\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

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[]\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)
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\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
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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
make[3]: [ltrharvest-pdf.aux] Error 1 (ignored)
Makefile:39: recipe for target 'ltrharvest-pdf.aux' failed
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
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(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
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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.

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LaTeX Warning: Reference `Examples' on page 1 undefined on input line 203.

[1] [2]

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[3] [4] [5]

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491.


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LaTeX Warning: Citation `vmatch' on page 6 undefined on input line 500.

[6]
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[]\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[] 

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[]\OT1/pcr/m/n/10 # args=-index chr02.19970727.fsa -v -out pred-chr02.fsa -outi
nner pred-inner-chr02.fsa[] 
[7]
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[]\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[] 

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[]\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[] 

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[]\OT1/pcr/m/n/10 $ gt ltrharvest -index chr02.19970727.fsa -seed 30 -xdrop 5 -
mat 2 -mis -2 -ins -3 
[8]
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[]\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.


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[]\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.


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[10]
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[]\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 .

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[][]
[11] [12] (./ltrharvest.aux)

LaTeX Warning: There were undefined references.


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 )
(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, 160863 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)
make[3]: [ltrharvest-pdf.bbl] Error 2 (ignored)
Makefile:32: recipe for target 'ltrharvest-pdf.bbl' failed
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 <2015/10/01> patch level 1
Babel <3.9m> 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)
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(/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
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[]\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[] 

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[]\OT1/pcr/m/n/10 # args=-index chr02.19970727.fsa -v -out pred-chr02.fsa -outi
nner pred-inner-chr02.fsa[] 
[7]
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[]\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[] 

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[]\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[] 

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[]\OT1/pcr/m/n/10 $ gt ltrharvest -index chr02.19970727.fsa -seed 30 -xdrop 5 -
mat 2 -mis -2 -ins -3 
[8]
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[]\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[] 

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[]\OT1/pcr/m/n/10 $ gt ltrharvest -index chrAll.19971001.fsa -seed 100 -minlenl
tr 100 -maxlenltr 1000 
[9] [10]
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[]\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 .

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[][]
[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
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b></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on ltrharvest.pdf (13 pages, 160039 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 <2015/10/01> patch level 1
Babel <3.9m> 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}]
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[5] [6]
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[]\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[] 

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[]\OT1/pcr/m/n/10 # args=-index chr02.19970727.fsa -v -out pred-chr02.fsa -outi
nner pred-inner-chr02.fsa[] 
[7]
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[]\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[] 

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[]\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]
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[]\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]
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[]\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 .

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[][]
[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/
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nts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/t
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b></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on ltrharvest.pdf (13 pages, 160039 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
make[3]: [ltrdigest-pdf.aux] Error 1 (ignored)
Makefile:39: recipe for target 'ltrdigest-pdf.aux' failed
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 <2015/10/01> patch level 1
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Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
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(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
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(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
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[]$\OT1/pcr/m/n/14.4 http : / / nar . oxfordjournals . org / cgi / content /
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]

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\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)

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[1]

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[2] [3] [4]
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\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

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[]\OT1/pcr/m/n/12 gt suffixerator -tis -des -dna -ssp -db genome.fas -indexname
 genome.fas 

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[]\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 ,

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\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
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b8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/
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Output written on ltrdigest.pdf (11 pages, 185702 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)
make[3]: [ltrdigest-pdf.bbl] Error 2 (ignored)
Makefile:32: recipe for target 'ltrdigest-pdf.bbl' failed
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 <2015/10/01> patch level 1
Babel <3.9m> 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)
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\OT1/ptm/m/n/12 trans-po-son it-self (\OT1/pcr/m/n/12 LTR[]retrotransposon \OT1
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[]\OT1/pcr/m/n/12 gt suffixerator -tis -des -dna -ssp -db genome.fas -indexname
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[]\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 ,

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enome.fas
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\OT1/ptm/m/n/12 se-quence fea-tures of LTR retro-trans-posons in pre-dicted can
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\OT1/ptm/m/n/12 trans-po-son it-self (\OT1/pcr/m/n/12 LTR[]retrotransposon \OT1
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[]\OT1/pcr/m/n/12 gt suffixerator -tis -des -dna -ssp -db genome.fas -indexname
 genome.fas 

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[]\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 ,

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\OT1/pcr/m/n/12 -hmms HMM*.hmm -outfileprefix mygenome-ltrs ltrs[]sorted.gff3 g
enome.fas
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test -e matstat-pdf.aux && mv matstat-pdf.aux matstat.aux
make[3]: [matstat-pdf.aux] Error 1 (ignored)
Makefile:39: recipe for target 'matstat-pdf.aux' failed
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 <2015/10/01> patch level 1
Babel <3.9m> 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
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(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
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(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
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(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (./optionman.sty)
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\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/
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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, 92633 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)
make[3]: [matstat-pdf.bbl] Error 2 (ignored)
Makefile:32: recipe for target 'matstat-pdf.bbl' failed
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 <2015/10/01> patch level 1
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(/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))
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(/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
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nts/map/pdftex/updmap/pdftex.map}]
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\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, 92633 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 <2015/10/01> patch level 1
Babel <3.9m> 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))
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(./matstat.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
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\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
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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, 92633 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
make[3]: [mgth-pdf.aux] Error 1 (ignored)
Makefile:39: recipe for target 'mgth-pdf.aux' failed
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 <2015/10/01> patch level 1
Babel <3.9m> and hyphenation patterns for 2 languages loaded.
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[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]

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\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]

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[]\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]
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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
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</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb></usr/s
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>
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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
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make[3]: [mgth-pdf.bbl] Error 2 (ignored)
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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)
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> \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}
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/fonts/type1/urw/times/utmri8a.pfb>
Output written on packedindex.pdf (7 pages, 159322 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)
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entering extended mode
(./packedindex.tex
LaTeX2e <2015/10/01> patch level 1
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Excluding comment 'comment') (./optionman.sty) (./packedindex.aux)
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*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
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nts/map/pdftex/updmap/pdftex.map}]
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\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]
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[]\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, 158691 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
make[3]: [repfind-pdf.aux] Error 1 (ignored)
Makefile:39: recipe for target 'repfind-pdf.aux' failed
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 <2015/10/01> patch level 1
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(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
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(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (./optionman.sty)
No file repfind.aux.
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*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
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[]\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 .

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[]\OT1/pcr/m/n/10 gt suffixerator -db repfinf-sample.seq -indexname repidx -dna
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[3]
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[]\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.


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[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, 103930 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)
make[3]: [repfind-pdf.bbl] Error 2 (ignored)
Makefile:32: recipe for target 'repfind-pdf.bbl' failed
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 <2015/10/01> patch level 1
Babel <3.9m> 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))
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(/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
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nts/map/pdftex/updmap/pdftex.map}] [2]
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[]\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 .

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[]\OT1/pcr/m/n/10 gt suffixerator -db repfinf-sample.seq -indexname repidx -dna
 -suf -tis -lcp -ssp -pl 
[3]
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[]\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></
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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, 103262 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 <2015/10/01> patch level 1
Babel <3.9m> 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))
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(/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]
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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 .

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[]\OT1/pcr/m/n/10 gt suffixerator -db repfinf-sample.seq -indexname repidx -dna
 -suf -tis -lcp -ssp -pl 
[3]
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[]\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, 103262 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
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LaTeX2e <2015/10/01> patch level 1
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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)
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(/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.
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*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.

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[]\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]
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[]\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
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Output written on tallymer-tmp.pdf (9 pages, 139957 bytes).
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pdflatex tallymer-tmp
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../../bin/gt packedindex mkindex -dna -dir rev -parts 12 -bsize 10 \
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bibtex genomediff
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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}
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(./genomediff.aux)
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(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/
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.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.pfb></
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are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/te
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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, 176522 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 '/«PKGBUILDDIR»/doc/manuals'
make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
   debian/rules override_dh_auto_test
make[1]: Entering directory '/«PKGBUILDDIR»'
bin/gt -test
seed=1189749392
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=1116785473
1328: gt sketch short test (unknown output format)                : ok
1326: gt sketch short test                                        : ok
1327: gt sketch short test (stdin)                                : ok
1329: gt sketch short test (unwriteable PNG file)                 : ok
1331: gt sketch short test (nonexistant style file)               : ok
1333: gt sketch prob 1                                            : ok
1332: gt sketch short test (invalid style file)                   : ok
1330: gt sketch short test (unwriteable PDF file)                 : ok
1334: gt sketch prob 2                                            : ok
1336: gt sketch multiline without parent                          : ok
1335: gt sketch track IDs to style file                           : ok
1337: gt sketch pipe                                              : ok
1340: gt sketch -showrecmaps (normal text size)                   : ok
1339: gt sketch -showrecmaps                                      : ok
1341: gt sketch -showrecmaps (narrow image)                       : ok
1342: gt sketch -showrecmaps (large text size)                    : ok
1343: gt sketch for transcript (neg. coords in ruler)             : ok
1345: sketch_constructed (C)                                      : ok
1346: sketch_parsed (C)                                           : ok
1347: sketch_parsed reverse order (C)                             : ok
1348: sketch_constructed (Lua)                                    : ok
1349: sketch_parsed (Lua)                                         : ok
1338: gt sketch streams <-> file output                           : ok
1344: gt sketch runtime Lua failures                              : ok
make[1]: Leaving directory '/«PKGBUILDDIR»'
 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 '/«PKGBUILDDIR»'
dh_auto_install -- installmanpages useshared=yes \
  64bit=no errorcheck=no prefix=/«PKGBUILDDIR»/debian/tmp/usr
	make -j1 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no installmanpages useshared=yes 64bit=no errorcheck=no prefix=/«PKGBUILDDIR»/debian/tmp/usr
make[2]: Entering directory '/«PKGBUILDDIR»'
[link libgenometools.so]
test -d /«PKGBUILDDIR»/debian/tmp/usr/bin || mkdir -p /«PKGBUILDDIR»/debian/tmp/usr/bin
cp bin/gt /«PKGBUILDDIR»/debian/tmp/usr/bin
strip /«PKGBUILDDIR»/debian/tmp/usr/bin/gt
cp -r gtdata /«PKGBUILDDIR»/debian/tmp/usr/bin
test -d /«PKGBUILDDIR»/debian/tmp/usr/include/genometools/core \
  || mkdir -p /«PKGBUILDDIR»/debian/tmp/usr/include/genometools/core
cp src/core/*_api.h /«PKGBUILDDIR»/debian/tmp/usr/include/genometools/core
test -d /«PKGBUILDDIR»/debian/tmp/usr/include/genometools/extended \
          || mkdir -p /«PKGBUILDDIR»/debian/tmp/usr/include/genometools/extended
cp src/extended/*_api.h /«PKGBUILDDIR»/debian/tmp/usr/include/genometools/extended
test -d /«PKGBUILDDIR»/debian/tmp/usr/include/genometools/annotationsketch \
          || mkdir -p /«PKGBUILDDIR»/debian/tmp/usr/include/genometools/annotationsketch
cp src/annotationsketch/*_api.h \
          /«PKGBUILDDIR»/debian/tmp/usr/include/genometools/annotationsketch
test -d /«PKGBUILDDIR»/debian/tmp/usr/include/genometools/ltr \
          || mkdir -p /«PKGBUILDDIR»/debian/tmp/usr/include/genometools/ltr
cp src/ltr/*_api.h /«PKGBUILDDIR»/debian/tmp/usr/include/genometools/ltr
cp obj/gt_config.h /«PKGBUILDDIR»/debian/tmp/usr/include/genometools
cp src/genometools.h /«PKGBUILDDIR»/debian/tmp/usr/include/genometools
test -d /«PKGBUILDDIR»/debian/tmp/usr/lib || mkdir -p /«PKGBUILDDIR»/debian/tmp/usr/lib
cp lib/libgenometools.a /«PKGBUILDDIR»/debian/tmp/usr/lib
cp lib/libgenometools.so.0 /«PKGBUILDDIR»/debian/tmp/usr/lib
ln -fs /«PKGBUILDDIR»/debian/tmp/usr/lib/libgenometools.so.0 /«PKGBUILDDIR»/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\\"/«PKGBUILDDIR»/debian/tmp/usr/include\\" -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/«PKGBUILDDIR»/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@!"2015-10-21 07:53:41"!' \
  -e 's!@SYSTEM@!Linux!' <src/genometools-config.in \
  >/«PKGBUILDDIR»/debian/tmp/usr/bin/genometools-config
chmod 755 /«PKGBUILDDIR»/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 /«PKGBUILDDIR»/doc/manpages || mkdir -p /«PKGBUILDDIR»/doc/manpages
rm -f /«PKGBUILDDIR»/doc/manpages/*
scripts/create_manpages /tmp/gtmanpages /«PKGBUILDDIR»/doc/manpages
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
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.............................................................................................
test ! -d /«PKGBUILDDIR»/doc/manpages || \
  ((test -d /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1 || mkdir -p /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1) \
    && cp /«PKGBUILDDIR»/doc/manpages/* /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1)
make[2]: Leaving directory '/«PKGBUILDDIR»'
dh_auto_install --sourcedirectory=gtpython \
  --destdir=/«PKGBUILDDIR»/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=/«PKGBUILDDIR»/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/__init__.py -> build/lib.linux-armv7l-2.7/gt
copying gt/dlload.py -> build/lib.linux-armv7l-2.7/gt
copying gt/props.py -> build/lib.linux-armv7l-2.7/gt
creating build/lib.linux-armv7l-2.7/gt/core
copying gt/core/__init__.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/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/error.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/gtstr.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/readmode.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/warning.py -> build/lib.linux-armv7l-2.7/gt/core
creating build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/__init__.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/canvas.py -> 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/custom_track_example.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/feature_index.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/graphics.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/layout.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/rec_map.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/style.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
creating build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/__init__.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/anno_db.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/custom_stream.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/custom_visitor.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/dup_feature_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/feature_index.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_stream.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/genome_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/gff3_out_stream.py -> 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/inter_feature_stream.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/node_visitor.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/region_node.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/sort_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/strand.py -> build/lib.linux-armv7l-2.7/gt/extended
running install_lib
creating /«PKGBUILDDIR»/debian/python-genometools/usr
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
copying build/lib.linux-armv7l-2.7/gt/__init__.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
copying build/lib.linux-armv7l-2.7/gt/dlload.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
copying build/lib.linux-armv7l-2.7/gt/props.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/__init__.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/alphabet.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/array.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/encseq.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/error.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/gtrange.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/gtstr.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/readmode.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/str_array.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/warning.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/__init__.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/block.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/canvas.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/color.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/custom_track.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/custom_track_example.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/diagram.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/feature_index.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/feature_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/graphics.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/image_info.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/layout.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/rec_map.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/style.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/__init__.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/add_introns_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/anno_db.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/comment_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_stream_example.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_visitor.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_visitor_example.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/dup_feature_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/eof_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/feature_index.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/feature_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/feature_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/genome_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/genome_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/gff3_in_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/gff3_out_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/gff3_visitor.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/inter_feature_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/merge_feature_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/meta_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/node_visitor.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/rdb.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/region_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/sequence_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/sort_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/strand.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
running install_egg_info
Writing /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/GenomeTools-0.1.egg-info
make[1]: Leaving directory '/«PKGBUILDDIR»'
   dh_install -a
   dh_installdocs -a
   dh_installchangelogs -a
   dh_installman -a
   dh_python2 -a
W: dh_python2:479: Please add dh-python package to Build-Depends
   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 '/«PKGBUILDDIR»'
dh_strip --dbg-package=genometools-dbg
make[1]: Leaving directory '/«PKGBUILDDIR»'
   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 libdl.so.2 (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 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-lpeg.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-des56.so.0 (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
dpkg-gencontrol: warning: Depends field of package python-genometools: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package python-genometools: unused substitution variable ${python:Provides}
dpkg-gencontrol: warning: package python-genometools: unused substitution variable ${python:Versions}
   dh_md5sums -a
   dh_builddeb -a
dpkg-deb: building package 'libgenometools0' in '../libgenometools0_1.5.7-2_armhf.deb'.
dpkg-deb: building package 'genometools' in '../genometools_1.5.7-2_armhf.deb'.
dpkg-deb: building package 'libgenometools0-dev' in '../libgenometools0-dev_1.5.7-2_armhf.deb'.
dpkg-deb: building package 'genometools-dbg' in '../genometools-dbg_1.5.7-2_armhf.deb'.
dpkg-deb: building package 'python-genometools' in '../python-genometools_1.5.7-2_armhf.deb'.
 dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../genometools_1.5.7-2_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build genometools-1.5.7
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20151021-0821

Finished
────────

I: Built successfully

┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot                                                            │
└──────────────────────────────────────────────────────────────────────────────┘


┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘


genometools_1.5.7-2_armhf.changes:
──────────────────────────────────

Format: 1.8
Date: Sat, 10 Oct 2015 12:04:37 +0000
Source: genometools
Binary: genometools genometools-common libgenometools0 libgenometools0-dev genometools-doc genometools-dbg python-genometools
Architecture: armhf
Version: 1.5.7-2
Distribution: stretch-staging
Urgency: low
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 (1.5.7-2) unstable; urgency=low
 .
   * disable parallel building
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 13cc4551feb50dfcbaa1e7d1bc1cc83a7b560cc0 76826 libgenometools0-dev_1.5.7-2_armhf.deb
 b07e26e7c6d31e62ae32b5bccd51372d228e85b6 1568278 libgenometools0_1.5.7-2_armhf.deb
 56b9e36641cbd34bbedfd40547961b94d5243ae1 30420 python-genometools_1.5.7-2_armhf.deb
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 c296d9e15b0704ddcd5e12d4d63d6422 1684204 science optional genometools_1.5.7-2_armhf.deb
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 30ec64b04092369f0951546b56f8fbcb 30420 python optional python-genometools_1.5.7-2_armhf.deb

┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents                                                             │
└──────────────────────────────────────────────────────────────────────────────┘


genometools-dbg_1.5.7-2_armhf.deb
─────────────────────────────────

 new debian package, version 2.0.
 size 4045870 bytes: control archive=713 bytes.
     623 bytes,    15 lines      control              
     341 bytes,     4 lines      md5sums              
 Package: genometools-dbg
 Source: genometools
 Version: 1.5.7-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 4506
 Depends: genometools (= 1.5.7-2) | libgenometools0 (= 1.5.7-2)
 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: 9c17ec1f0d99a56b33524203cd2a2f8ff0bfc45a

drwxr-xr-x root/root         0 2015-10-21 08:20 ./
drwxr-xr-x root/root         0 2015-10-21 08:20 ./usr/
drwxr-xr-x root/root         0 2015-10-21 08:20 ./usr/lib/
drwxr-xr-x root/root         0 2015-10-21 08:20 ./usr/lib/debug/
drwxr-xr-x root/root         0 2015-10-21 08:20 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2015-10-21 08:20 ./usr/lib/debug/.build-id/9c/
-rw-r--r-- root/root   4589892 2015-10-21 08:20 ./usr/lib/debug/.build-id/9c/17ec1f0d99a56b33524203cd2a2f8ff0bfc45a.debug
drwxr-xr-x root/root         0 2015-10-21 08:19 ./usr/share/
drwxr-xr-x root/root         0 2015-10-21 08:19 ./usr/share/doc/
drwxr-xr-x root/root         0 2015-10-21 08:20 ./usr/share/doc/genometools-dbg/
-rw-r--r-- root/root      2004 2015-10-10 12:05 ./usr/share/doc/genometools-dbg/changelog.Debian.gz
-rw-r--r-- root/root      5926 2015-09-12 10:16 ./usr/share/doc/genometools-dbg/changelog.gz
-rw-r--r-- root/root      5077 2014-12-12 20:59 ./usr/share/doc/genometools-dbg/copyright


genometools_1.5.7-2_armhf.deb
─────────────────────────────

 new debian package, version 2.0.
 size 1684204 bytes: control archive=3532 bytes.
     887 bytes,    16 lines      control              
    7176 bytes,   100 lines      md5sums              
 Package: genometools
 Version: 1.5.7-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 5380
 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 2015-10-21 08:20 ./
drwxr-xr-x root/root         0 2015-10-21 08:19 ./usr/
drwxr-xr-x root/root         0 2015-10-21 08:20 ./usr/bin/
-rwxr-xr-x root/root   5345572 2015-10-21 08:20 ./usr/bin/gt
drwxr-xr-x root/root         0 2015-10-21 08:19 ./usr/share/
drwxr-xr-x root/root         0 2015-10-21 08:19 ./usr/share/doc/
drwxr-xr-x root/root         0 2015-10-21 08:20 ./usr/share/doc/genometools/
-rw-r--r-- root/root       833 2015-09-12 10:16 ./usr/share/doc/genometools/CONTRIBUTORS
-rw-r--r-- root/root      1772 2015-09-12 10:16 ./usr/share/doc/genometools/README
-rw-r--r-- root/root         6 2015-09-12 10:16 ./usr/share/doc/genometools/VERSION
-rw-r--r-- root/root      2004 2015-10-10 12:05 ./usr/share/doc/genometools/changelog.Debian.gz
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libgenometools0-dev_1.5.7-2_armhf.deb
─────────────────────────────────────

 new debian package, version 2.0.
 size 76826 bytes: control archive=5113 bytes.
     672 bytes,    18 lines      control              
   13509 bytes,   160 lines      md5sums              
 Package: libgenometools0-dev
 Source: genometools
 Version: 1.5.7-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 559
 Depends: libgenometools0 (= 1.5.7-2)
 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.

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-rw-r--r-- root/root      6539 2015-10-21 07:53 ./usr/include/genometools/genometools.h
-rw-r--r-- root/root      1964 2015-10-21 07:53 ./usr/include/genometools/gt_config.h
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-rw-r--r-- root/root      3939 2015-10-21 07:53 ./usr/include/genometools/ltr/ltr_refseq_match_stream_api.h
drwxr-xr-x root/root         0 2015-10-21 08:20 ./usr/lib/
lrwxrwxrwx root/root         0 2015-10-21 08:20 ./usr/lib/libgenometools.so -> libgenometools.so.0
drwxr-xr-x root/root         0 2015-10-21 08:19 ./usr/share/
drwxr-xr-x root/root         0 2015-10-21 08:19 ./usr/share/doc/
drwxr-xr-x root/root         0 2015-10-21 08:20 ./usr/share/doc/libgenometools0-dev/
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-rw-r--r-- root/root      5077 2014-12-12 20:59 ./usr/share/doc/libgenometools0-dev/copyright


libgenometools0_1.5.7-2_armhf.deb
─────────────────────────────────

 new debian package, version 2.0.
 size 1568278 bytes: control archive=1489 bytes.
    1006 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: 1.5.7-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 5263
 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.

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drwxr-xr-x root/root         0 2015-10-21 08:19 ./usr/share/doc/
drwxr-xr-x root/root         0 2015-10-21 08:20 ./usr/share/doc/libgenometools0/
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-rw-r--r-- root/root      5077 2014-12-12 20:59 ./usr/share/doc/libgenometools0/copyright


python-genometools_1.5.7-2_armhf.deb
────────────────────────────────────

 new debian package, version 2.0.
 size 30420 bytes: control archive=2524 bytes.
     672 bytes,    15 lines      control              
    5371 bytes,    58 lines      md5sums              
     168 bytes,     9 lines   *  postinst             #!/bin/sh
     273 bytes,    14 lines   *  prerm                #!/bin/sh
 Package: python-genometools
 Source: genometools
 Version: 1.5.7-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 221
 Depends: python (>= 2.7), python (<< 2.8), python-ctypes, libgenometools0
 Section: python
 Priority: optional
 Homepage: http://genometools.org
 Description: Python bindings for genometools
  Partial Python2 bindings for the GenomeTools library. 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.

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drwxr-xr-x root/root         0 2015-10-21 08:19 ./usr/share/doc/
drwxr-xr-x root/root         0 2015-10-21 08:20 ./usr/share/doc/python-genometools/
-rw-r--r-- root/root      2004 2015-10-10 12:05 ./usr/share/doc/python-genometools/changelog.Debian.gz
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-rw-r--r-- root/root      5077 2014-12-12 20:59 ./usr/share/doc/python-genometools/copyright


┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build                                                                   │
└──────────────────────────────────────────────────────────────────────────────┘


┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use

┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

Build Architecture: armhf
Build-Space: 259056
Build-Time: 3973
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 1623
Job: genometools_1.5.7-2
Machine Architecture: armhf
Package: genometools
Package-Time: 5668
Source-Version: 1.5.7-2
Space: 259056
Status: successful
Version: 1.5.7-2
────────────────────────────────────────────────────────────────────────────────
Finished at 20151021-0821
Build needed 01:34:28, 259056k disc space

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