Build log for genometools (1.5.8-1) on armhf

genometools → 1.5.8-1 → armhf → 2016-01-13 06:45:55

sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-02

╔══════════════════════════════════════════════════════════════════════════════╗
║ genometools 1.5.8-1 (armhf)                                13 Jan 2016 05:08 ║
╚══════════════════════════════════════════════════════════════════════════════╝

Package: genometools
Version: 1.5.8-1
Source Version: 1.5.8-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'build/genometools-Xvdw77/genometools-1.5.8' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/genometools-Xvdw77' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-4a6fd27c-4b81-4f61-ae0c-e7ebdcdec1e4' with '«CHROOT»'

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

Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [8608 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [10.6 MB]
Fetched 19.3 MB in 22s (857 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges

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│ Fetch source files                                                           │
└──────────────────────────────────────────────────────────────────────────────┘


Check APT
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Checking available source versions...

Download source files with APT
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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 13.3 MB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main genometools 1.5.8-1 (dsc) [3483 B]
Get:2 http://172.17.0.1/private stretch-staging/main genometools 1.5.8-1 (tar) [13.3 MB]
Get:3 http://172.17.0.1/private stretch-staging/main genometools 1.5.8-1 (diff) [20.9 kB]
Fetched 13.3 MB in 1s (11.1 MB/s)
Download complete and in download only mode

Check architectures
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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-LMWZn6/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/«BUILDDIR»/resolver-LMWZn6/apt_archive ./ InRelease
Ign:1 file:/«BUILDDIR»/resolver-LMWZn6/apt_archive ./ InRelease
Get:2 file:/«BUILDDIR»/resolver-LMWZn6/apt_archive ./ Release [2119 B]
Get:2 file:/«BUILDDIR»/resolver-LMWZn6/apt_archive ./ Release [2119 B]
Get:3 file:/«BUILDDIR»/resolver-LMWZn6/apt_archive ./ Release.gpg [299 B]
Get:3 file:/«BUILDDIR»/resolver-LMWZn6/apt_archive ./ Release.gpg [299 B]
Get:4 file:/«BUILDDIR»/resolver-LMWZn6/apt_archive ./ Sources [188 B]
Get:5 file:/«BUILDDIR»/resolver-LMWZn6/apt_archive ./ Packages [509 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  libapt-pkg4.16 libisl13 libprocps4
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 7 not upgraded.
Need to get 0 B/768 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/«BUILDDIR»/resolver-LMWZn6/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
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(Reading database ... 13660 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
Merged Build-Depends: 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, libsqlite3-dev, libbam-dev, libpango1.0-dev, libtre-dev, texlive-latex-base, texlive-latex-extra, texlive-fonts-extra, latex-xcolor, texlive-fonts-recommended, python, asciidoc, libxml2-utils, xsltproc, ruby, docbook-xsl, faketime, imagemagick
Filtered Build-Depends: 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, libsqlite3-dev, libbam-dev, libpango1.0-dev, libtre-dev, texlive-latex-base, texlive-latex-extra, texlive-fonts-extra, latex-xcolor, texlive-fonts-recommended, python, asciidoc, libxml2-utils, xsltproc, ruby, docbook-xsl, faketime, imagemagick
dpkg-deb: building package 'sbuild-build-depends-genometools-dummy' in '/«BUILDDIR»/resolver-sDG9Nt/apt_archive/sbuild-build-depends-genometools-dummy.deb'.
OK
Get:1 file:/«BUILDDIR»/resolver-sDG9Nt/apt_archive ./ InRelease
Ign:1 file:/«BUILDDIR»/resolver-sDG9Nt/apt_archive ./ InRelease
Get:2 file:/«BUILDDIR»/resolver-sDG9Nt/apt_archive ./ Release [2119 B]
Get:2 file:/«BUILDDIR»/resolver-sDG9Nt/apt_archive ./ Release [2119 B]
Get:3 file:/«BUILDDIR»/resolver-sDG9Nt/apt_archive ./ Release.gpg [299 B]
Get:3 file:/«BUILDDIR»/resolver-sDG9Nt/apt_archive ./ Release.gpg [299 B]
Get:4 file:/«BUILDDIR»/resolver-sDG9Nt/apt_archive ./ Sources [460 B]
Get:5 file:/«BUILDDIR»/resolver-sDG9Nt/apt_archive ./ Packages [718 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  libapt-pkg4.16 libisl13 libprocps4
Use 'apt autoremove' to remove them.
The following additional 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-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-roboto-hinted fonts-sil-gentium fonts-sil-gentium-basic
  fonts-sil-gentiumplus fonts-stix gettext gettext-base gir1.2-freedesktop
  gir1.2-glib-2.0 gir1.2-pango-1.0 groff-base hicolor-icon-theme imagemagick
  imagemagick-6.q16 imagemagick-common intltool-debian libarchive-zip-perl
  libavahi-client3 libavahi-common-data libavahi-common3 libbam-dev libbz2-dev
  libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev
  libcroco3 libcups2 libcupsfilters1 libcupsimage2 libdatrie1 libelf1
  libexpat1 libexpat1-dev libfaketime libffi6 libfftw3-double3
  libfile-stripnondeterminism-perl libfontconfig1 libfontconfig1-dev
  libfreetype6 libfreetype6-dev libgirepository-1.0-1 libglib2.0-0
  libglib2.0-bin libglib2.0-data libglib2.0-dev 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 liblqr-1-0 libltdl7 liblua5.1-0 liblua5.1-0-dev liblzo2-2
  libmagic1 libmagickcore-6.q16-2 libmagickwand-6.q16-2 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 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0
  libpixman-1-dev libpng12-dev libpoppler57 libpotrace0 libptexenc1
  libpthread-stubs0-dev libpython-stdlib libpython2.7-minimal
  libpython2.7-stdlib libreadline-dev libreadline6-dev libruby2.2 libsasl2-2
  libsasl2-modules-db libsm-dev libsm6 libsqlite3-0 libsqlite3-dev libssl1.0.2
  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 ruby-minitest ruby-power-assert ruby-test-unit
  ruby2.2 rubygems-integration sgml-base t1utils tex-common texlive-base
  texlive-binaries texlive-fonts-extra texlive-fonts-recommended
  texlive-latex-base texlive-latex-extra texlive-latex-recommended
  texlive-pictures ttf-adf-accanthis ttf-adf-gillius ttf-adf-universalis ucf
  x11-common x11proto-core-dev x11proto-input-dev x11proto-kb-dev
  x11proto-render-dev x11proto-xext-dev xdg-utils xml-core xorg-sgml-doctools
  xsltproc xtrans-dev zlib1g-dev
Suggested packages:
  source-highlight vim-addon-manager wamerican | wordlist whois vacation
  dh-make dbtoepub docbook-xsl-doc-html | docbook-xsl-doc-pdf
  | docbook-xsl-doc-text | docbook-xsl-doc docbook-xsl-saxon fop libsaxon-java
  libxalan2-java libxslthl-java xalan fontforge gettext-doc autopoint
  libasprintf-dev libgettextpo-dev groff imagemagick-doc autotrace cups-bsd
  | lpr | lprng curl enscript ffmpeg gimp gnuplot grads graphviz hp2xx html2ps
  libwmf-bin mplayer povray radiance sane-utils transfig ufraw-batch
  libcairo2-doc cups-common libfftw3-bin libfftw3-dev libglib2.0-doc
  gnutls-bin krb5-doc krb5-user libice-doc liblcms2-utils
  libmagickcore-6.q16-2-extra libpango1.0-doc readline-doc libsm-doc
  sqlite3-doc tre-agrep libxcb-doc libxext-doc less www-browser
  libmail-box-perl poppler-utils ghostscript fonts-japanese-mincho
  | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic
  fonts-arphic-ukai fonts-arphic-uming fonts-nanum python-doc python-tk
  python2.7-doc binfmt-support ri ruby-dev bundler sgml-base-doc perl-tk gv
  | postscript-viewer xpdf-reader | pdf-viewer cm-super libfile-which-perl
  libspreadsheet-parseexcel-perl python-pygments texlive-pstricks dot2tex
  libtcltk-ruby prerex gvfs-bin
Recommended packages:
  dblatex docbook-utils xmlto docbook-xml fonts-roboto-unhinted curl | wget
  | lynx-cur libmagickcore-6.q16-2-extra ghostscript netpbm bzip2-doc
  shared-mime-info xdg-user-dirs fonts-droid krb5-locales libtool libtool-bin
  gsfonts libsasl2-modules libx11-doc libmail-sendmail-perl libjs-jquery
  lmodern wish texlive-fonts-extra-doc tipa tex-gyre
  texlive-fonts-recommended-doc texlive-latex-base-doc texlive-latex-extra-doc
  texlive-latex-recommended-doc prosper texlive-pictures-doc tk
  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-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-roboto-hinted fonts-sil-gentium fonts-sil-gentium-basic
  fonts-sil-gentiumplus fonts-stix gettext gettext-base gir1.2-freedesktop
  gir1.2-glib-2.0 gir1.2-pango-1.0 groff-base hicolor-icon-theme imagemagick
  imagemagick-6.q16 imagemagick-common intltool-debian libarchive-zip-perl
  libavahi-client3 libavahi-common-data libavahi-common3 libbam-dev libbz2-dev
  libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev
  libcroco3 libcups2 libcupsfilters1 libcupsimage2 libdatrie1 libelf1
  libexpat1 libexpat1-dev libfaketime libffi6 libfftw3-double3
  libfile-stripnondeterminism-perl libfontconfig1 libfontconfig1-dev
  libfreetype6 libfreetype6-dev libgirepository-1.0-1 libglib2.0-0
  libglib2.0-bin libglib2.0-data libglib2.0-dev 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 liblqr-1-0 libltdl7 liblua5.1-0 liblua5.1-0-dev liblzo2-2
  libmagic1 libmagickcore-6.q16-2 libmagickwand-6.q16-2 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 libpoppler57 libpotrace0 libptexenc1
  libpthread-stubs0-dev libpython-stdlib libpython2.7-minimal
  libpython2.7-stdlib libreadline-dev libreadline6-dev libruby2.2 libsasl2-2
  libsasl2-modules-db libsm-dev libsm6 libsqlite3-0 libsqlite3-dev libssl1.0.2
  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 ruby-minitest ruby-power-assert ruby-test-unit
  ruby2.2 rubygems-integration sbuild-build-depends-genometools-dummy
  sgml-base t1utils tex-common texlive-base texlive-binaries
  texlive-fonts-extra texlive-fonts-recommended texlive-latex-base
  texlive-latex-extra texlive-latex-recommended texlive-pictures
  ttf-adf-accanthis ttf-adf-gillius ttf-adf-universalis ucf x11-common
  x11proto-core-dev x11proto-input-dev x11proto-kb-dev x11proto-render-dev
  x11proto-xext-dev xdg-utils xml-core xorg-sgml-doctools xsltproc xtrans-dev
  zlib1g-dev
The following packages will be upgraded:
  libpcre3
1 upgraded, 242 newly installed, 0 to remove and 6 not upgraded.
Need to get 372 MB/372 MB of archives.
After this operation, 1172 MB of additional disk space will be used.
Get:1 file:/«BUILDDIR»/resolver-sDG9Nt/apt_archive ./ sbuild-build-depends-genometools-dummy 0.invalid.0 [982 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf libpcre3 armhf 2:8.38-1 [308 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-5 [1083 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.6 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.11-2 [380 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.11-2 [1081 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-1 [40.0 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.59 [36.4 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.1.0-7 [59.8 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-0 armhf 3.9.2-1 [404 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libssl1.0.2 armhf 1.0.2e-1 [883 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.11-2 [1836 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.11-2 [266 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-1 [19.5 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.11-1 [150 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libfreetype6 armhf 2.6.1-0.1 [411 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf ucf all 3.0031 [68.9 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf fonts-dejavu-core all 2.35-1 [1064 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf fontconfig-config all 2.11.0-6.3 [273 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libfontconfig1 armhf 2.11.0-6.3 [311 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf fontconfig armhf 2.11.0-6.3 [402 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf fonts-lato all 2.0-1 [2684 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf imagemagick-common all 8:6.8.9.9-6 [149 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libfftw3-double3 armhf 3.3.4-2+rpi1 [434 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf liblcms2-2 armhf 2.6-3 [113 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.46.2-3 [2482 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf liblqr-1-0 armhf 0.4.2-2 [20.9 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libltdl7 armhf 2.4.2-1.11 [42.5 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf liblzo2-2 armhf 2.08-1.2 [47.6 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.4.1-2 [103 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libtiff5 armhf 4.0.6-1 [201 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libxdmcp6 armhf 1:1.1.2-1 [25.0 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libxcb1 armhf 1.10-3+b1 [40.6 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libx11-data all 2:1.6.3-1 [128 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libicu55 armhf 55.1-7 [7380 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.3+dfsg1-1 [800 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libmagickcore-6.q16-2 armhf 8:6.8.9.9-6+b1 [1517 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libmagickwand-6.q16-2 armhf 8:6.8.9.9-6+b1 [378 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libpaper1 armhf 1.1.24+nmu4 [21.4 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libpcrecpp0v5 armhf 2:8.38-1 [148 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libtre5 armhf 0.8.0-4 [51.3 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libxrender1 armhf 1:0.9.9-2 [28.9 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libxft2 armhf 2.3.2-1 [48.3 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libyaml-0-2 armhf 0.1.6-3 [41.5 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libzzip-0-13 armhf 0.13.62-3 [51.3 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf lua-md5 armhf 1.2+git+1+8d87fee-1 [14.6 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf lua-md5-dev armhf 1.2+git+1+8d87fee-1 [22.3 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf poppler-data all 0.4.7-7 [1466 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf sgml-base all 1.26+nmu4 [14.6 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libfaketime armhf 0.9.6-4 [24.9 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf faketime armhf 0.9.6-4 [13.1 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libtrio2 armhf 1.16+dfsg1-3 [39.0 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libnettle6 armhf 3.1.1-4 [200 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libhogweed4 armhf 3.1.1-4 [126 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libp11-kit0 armhf 0.23.2-3 [93.3 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libtasn1-6 armhf 4.7-3 [44.4 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libgnutls-deb0-28 armhf 3.3.19-1 [647 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-8 [11.5 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.13.2+dfsg-4+b1 [56.5 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.13.2+dfsg-4+b1 [110 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.13.2+dfsg-4+b1 [261 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.13.2+dfsg-4+b1 [129 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf libidn11 armhf 1.32-3 [110 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf libsasl2-modules-db armhf 2.1.26.dfsg1-14+b1 [65.8 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf libsasl2-2 armhf 2.1.26.dfsg1-14+b1 [97.1 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libldap-2.4-2 armhf 2.4.42+dfsg-2+rpi1+b1 [199 kB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf asciidoc all 8.6.9-3 [830 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf openssl armhf 1.0.2e-1 [662 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf ca-certificates all 20160104 [200 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:82 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:83 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:84 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.18 [248 kB]
Get:85 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.56-2 [94.9 kB]
Get:86 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
Get:87 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.014-1 [7472 B]
Get:88 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20151225 [830 kB]
Get:89 http://172.17.0.1/private stretch-staging/main armhf xml-core all 0.13+nmu2 [24.2 kB]
Get:90 http://172.17.0.1/private stretch-staging/main armhf docbook-xsl all 1.78.1+dfsg-1.1 [1230 kB]
Get:91 http://172.17.0.1/private stretch-staging/main armhf fonts-cabin all 1.5-2 [139 kB]
Get:92 http://172.17.0.1/private stretch-staging/main armhf fonts-comfortaa all 2.003-1 [133 kB]
Get:93 http://172.17.0.1/private stretch-staging/main armhf fonts-crosextra-caladea all 20130214-1 [82.1 kB]
Get:94 http://172.17.0.1/private stretch-staging/main armhf fonts-crosextra-carlito all 20130920-1 [745 kB]
Get:95 http://172.17.0.1/private stretch-staging/main armhf fonts-dejavu-extra all 2.35-1 [1787 kB]
Get:96 http://172.17.0.1/private stretch-staging/main armhf fonts-ebgaramond all 0.015+git20130628-3 [415 kB]
Get:97 http://172.17.0.1/private stretch-staging/main armhf fonts-ebgaramond-extra all 0.015+git20130628-3 [680 kB]
Get:98 http://172.17.0.1/private stretch-staging/main armhf fonts-font-awesome all 4.4.0~dfsg-1 [493 kB]
Get:99 http://172.17.0.1/private stretch-staging/main armhf fonts-freefont-otf all 20120503-4 [3186 kB]
Get:100 http://172.17.0.1/private stretch-staging/main armhf fonts-freefont-ttf all 20120503-4 [4262 kB]
Get:101 http://172.17.0.1/private stretch-staging/main armhf fonts-gfs-artemisia all 1.1-5 [259 kB]
Get:102 http://172.17.0.1/private stretch-staging/main armhf fonts-gfs-complutum all 1.1-6 [41.6 kB]
Get:103 http://172.17.0.1/private stretch-staging/main armhf fonts-gfs-didot all 1.1-6 [278 kB]
Get:104 http://172.17.0.1/private stretch-staging/main armhf fonts-gfs-neohellenic all 1.1-6 [215 kB]
Get:105 http://172.17.0.1/private stretch-staging/main armhf fonts-gfs-olga all 1.1-5 [33.2 kB]
Get:106 http://172.17.0.1/private stretch-staging/main armhf fonts-gfs-solomos all 1.1-5 [40.6 kB]
Get:107 http://172.17.0.1/private stretch-staging/main armhf fonts-inconsolata all 001.010-5 [61.6 kB]
Get:108 http://172.17.0.1/private stretch-staging/main armhf fonts-junicode all 0.7.8-2 [643 kB]
Get:109 http://172.17.0.1/private stretch-staging/main armhf fonts-linuxlibertine all 5.3.0-2 [1713 kB]
Get:110 http://172.17.0.1/private stretch-staging/main armhf fonts-lobster all 2.0-2 [39.5 kB]
Get:111 http://172.17.0.1/private stretch-staging/main armhf fonts-lobstertwo all 2.0-2 [94.0 kB]
Get:112 http://172.17.0.1/private stretch-staging/main armhf fonts-oflb-asana-math all 000.907-6 [245 kB]
Get:113 http://172.17.0.1/private stretch-staging/main armhf fonts-roboto-hinted all 2:0~20151012-1 [2941 kB]
Get:114 http://172.17.0.1/private stretch-staging/main armhf fonts-roboto all 2:0~20151012-1 [5178 B]
Get:115 http://172.17.0.1/private stretch-staging/main armhf fonts-sil-gentium all 20081126:1.03-1 [251 kB]
Get:116 http://172.17.0.1/private stretch-staging/main armhf fonts-sil-gentium-basic all 1.1-7 [382 kB]
Get:117 http://172.17.0.1/private stretch-staging/main armhf fonts-sil-gentiumplus all 5.000-1 [2811 kB]
Get:118 http://172.17.0.1/private stretch-staging/main armhf libgirepository-1.0-1 armhf 1.46.0-3 [83.4 kB]
Get:119 http://172.17.0.1/private stretch-staging/main armhf gir1.2-glib-2.0 armhf 1.46.0-3 [143 kB]
Get:120 http://172.17.0.1/private stretch-staging/main armhf libpixman-1-0 armhf 0.33.4-1 [453 kB]
Get:121 http://172.17.0.1/private stretch-staging/main armhf libxcb-render0 armhf 1.10-3+b1 [16.9 kB]
Get:122 http://172.17.0.1/private stretch-staging/main armhf libxcb-shm0 armhf 1.10-3+b1 [11.4 kB]
Get:123 http://172.17.0.1/private stretch-staging/main armhf libcairo2 armhf 1.14.4-1 [687 kB]
Get:124 http://172.17.0.1/private stretch-staging/main armhf libcairo-gobject2 armhf 1.14.4-1 [331 kB]
Get:125 http://172.17.0.1/private stretch-staging/main armhf gir1.2-freedesktop armhf 1.46.0-3 [22.5 kB]
Get:126 http://172.17.0.1/private stretch-staging/main armhf libthai-data all 0.1.24-1 [163 kB]
Get:127 http://172.17.0.1/private stretch-staging/main armhf libdatrie1 armhf 0.2.10-1 [32.2 kB]
Get:128 http://172.17.0.1/private stretch-staging/main armhf libthai0 armhf 0.1.24-1 [46.2 kB]
Get:129 http://172.17.0.1/private stretch-staging/main armhf libpango-1.0-0 armhf 1.38.1-1 [292 kB]
Get:130 http://172.17.0.1/private stretch-staging/main armhf libgraphite2-3 armhf 1.3.4-2 [61.5 kB]
Get:131 http://172.17.0.1/private stretch-staging/main armhf libharfbuzz0b armhf 1.0.1-1+b1 [501 kB]
Get:132 http://172.17.0.1/private stretch-staging/main armhf libpangoft2-1.0-0 armhf 1.38.1-1 [229 kB]
Get:133 http://172.17.0.1/private stretch-staging/main armhf libpangocairo-1.0-0 armhf 1.38.1-1 [218 kB]
Get:134 http://172.17.0.1/private stretch-staging/main armhf libpangoxft-1.0-0 armhf 1.38.1-1 [214 kB]
Get:135 http://172.17.0.1/private stretch-staging/main armhf gir1.2-pango-1.0 armhf 1.38.1-1 [222 kB]
Get:136 http://172.17.0.1/private stretch-staging/main armhf hicolor-icon-theme all 0.13-1 [8600 B]
Get:137 http://172.17.0.1/private stretch-staging/main armhf imagemagick-6.q16 armhf 8:6.8.9.9-6+b1 [511 kB]
Get:138 http://172.17.0.1/private stretch-staging/main armhf imagemagick armhf 8:6.8.9.9-6+b1 [155 kB]
Get:139 http://172.17.0.1/private stretch-staging/main armhf libavahi-common-data armhf 0.6.32~rc+dfsg-1 [99.5 kB]
Get:140 http://172.17.0.1/private stretch-staging/main armhf libavahi-common3 armhf 0.6.32~rc+dfsg-1 [48.1 kB]
Get:141 http://172.17.0.1/private stretch-staging/main armhf libavahi-client3 armhf 0.6.32~rc+dfsg-1 [50.7 kB]
Get:142 http://172.17.0.1/private stretch-staging/main armhf libbam-dev armhf 0.1.19-2 [109 kB]
Get:143 http://172.17.0.1/private stretch-staging/main armhf libbz2-dev armhf 1.0.6-8 [27.8 kB]
Get:144 http://172.17.0.1/private stretch-staging/main armhf libcairo-script-interpreter2 armhf 1.14.4-1 [360 kB]
Get:145 http://172.17.0.1/private stretch-staging/main armhf libexpat1-dev armhf 2.1.0-7 [114 kB]
Get:146 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:147 http://172.17.0.1/private stretch-staging/main armhf libpng12-dev armhf 1.2.54-1 [233 kB]
Get:148 http://172.17.0.1/private stretch-staging/main armhf libfreetype6-dev armhf 2.6.1-0.1 [941 kB]
Get:149 http://172.17.0.1/private stretch-staging/main armhf pkg-config armhf 0.29-2 [58.8 kB]
Get:150 http://172.17.0.1/private stretch-staging/main armhf libfontconfig1-dev armhf 2.11.0-6.3 [875 kB]
Get:151 http://172.17.0.1/private stretch-staging/main armhf xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:152 http://172.17.0.1/private stretch-staging/main armhf x11proto-core-dev all 7.0.27-1 [729 kB]
Get:153 http://172.17.0.1/private stretch-staging/main armhf libxau-dev armhf 1:1.0.8-1 [23.0 kB]
Get:154 http://172.17.0.1/private stretch-staging/main armhf libxdmcp-dev armhf 1:1.1.2-1 [40.3 kB]
Get:155 http://172.17.0.1/private stretch-staging/main armhf x11proto-input-dev all 2.3.1-1 [157 kB]
Get:156 http://172.17.0.1/private stretch-staging/main armhf x11proto-kb-dev all 1.0.7-1 [233 kB]
Get:157 http://172.17.0.1/private stretch-staging/main armhf xtrans-dev all 1.3.5-1 [100 kB]
Get:158 http://172.17.0.1/private stretch-staging/main armhf libpthread-stubs0-dev armhf 0.3-4 [4042 B]
Get:159 http://172.17.0.1/private stretch-staging/main armhf libxcb1-dev armhf 1.10-3+b1 [79.5 kB]
Get:160 http://172.17.0.1/private stretch-staging/main armhf libx11-dev armhf 2:1.6.3-1 [749 kB]
Get:161 http://172.17.0.1/private stretch-staging/main armhf x11proto-render-dev all 2:0.11.1-2 [20.8 kB]
Get:162 http://172.17.0.1/private stretch-staging/main armhf libxrender-dev armhf 1:0.9.9-2 [36.5 kB]
Get:163 http://172.17.0.1/private stretch-staging/main armhf x11proto-xext-dev all 7.3.0-1 [212 kB]
Get:164 http://172.17.0.1/private stretch-staging/main armhf libxext-dev armhf 2:1.3.3-1 [102 kB]
Get:165 http://172.17.0.1/private stretch-staging/main armhf x11-common all 1:7.7+12 [251 kB]
Get:166 http://172.17.0.1/private stretch-staging/main armhf libice6 armhf 2:1.0.9-1+b1 [51.9 kB]
Get:167 http://172.17.0.1/private stretch-staging/main armhf libsm6 armhf 2:1.2.2-1+b1 [31.2 kB]
Get:168 http://172.17.0.1/private stretch-staging/main armhf libice-dev armhf 2:1.0.9-1+b1 [59.0 kB]
Get:169 http://172.17.0.1/private stretch-staging/main armhf libsm-dev armhf 2:1.2.2-1+b1 [33.5 kB]
Get:170 http://172.17.0.1/private stretch-staging/main armhf libpixman-1-dev armhf 0.33.4-1 [475 kB]
Get:171 http://172.17.0.1/private stretch-staging/main armhf libxcb-render0-dev armhf 1.10-3+b1 [22.3 kB]
Get:172 http://172.17.0.1/private stretch-staging/main armhf libxcb-shm0-dev armhf 1.10-3+b1 [12.8 kB]
Get:173 http://172.17.0.1/private stretch-staging/main armhf libelf1 armhf 0.163-5.1 [162 kB]
Get:174 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-data all 2.46.2-3 [2418 kB]
Get:175 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-bin armhf 2.46.2-3 [1566 kB]
Get:176 http://172.17.0.1/private stretch-staging/main armhf libpcre16-3 armhf 2:8.38-1 [229 kB]
Get:177 http://172.17.0.1/private stretch-staging/main armhf libpcre32-3 armhf 2:8.38-1 [222 kB]
Get:178 http://172.17.0.1/private stretch-staging/main armhf libpcre3-dev armhf 2:8.38-1 [556 kB]
Get:179 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-dev armhf 2.46.2-3 [2715 kB]
Get:180 http://172.17.0.1/private stretch-staging/main armhf libcairo2-dev armhf 1.14.4-1 [810 kB]
Get:181 http://172.17.0.1/private stretch-staging/main armhf libcups2 armhf 2.1.2-1 [266 kB]
Get:182 http://172.17.0.1/private stretch-staging/main armhf libcupsimage2 armhf 2.1.2-1 [116 kB]
Get:183 http://172.17.0.1/private stretch-staging/main armhf libcupsfilters1 armhf 1.4.0-1 [107 kB]
Get:184 http://172.17.0.1/private stretch-staging/main armhf libijs-0.35 armhf 0.35-11 [16.1 kB]
Get:185 http://172.17.0.1/private stretch-staging/main armhf libjbig2dec0 armhf 0.12+20150918-1 [50.7 kB]
Get:186 http://172.17.0.1/private stretch-staging/main armhf libgs9-common all 9.16~dfsg-2 [2983 kB]
Get:187 http://172.17.0.1/private stretch-staging/main armhf libgs9 armhf 9.16~dfsg-2 [1699 kB]
Get:188 http://172.17.0.1/private stretch-staging/main armhf libharfbuzz-icu0 armhf 1.0.1-1+b1 [390 kB]
Get:189 http://172.17.0.1/private stretch-staging/main armhf libharfbuzz-gobject0 armhf 1.0.1-1+b1 [395 kB]
Get:190 http://172.17.0.1/private stretch-staging/main armhf libharfbuzz-dev armhf 1.0.1-1+b1 [548 kB]
Get:191 http://172.17.0.1/private stretch-staging/main armhf libkpathsea6 armhf 2015.20150524.37493-7+b1 [148 kB]
Get:192 http://172.17.0.1/private stretch-staging/main armhf liblua5.1-0 armhf 5.1.5-8 [83.3 kB]
Get:193 http://172.17.0.1/private stretch-staging/main armhf libtinfo-dev armhf 6.0+20151024-2 [65.8 kB]
Get:194 http://172.17.0.1/private stretch-staging/main armhf libreadline6-dev armhf 6.3-8+b3 [105 kB]
Get:195 http://172.17.0.1/private stretch-staging/main armhf libreadline-dev armhf 6.3-8+b3 [958 B]
Get:196 http://172.17.0.1/private stretch-staging/main armhf liblua5.1-0-dev armhf 5.1.5-8 [115 kB]
Get:197 http://172.17.0.1/private stretch-staging/main armhf libxft-dev armhf 2.3.2-1 [59.1 kB]
Get:198 http://172.17.0.1/private stretch-staging/main armhf libpango1.0-dev armhf 1.38.1-1 [450 kB]
Get:199 http://172.17.0.1/private stretch-staging/main armhf libpaper-utils armhf 1.1.24+nmu4 [17.2 kB]
Get:200 http://172.17.0.1/private stretch-staging/main armhf libopenjpeg5 armhf 1:1.5.2-3.1+b4 [93.0 kB]
Get:201 http://172.17.0.1/private stretch-staging/main armhf libpoppler57 armhf 0.38.0-2 [1117 kB]
Get:202 http://172.17.0.1/private stretch-staging/main armhf libpotrace0 armhf 1.13-2 [22.8 kB]
Get:203 http://172.17.0.1/private stretch-staging/main armhf libptexenc1 armhf 2015.20150524.37493-7+b1 [53.8 kB]
Get:204 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-dev armhf 3.9.2-1 [525 kB]
Get:205 http://172.17.0.1/private stretch-staging/main armhf libsynctex1 armhf 2015.20150524.37493-7+b1 [56.4 kB]
Get:206 http://172.17.0.1/private stretch-staging/main armhf libtexlua52 armhf 2015.20150524.37493-7+b1 [84.1 kB]
Get:207 http://172.17.0.1/private stretch-staging/main armhf libtexluajit2 armhf 2015.20150524.37493-7+b1 [186 kB]
Get:208 http://172.17.0.1/private stretch-staging/main armhf libtre-dev armhf 0.8.0-4 [27.1 kB]
Get:209 http://172.17.0.1/private stretch-staging/main armhf libxt6 armhf 1:1.1.5-1 [155 kB]
Get:210 http://172.17.0.1/private stretch-staging/main armhf libxmu6 armhf 2:1.1.2-2 [52.0 kB]
Get:211 http://172.17.0.1/private stretch-staging/main armhf libxpm4 armhf 1:3.5.11-1+b1 [42.4 kB]
Get:212 http://172.17.0.1/private stretch-staging/main armhf libxaw7 armhf 2:1.0.13-1 [164 kB]
Get:213 http://172.17.0.1/private stretch-staging/main armhf libxi6 armhf 2:1.7.5-1 [75.4 kB]
Get:214 http://172.17.0.1/private stretch-staging/main armhf libxml2-utils armhf 2.9.3+dfsg1-1 [101 kB]
Get:215 http://172.17.0.1/private stretch-staging/main armhf libxslt1.1 armhf 1.1.28-2.1 [211 kB]
Get:216 http://172.17.0.1/private stretch-staging/main armhf lua-filesystem armhf 1.6.3-1 [9984 B]
Get:217 http://172.17.0.1/private stretch-staging/main armhf lua-filesystem-dev armhf 1.6.3-1 [24.4 kB]
Get:218 http://172.17.0.1/private stretch-staging/main armhf lua-lpeg armhf 0.12.2-1 [25.4 kB]
Get:219 http://172.17.0.1/private stretch-staging/main armhf lua-lpeg-dev armhf 0.12.2-1 [44.3 kB]
Get:220 http://172.17.0.1/private stretch-staging/main armhf tex-common all 6.04 [564 kB]
Get:221 http://172.17.0.1/private stretch-staging/main armhf preview-latex-style all 11.87-3+deb8u1 [318 kB]
Get:222 http://172.17.0.1/private stretch-staging/main armhf rubygems-integration all 1.10 [4882 B]
Get:223 http://172.17.0.1/private stretch-staging/main armhf ruby-power-assert all 0.2.6-1 [7384 B]
Get:224 http://172.17.0.1/private stretch-staging/main armhf ruby-test-unit all 3.1.5-1 [68.6 kB]
Get:225 http://172.17.0.1/private stretch-staging/main armhf ruby-minitest all 5.8.3-1 [49.9 kB]
Get:226 http://172.17.0.1/private stretch-staging/main armhf libruby2.2 armhf 2.2.3-2 [2842 kB]
Get:227 http://172.17.0.1/private stretch-staging/main armhf ruby2.2 armhf 2.2.3-2 [218 kB]
Get:228 http://172.17.0.1/private stretch-staging/main armhf ruby all 1:2.2.4 [9798 B]
Get:229 http://172.17.0.1/private stretch-staging/main armhf t1utils armhf 1.39-2 [52.7 kB]
Get:230 http://172.17.0.1/private stretch-staging/main armhf texlive-binaries armhf 2015.20150524.37493-7+b1 [6842 kB]
Get:231 http://172.17.0.1/private stretch-staging/main armhf xdg-utils all 1.1.1-1 [71.1 kB]
Get:232 http://172.17.0.1/private stretch-staging/main armhf texlive-base all 2015.20151225-1 [18.1 MB]
Get:233 http://172.17.0.1/private stretch-staging/main armhf ttf-adf-accanthis all 0.20090423-2 [401 kB]
Get:234 http://172.17.0.1/private stretch-staging/main armhf ttf-adf-gillius all 0.20090423-2 [400 kB]
Get:235 http://172.17.0.1/private stretch-staging/main armhf ttf-adf-universalis all 0.20090423-2 [221 kB]
Get:236 http://172.17.0.1/private stretch-staging/main armhf fonts-stix all 1.1.1-4 [590 kB]
Get:237 http://172.17.0.1/private stretch-staging/main armhf texlive-fonts-extra all 2015.20151225-2 [222 MB]
Get:238 http://172.17.0.1/private stretch-staging/main armhf texlive-fonts-recommended all 2015.20151225-1 [5685 kB]
Get:239 http://172.17.0.1/private stretch-staging/main armhf texlive-latex-base all 2015.20151225-1 [897 kB]
Get:240 http://172.17.0.1/private stretch-staging/main armhf texlive-latex-recommended all 2015.20151225-1 [8436 kB]
Get:241 http://172.17.0.1/private stretch-staging/main armhf texlive-pictures all 2015.20151225-1 [3154 kB]
Get:242 http://172.17.0.1/private stretch-staging/main armhf texlive-latex-extra all 2015.20151225-2 [10.9 MB]
Get:243 http://172.17.0.1/private stretch-staging/main armhf xsltproc armhf 1.1.28-2.1 [118 kB]
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Processing triggers for libc-bin (2.21-6) ...
Processing triggers for systemd (228-2) ...
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Setting up bsdmainutils (9.0.6) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up libffi6:armhf (3.2.1-4) ...
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Setting up libssl1.0.2:armhf (1.0.2e-1) ...
Setting up libpython2.7-stdlib:armhf (2.7.11-2) ...
Setting up python2.7 (2.7.11-2) ...
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Setting up python (2.7.11-1) ...
Setting up libfreetype6:armhf (2.6.1-0.1) ...
Setting up ucf (3.0031) ...
Setting up fonts-dejavu-core (2.35-1) ...
Setting up fontconfig-config (2.11.0-6.3) ...
Setting up libfontconfig1:armhf (2.11.0-6.3) ...
Setting up fontconfig (2.11.0-6.3) ...
Regenerating fonts cache... done.
Setting up fonts-lato (2.0-1) ...
Setting up imagemagick-common (8:6.8.9.9-6) ...
Setting up libfftw3-double3:armhf (3.3.4-2+rpi1) ...
Setting up libjbig0:armhf (2.1-3.1) ...
Setting up liblcms2-2:armhf (2.6-3) ...
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No schema files found: doing nothing.
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Setting up liblzo2-2:armhf (2.08-1.2) ...
Setting up libjpeg62-turbo:armhf (1:1.4.1-2) ...
Setting up libtiff5:armhf (4.0.6-1) ...
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Setting up libxcb1:armhf (1.10-3+b1) ...
Setting up libx11-data (2:1.6.3-1) ...
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Setting up libxext6:armhf (2:1.3.3-1) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1) ...
Setting up libmagickcore-6.q16-2:armhf (8:6.8.9.9-6+b1) ...
Setting up libmagickwand-6.q16-2:armhf (8:6.8.9.9-6+b1) ...
Setting up libpaper1:armhf (1.1.24+nmu4) ...

Creating config file /etc/papersize with new version
Setting up libpcrecpp0v5:armhf (2:8.38-1) ...
Setting up libtre5:armhf (0.8.0-4) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libxrender1:armhf (1:0.9.9-2) ...
Setting up libxft2:armhf (2.3.2-1) ...
Setting up libyaml-0-2:armhf (0.1.6-3) ...
Setting up libzzip-0-13:armhf (0.13.62-3) ...
Setting up lua-md5:armhf (1.2+git+1+8d87fee-1) ...
Setting up lua-md5-dev:armhf (1.2+git+1+8d87fee-1) ...
Setting up poppler-data (0.4.7-7) ...
Setting up sgml-base (1.26+nmu4) ...
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Setting up faketime (0.9.6-4) ...
Setting up libtrio2:armhf (1.16+dfsg1-3) ...
Setting up libmagic1:armhf (1:5.25-2) ...
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Setting up libnettle6:armhf (3.1.1-4) ...
Setting up libhogweed4:armhf (3.1.1-4) ...
Setting up libp11-kit0:armhf (0.23.2-3) ...
Setting up libtasn1-6:armhf (4.7-3) ...
Setting up libgnutls-deb0-28:armhf (3.3.19-1) ...
Setting up libkeyutils1:armhf (1.5.9-8) ...
Setting up libkrb5support0:armhf (1.13.2+dfsg-4+b1) ...
Setting up libk5crypto3:armhf (1.13.2+dfsg-4+b1) ...
Setting up libkrb5-3:armhf (1.13.2+dfsg-4+b1) ...
Setting up libgssapi-krb5-2:armhf (1.13.2+dfsg-4+b1) ...
Setting up libidn11:armhf (1.32-3) ...
Setting up libsasl2-modules-db:armhf (2.1.26.dfsg1-14+b1) ...
Setting up libsasl2-2:armhf (2.1.26.dfsg1-14+b1) ...
Setting up libldap-2.4-2:armhf (2.4.42+dfsg-2+rpi1+b1) ...
Setting up asciidoc (8.6.9-3) ...
Setting up openssl (1.0.2e-1) ...
Setting up ca-certificates (20160104) ...
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.18) ...
Setting up libarchive-zip-perl (1.56-2) ...
Setting up libfile-stripnondeterminism-perl (0.014-1) ...
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) ...
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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) ...
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Setting up fonts-lobstertwo (2.0-2) ...
Setting up fonts-oflb-asana-math (000.907-6) ...
Setting up fonts-roboto-hinted (2:0~20151012-1) ...
Setting up fonts-roboto (2:0~20151012-1) ...
Setting up fonts-sil-gentium (20081126:1.03-1) ...
Setting up fonts-sil-gentium-basic (1.1-7) ...
Setting up fonts-sil-gentiumplus (5.000-1) ...
Setting up libgirepository-1.0-1:armhf (1.46.0-3) ...
Setting up gir1.2-glib-2.0:armhf (1.46.0-3) ...
Setting up libpixman-1-0:armhf (0.33.4-1) ...
Setting up libxcb-render0:armhf (1.10-3+b1) ...
Setting up libxcb-shm0:armhf (1.10-3+b1) ...
Setting up libcairo2:armhf (1.14.4-1) ...
Setting up libcairo-gobject2:armhf (1.14.4-1) ...
Setting up gir1.2-freedesktop:armhf (1.46.0-3) ...
Setting up libthai-data (0.1.24-1) ...
Setting up libdatrie1:armhf (0.2.10-1) ...
Setting up libthai0:armhf (0.1.24-1) ...
Setting up libpango-1.0-0:armhf (1.38.1-1) ...
Setting up libgraphite2-3:armhf (1.3.4-2) ...
Setting up libharfbuzz0b:armhf (1.0.1-1+b1) ...
Setting up libpangoft2-1.0-0:armhf (1.38.1-1) ...
Setting up libpangocairo-1.0-0:armhf (1.38.1-1) ...
Setting up libpangoxft-1.0-0:armhf (1.38.1-1) ...
Setting up gir1.2-pango-1.0:armhf (1.38.1-1) ...
Setting up hicolor-icon-theme (0.13-1) ...
Setting up imagemagick-6.q16 (8:6.8.9.9-6+b1) ...
Setting up imagemagick (8:6.8.9.9-6+b1) ...
update-alternatives: using /usr/bin/compare-im6 to provide /usr/bin/compare (compare) in auto mode
update-alternatives: using /usr/bin/animate-im6 to provide /usr/bin/animate (animate) in auto mode
update-alternatives: using /usr/bin/convert-im6 to provide /usr/bin/convert (convert) in auto mode
update-alternatives: using /usr/bin/composite-im6 to provide /usr/bin/composite (composite) in auto mode
update-alternatives: using /usr/bin/conjure-im6 to provide /usr/bin/conjure (conjure) in auto mode
update-alternatives: using /usr/bin/import-im6 to provide /usr/bin/import (import) in auto mode
update-alternatives: using /usr/bin/identify-im6 to provide /usr/bin/identify (identify) in auto mode
update-alternatives: using /usr/bin/stream-im6 to provide /usr/bin/stream (stream) in auto mode
update-alternatives: using /usr/bin/display-im6 to provide /usr/bin/display (display) in auto mode
update-alternatives: using /usr/bin/montage-im6 to provide /usr/bin/montage (montage) in auto mode
update-alternatives: using /usr/bin/mogrify-im6 to provide /usr/bin/mogrify (mogrify) in auto mode
Setting up libavahi-common-data:armhf (0.6.32~rc+dfsg-1) ...
Setting up libavahi-common3:armhf (0.6.32~rc+dfsg-1) ...
Setting up libavahi-client3:armhf (0.6.32~rc+dfsg-1) ...
Setting up libbam-dev (0.1.19-2) ...
Setting up libbz2-dev:armhf (1.0.6-8) ...
Setting up libcairo-script-interpreter2:armhf (1.14.4-1) ...
Setting up libexpat1-dev:armhf (2.1.0-7) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up libpng12-dev:armhf (1.2.54-1) ...
Setting up libfreetype6-dev (2.6.1-0.1) ...
Setting up pkg-config (0.29-2) ...
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 (1.0.7-1) ...
Setting up xtrans-dev (1.3.5-1) ...
Setting up libpthread-stubs0-dev:armhf (0.3-4) ...
Setting up libxcb1-dev:armhf (1.10-3+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 (1:0.9.9-2) ...
Setting up x11proto-xext-dev (7.3.0-1) ...
Setting up libxext-dev:armhf (2:1.3.3-1) ...
Setting up x11-common (1:7.7+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 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 (0.33.4-1) ...
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 (2.46.2-3) ...
Setting up libglib2.0-bin (2.46.2-3) ...
Setting up libpcre16-3:armhf (2:8.38-1) ...
Setting up libpcre32-3:armhf (2:8.38-1) ...
Setting up libpcre3-dev:armhf (2:8.38-1) ...
Setting up libglib2.0-dev (2.46.2-3) ...
Setting up libcairo2-dev (1.14.4-1) ...
Setting up libcups2:armhf (2.1.2-1) ...
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:armhf (2015.20150524.37493-7+b1) ...
Setting up liblua5.1-0:armhf (5.1.5-8) ...
Setting up libtinfo-dev:armhf (6.0+20151024-2) ...
Setting up libreadline6-dev:armhf (6.3-8+b3) ...
Setting up libreadline-dev:armhf (6.3-8+b3) ...
Setting up liblua5.1-0-dev:armhf (5.1.5-8) ...
Setting up libxft-dev (2.3.2-1) ...
Setting up libpango1.0-dev (1.38.1-1) ...
Setting up libpaper-utils (1.1.24+nmu4) ...
Setting up libopenjpeg5:armhf (1:1.5.2-3.1+b4) ...
Setting up libpoppler57:armhf (0.38.0-2) ...
Setting up libpotrace0 (1.13-2) ...
Setting up libptexenc1:armhf (2015.20150524.37493-7+b1) ...
Setting up libsqlite3-dev:armhf (3.9.2-1) ...
Setting up libsynctex1:armhf (2015.20150524.37493-7+b1) ...
Setting up libtexlua52:armhf (2015.20150524.37493-7+b1) ...
Setting up libtexluajit2:armhf (2015.20150524.37493-7+b1) ...
Setting up libtre-dev (0.8.0-4) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up libxmu6:armhf (2:1.1.2-2) ...
Setting up libxpm4:armhf (1:3.5.11-1+b1) ...
Setting up libxaw7:armhf (2:1.0.13-1) ...
Setting up libxi6:armhf (2:1.7.5-1) ...
Setting up libxml2-utils (2.9.3+dfsg1-1) ...
Setting up libxslt1.1:armhf (1.1.28-2.1) ...
Setting up lua-filesystem:armhf (1.6.3-1) ...
Setting up lua-filesystem-dev:armhf (1.6.3-1) ...
Setting up lua-lpeg:armhf (0.12.2-1) ...
Setting up lua-lpeg-dev:armhf (0.12.2-1) ...
Setting up tex-common (6.04) ...
update-language: texlive-base not installed and configured, doing nothing!
Setting up preview-latex-style (11.87-3+deb8u1) ...
update-language: texlive-base not installed and configured, doing nothing!
Regenerating '/var/lib/texmf/fmtutil.cnf-DEBIAN'... done.
Regenerating '/var/lib/texmf/fmtutil.cnf-TEXLIVEDIST'... done.
update-fmtutil has updated the following file(s):
	/var/lib/texmf/fmtutil.cnf-DEBIAN
	/var/lib/texmf/fmtutil.cnf-TEXLIVEDIST
If you want to activate the changes in the above file(s),
you should run fmtutil-sys or fmtutil.
Setting up rubygems-integration (1.10) ...
Setting up t1utils (1.39-2) ...
Setting up xdg-utils (1.1.1-1) ...
Setting up ttf-adf-accanthis (0.20090423-2) ...
Setting up ttf-adf-gillius (0.20090423-2) ...
Setting up ttf-adf-universalis (0.20090423-2) ...
Setting up fonts-stix (1.1.1-4) ...
Setting up xsltproc (1.1.28-2.1) ...
Processing triggers for sgml-base (1.26+nmu4) ...
Setting up docbook-xsl (1.78.1+dfsg-1.1) ...
Setting up ruby2.2 (2.2.3-2) ...
Setting up ruby (1:2.2.4) ...
Setting up dh-strip-nondeterminism (0.014-1) ...
Setting up debhelper (9.20151225) ...
Setting up libcupsimage2:armhf (2.1.2-1) ...
Setting up libcupsfilters1:armhf (1.4.0-1) ...
Setting up libgs9 (9.16~dfsg-2) ...
Setting up ruby-power-assert (0.2.6-1) ...
Setting up ruby-minitest (5.8.3-1) ...
Setting up ruby-test-unit (3.1.5-1) ...
Setting up texlive-binaries (2015.20150524.37493-7+b1) ...
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
Setting up libruby2.2:armhf (2.2.3-2) ...
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 (2015.20151225-1) ...
/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 (2015.20151225-1) ...
Setting up texlive-latex-base (2015.20151225-1) ...
Setting up texlive-fonts-extra (2015.20151225-2) ...
Processing triggers for tex-common (6.04) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Building format(s) --all.
	This may take some time... done.
Setting up texlive-latex-recommended (2015.20151225-1) ...
Setting up texlive-pictures (2015.20151225-1) ...
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 (2015.20151225-2) ...
Processing triggers for tex-common (6.04) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Setting up sbuild-build-depends-genometools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.21-6) ...
Processing triggers for ca-certificates (20160104) ...
Updating certificates in /etc/ssl/certs...
173 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for systemd (228-2) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25.90.20160101-1 dpkg-dev_1.18.4 g++-5_5.3.1-5+rpi1 gcc-5_5.3.1-5+rpi1 libc6-dev_2.21-6 libstdc++-4.9-dev_4.9.3-10 libstdc++-5-dev_5.3.1-5+rpi1 libstdc++6_5.3.1-5+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.1.10 asciidoc_8.6.9-3 base-files_9.4+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.25.90.20160101-1 bsdmainutils_9.0.6 bsdutils_1:2.27.1-1 build-essential_11.7 bzip2_1.0.6-8 ca-certificates_20160104 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-5+rpi1 dash_0.5.7-4 debconf_1.5.58 debfoster_2.7-2 debhelper_9.20151225 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-3 dmsetup_2:1.02.114-1 docbook-xsl_1.78.1+dfsg-1.1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 faketime_0.9.6-4 file_1:5.25-2 findutils_4.4.2-10 fontconfig_2.11.0-6.3 fontconfig-config_2.11.0-6.3 fonts-cabin_1.5-2 fonts-comfortaa_2.003-1 fonts-crosextra-caladea_20130214-1 fonts-crosextra-carlito_20130920-1 fonts-dejavu-core_2.35-1 fonts-dejavu-extra_2.35-1 fonts-ebgaramond_0.015+git20130628-3 fonts-ebgaramond-extra_0.015+git20130628-3 fonts-font-awesome_4.4.0~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_2:0~20151012-1 fonts-roboto-hinted_2:0~20151012-1 fonts-sil-gentium_20081126:1.03-1 fonts-sil-gentium-basic_1.1-7 fonts-sil-gentiumplus_5.000-1 fonts-stix_1.1.1-4 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-5+rpi1 gcc_4:5.3.1-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-3 gcc-4.9-base_4.9.3-10 gcc-5_5.3.1-5+rpi1 gcc-5-base_5.3.1-5+rpi1 gettext_0.19.7-2 gettext-base_0.19.7-2 gir1.2-freedesktop_1.46.0-3 gir1.2-glib-2.0_1.46.0-3 gir1.2-pango-1.0_1.38.1-1 gnupg_1.4.20-1 gpgv_1.4.20-1 grep_2.22-1 groff-base_1.22.3-5 gzip_1.6-4 hicolor-icon-theme_0.13-1 hostname_3.16 imagemagick_8:6.8.9.9-6+b1 imagemagick-6.q16_8:6.8.9.9-6+b1 imagemagick-common_8:6.8.9.9-6 init_1.24 init-system-helpers_1.24 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-4+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.10-2+b3 libapt-pkg4.12_1.0.9.10 libapt-pkg4.16_1.0.10.2 libapt-pkg5.0_1.1.10 libarchive-zip-perl_1.56-2 libasan1_4.9.3-10 libasan2_5.3.1-5+rpi1 libatomic1_5.3.1-5+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libavahi-client3_0.6.32~rc+dfsg-1 libavahi-common-data_0.6.32~rc+dfsg-1 libavahi-common3_0.6.32~rc+dfsg-1 libbam-dev_0.1.19-2 libblkid1_2.27.1-1 libbz2-1.0_1.0.6-8 libbz2-dev_1.0.6-8 libc-bin_2.21-6 libc-dev-bin_2.21-6 libc6_2.21-6 libc6-dev_2.21-6 libcairo-gobject2_1.14.4-1 libcairo-script-interpreter2_1.14.4-1 libcairo2_1.14.4-1 libcairo2-dev_1.14.4-1 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-5+rpi1 libcomerr2_1.42.13-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.6.6-5 libcups2_2.1.2-1 libcupsfilters1_1.4.0-1 libcupsimage2_2.1.2-1 libdatrie1_0.2.10-1 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1 libdebconfclient0_0.201 libdevmapper1.02.1_2:1.02.114-1 libdpkg-perl_1.18.4 libdrm2_2.4.65-3 libelf1_0.163-5.1 libexpat1_2.1.0-7 libexpat1-dev_2.1.0-7 libfakeroot_1.20.2-1 libfaketime_0.9.6-4 libfdisk1_2.27.1-1 libffi6_3.2.1-4 libfftw3-double3_3.3.4-2+rpi1 libfile-stripnondeterminism-perl_0.014-1 libfontconfig1_2.11.0-6.3 libfontconfig1-dev_2.11.0-6.3 libfreetype6_2.6.1-0.1 libfreetype6-dev_2.6.1-0.1 libgc1c2_1:7.4.2-7.3 libgcc-4.9-dev_4.9.3-10 libgcc-5-dev_5.3.1-5+rpi1 libgcc1_1:5.3.1-5+rpi1 libgcrypt20_1.6.4-4 libgdbm3_1.8.3-13.1 libgirepository-1.0-1_1.46.0-3 libglib2.0-0_2.46.2-3 libglib2.0-bin_2.46.2-3 libglib2.0-data_2.46.2-3 libglib2.0-dev_2.46.2-3 libgmp10_2:6.1.0+dfsg-2 libgnutls-deb0-28_3.3.19-1 libgomp1_5.3.1-5+rpi1 libgpg-error0_1.21-1 libgraphite2-3_1.3.4-2 libgs9_9.16~dfsg-2 libgs9-common_9.16~dfsg-2 libgssapi-krb5-2_1.13.2+dfsg-4+b1 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_55.1-7 libidn11_1.32-3 libijs-0.35_0.35-11 libisl13_0.14-2 libisl15_0.15-3 libjbig0_2.1-3.1 libjbig2dec0_0.12+20150918-1 libjpeg62-turbo_1:1.4.1-2 libk5crypto3_1.13.2+dfsg-4+b1 libkeyutils1_1.5.9-8 libklibc_2.0.4-4+rpi1 libkmod2_21-1 libkpathsea6_2015.20150524.37493-7+b1 libkrb5-3_1.13.2+dfsg-4+b1 libkrb5support0_1.13.2+dfsg-4+b1 liblcms2-2_2.6-3 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b1 liblqr-1-0_0.4.2-2 libltdl7_2.4.2-1.11 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 libmagickcore-6.q16-2_8:6.8.9.9-6+b1 libmagickwand-6.q16-2_8:6.8.9.9-6+b1 libmount1_2.27.1-1 libmpc3_1.0.3-1 libmpfr4_3.1.3-2 libncurses5_6.0+20151024-2 libncursesw5_6.0+20151024-2 libnettle6_3.1.1-4 libopenjpeg5_1:1.5.2-3.1+b4 libp11-kit0_0.23.2-3 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_1.38.1-1 libpango1.0-dev_1.38.1-1 libpangocairo-1.0-0_1.38.1-1 libpangoft2-1.0-0_1.38.1-1 libpangoxft-1.0-0_1.38.1-1 libpaper-utils_1.1.24+nmu4 libpaper1_1.1.24+nmu4 libpcre16-3_2:8.38-1 libpcre3_2:8.38-1 libpcre3-dev_2:8.38-1 libpcre32-3_2:8.38-1 libpcrecpp0v5_2:8.38-1 libperl5.22_5.22.1-3 libpipeline1_1.4.1-2 libpixman-1-0_0.33.4-1 libpixman-1-dev_0.33.4-1 libpng12-0_1.2.54-1 libpng12-dev_1.2.54-1 libpoppler57_0.38.0-2 libpotrace0_1.13-2 libprocps3_2:3.3.9-9 libprocps4_2:3.3.10-2 libprocps5_2:3.3.11-3 libptexenc1_2015.20150524.37493-7+b1 libpthread-stubs0-dev_0.3-4 libpython-stdlib_2.7.11-1 libpython2.7-minimal_2.7.11-2 libpython2.7-stdlib_2.7.11-2 libreadline-dev_6.3-8+b3 libreadline6_6.3-8+b3 libreadline6-dev_6.3-8+b3 libruby2.2_2.2.3-2 libsasl2-2_2.1.26.dfsg1-14+b1 libsasl2-modules-db_2.1.26.dfsg1-14+b1 libseccomp2_2.2.3-2 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libslang2_2.3.0-2+b1 libsm-dev_2:1.2.2-1+b1 libsm6_2:1.2.2-1+b1 libsmartcols1_2.27.1-1 libsqlite3-0_3.9.2-1 libsqlite3-dev_3.9.2-1 libss2_1.42.13-1 libssl1.0.2_1.0.2e-1 libstdc++-4.9-dev_4.9.3-10 libstdc++-5-dev_5.3.1-5+rpi1 libstdc++6_5.3.1-5+rpi1 libsynctex1_2015.20150524.37493-7+b1 libsystemd0_228-2 libtasn1-6_4.7-3 libtexlua52_2015.20150524.37493-7+b1 libtexluajit2_2015.20150524.37493-7+b1 libthai-data_0.1.24-1 libthai0_0.1.24-1 libtiff5_4.0.6-1 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20151024-2 libtinfo5_6.0+20151024-2 libtre-dev_0.8.0-4 libtre5_0.8.0-4 libtrio2_1.16+dfsg1-3 libubsan0_5.3.1-5+rpi1 libudev1_228-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1 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_2.9.3+dfsg1-1 libxml2-utils_2.9.3+dfsg1-1 libxmu6_2:1.1.2-2 libxpm4_1:3.5.11-1+b1 libxrender-dev_1:0.9.9-2 libxrender1_1:0.9.9-2 libxslt1.1_1.1.28-2.1 libxt6_1:1.1.5-1 libyaml-0-2_0.1.6-3 libzzip-0-13_0.13.62-3 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_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_2.7.5-1 manpages_3.74-1 mawk_1.3.3-17 mime-support_3.59 mount_2.27.1-1 multiarch-support_2.21-6 nano_2.4.2-1 ncurses-base_6.0+20151024-2 ncurses-bin_6.0+20151024-2 openssl_1.0.2e-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-3 perl-base_5.22.1-3 perl-modules-5.22_5.22.1-3 pkg-config_0.29-2 po-debconf_1.0.18 poppler-data_0.4.7-7 preview-latex-style_11.87-3+deb8u1 procps_2:3.3.11-3 python_2.7.11-1 python-minimal_2.7.11-1 python2.7_2.7.11-2 python2.7-minimal_2.7.11-2 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 ruby_1:2.2.4 ruby-minitest_5.8.3-1 ruby-power-assert_0.2.6-1 ruby-test-unit_3.1.5-1 ruby2.2_2.2.3-2 rubygems-integration_1.10 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-genometools-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 sgml-base_1.26+nmu4 startpar_0.59-3 systemd_228-2 systemd-sysv_228-2 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 t1utils_1.39-2 tar_1.28-2.1 tex-common_6.04 texlive-base_2015.20151225-1 texlive-binaries_2015.20150524.37493-7+b1 texlive-fonts-extra_2015.20151225-2 texlive-fonts-recommended_2015.20151225-1 texlive-latex-base_2015.20151225-1 texlive-latex-extra_2015.20151225-2 texlive-latex-recommended_2015.20151225-1 texlive-pictures_2015.20151225-1 ttf-adf-accanthis_0.20090423-2 ttf-adf-gillius_0.20090423-2 ttf-adf-universalis_0.20090423-2 tzdata_2015g-1 ucf_3.0031 udev_228-2 util-linux_2.27.1-1 x11-common_1:7.7+12 x11proto-core-dev_7.0.27-1 x11proto-input-dev_2.3.1-1 x11proto-kb-dev_1.0.7-1 x11proto-render-dev_2:0.11.1-2 x11proto-xext-dev_7.3.0-1 xdg-utils_1.1.1-1 xml-core_0.13+nmu2 xorg-sgml-doctools_1:1.11-1 xsltproc_1.1.28-2.1 xtrans-dev_1.3.5-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1

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


Unpack source
─────────────

gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Thu Jan  7 23:03:53 2016 UTC using RSA key ID 04A3610B
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./genometools_1.5.8-1.dsc
dpkg-source: info: extracting genometools in genometools-1.5.8
dpkg-source: info: unpacking genometools_1.5.8.orig.tar.gz
dpkg-source: info: unpacking genometools_1.5.8-1.debian.tar.xz
dpkg-source: info: applying spelling
dpkg-source: info: applying remove_png_timestamps
dpkg-source: info: applying adding_soname
dpkg-source: info: applying libbam-fix
dpkg-source: info: applying remove-gitignores
dpkg-source: info: applying fix-exports
dpkg-source: info: applying split-manuals
dpkg-source: info: applying use-mx32

Check disc space
────────────────

Sufficient free space for build

User Environment
────────────────

DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-4a6fd27c-4b81-4f61-ae0c-e7ebdcdec1e4
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd

dpkg-buildpackage
─────────────────

dpkg-buildpackage: source package genometools
dpkg-buildpackage: source version 1.5.8-1
dpkg-buildpackage: source distribution unstable
 dpkg-source --before-build genometools-1.5.8
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.*
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      -name '*.ssp' -or -name '*.des' -or -name "*.md5"  \) -and \( -not \
      -name '*foo.32.*' -not -name '*foo.64.*' \) -delete
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      www/genometools.org/htdocs/images/constructed.png \
      doc/manuals/annotationsketch.pdf
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      www/genometools.org/htdocs/examples.html \
      www/genometools.org/htdocs/libgenometools.html \
      www/genometools.org/htdocs/tools/gt.html
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make[1]: Leaving directory '/«PKGBUILDDIR»'
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 debian/rules build-arch
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make[1]: Entering directory '/«PKGBUILDDIR»'
faketime -f "`TZ=UTC date -d @1452205111 +'%Y-%m-%d %H:%M:%S'`" dh_auto_build -- useshared=yes x32=no 64bit=no errorcheck=no all docs manuals
	make -j1 useshared=yes x32=no 64bit=no errorcheck=no all docs manuals
make[2]: Entering directory '/«PKGBUILDDIR»'
[create obj/gt_config.h]
[compile alphabet.o]
[compile array.o]
[compile array2dim.o]
[compile array2dim_sparse.o]
[compile array3dim.o]
[compile basename.o]
[compile bioseq.o]
[compile bioseq_col.o]
[compile bioseq_iterator.o]
[compile bitbuffer.o]
[compile bitpackstringop.o]
[compile bitpackstringop16.o]
[compile bitpackstringop32.o]
[compile bitpackstringop64.o]
[compile bitpackstringop8.o]
[compile bittab.o]
[compile bool_matrix.o]
[compile bsearch.o]
[compile byte_popcount.o]
[compile byte_select.o]
[compile checkbitpackarray.o]
[compile checkbitpackstring-int.o]
[compile checkbitpackstring.o]
[compile checkbitpackstring16.o]
[compile checkbitpackstring32.o]
[compile checkbitpackstring64.o]
[compile checkbitpackstring8.o]
[compile class_alloc.o]
[compile class_alloc_lock.o]
[compile codon_iterator.o]
[compile codon_iterator_encseq.o]
[compile codon_iterator_simple.o]
[compile colorspace.o]
[compile combinatorics.o]
[compile compact_ulong_store.o]
[compile compat.o]
[compile complement.o]
[compile countingsort.o]
[compile cstr.o]
[compile cstr_array.o]
[compile cstr_table.o]
[compile desc_buffer.o]
[compile disc_distri.o]
[compile dlist.o]
[compile dual-pivot-qsort.o]
[compile dyn_bittab.o]
[compile dynalloc.o]
[compile eansi.o]
[compile ebzlib.o]
[compile encseq.o]
[compile encseq_access_type.o]
[compile encseq_col.o]
[compile encseq_metadata.o]
[compile encseq_options.o]
[compile encseq_ptr.o]
[compile endianess.o]
[compile error.o]
[compile example.o]
[compile example_a.o]
[compile example_b.o]
[compile ezlib.o]
[compile fa.o]
[compile fasta.o]
[compile fasta_reader.o]
[compile fasta_reader_fsm.o]
[compile fasta_reader_rec.o]
[compile fasta_reader_seqit.o]
[compile fastq.o]
[compile file.o]
[compile fileutils.o]
[compile gc_content.o]
[compile grep.o]
[compile gtdatapath.o]
[compile hashmap.o]
[compile hashtable.o]
[compile init.o]
[compile interval_tree.o]
[compile io.o]
[compile log.o]
[compile logger.o]
[compile ma.o]
[compile mapspec.o]
[compile mathsupport.o]
[compile md5_encoder.o]
[compile md5_fingerprint.o]
[compile md5_seqid.o]
[compile md5_tab.o]
[compile msort.o]
[compile multithread.o]
[compile option.o]
[compile orf.o]
[compile output_file.o]
[compile parseutils.o]
[compile password_entry.o]
[compile phase.o]
[compile process.o]
[compile progressbar.o]
[compile qsort-ulong.o]
[compile qsort_r.o]
[compile quality.o]
[compile queue.o]
[compile radix_sort.o]
[compile range.o]
[compile readmode.o]
[compile safearith.o]
[compile score_function.o]
[compile score_matrix.o]
[compile seq.o]
[compile seq_col.o]
[compile seq_info_cache.o]
[compile seq_iterator.o]
[compile seq_iterator_fastq.o]
[compile seq_iterator_sequence_buffer.o]
[compile sequence_buffer.o]
[compile sequence_buffer_embl.o]
[compile sequence_buffer_fasta.o]
[compile sequence_buffer_fastq.o]
[compile sequence_buffer_gb.o]
[compile sequence_buffer_plain.o]
[compile showtime.o]
[compile sig.o]
[compile spacepeak.o]
[compile splitter.o]
[compile str.o]
[compile str_array.o]
[compile str_cache.o]
[compile strand.o]
[compile strcmp.o]
[compile string_distri.o]
[compile symbol.o]
[compile thread.o]
[compile timer.o]
[compile tokenizer.o]
[compile tool.o]
[compile tool_iterator.o]
[compile toolbox.o]
[compile tooldriver.o]
[compile trans_table.o]
[compile translator.o]
[compile unit_testing.o]
[compile version.o]
[compile versionfunc.o]
[compile warning.o]
[compile xansi.o]
[compile xbsd.o]
[compile xbzlib.o]
[compile xposix.o]
[compile xzlib.o]
[compile yarandom.o]
[compile add_ids_stream.o]
[compile add_ids_visitor.o]
[compile add_introns_stream.o]
[compile affinealign.o]
[compile aligned_segment.o]
[compile aligned_segments_pile.o]
[compile alignment.o]
[compile anno_db_gfflike.o]
[compile anno_db_schema.o]
[compile array_in_stream.o]
[compile array_out_stream.o]
[compile assembly_stats_calculator.o]
[compile bed_in_stream.o]
[compile bed_parser.o]
[compile bitinstream.o]
[compile bitoutstream.o]
[compile blast_process_call.o]
[compile buffer_stream.o]
[compile cds_check_stream.o]
[compile cds_check_visitor.o]
[compile cds_stream.o]
[compile cds_visitor.o]
[compile chain.o]
[compile check_boundaries_visitor.o]
[compile chseqids_stream.o]
[compile clustered_set.o]
[compile clustered_set_uf.o]
[compile coin_hmm.o]
[compile collect_ids_visitor.o]
[compile comment_node.o]
[compile compressed_bitsequence.o]
[compile condenseq.o]
[compile condenseq_creator.o]
[compile condenseq_search_arguments.o]
[compile consensus_sa.o]
[compile csa_gene.o]
[compile csa_splice_form.o]
[compile csa_stream.o]
[compile csa_variable_strands.o]
[compile csa_visitor.o]
[compile cstr_iterator.o]
[compile diagonalbandalign.o]
[compile diagonalbandalign_affinegapcost.o]
[compile dice_hmm.o]
[compile dot_out_stream.o]
[compile dot_visitor.o]
[compile dup_feature_stream.o]
[compile dup_feature_visitor.o]
[compile editscript.o]
[compile elias_gamma.o]
[compile encdesc.o]
[compile encdesc_header_io.o]
[compile eof_node.o]
[compile evaluator.o]
[compile extract_feature_sequence.o]
[compile extract_feature_stream.o]
[compile extract_feature_visitor.o]
[compile fasta_header_iterator.o]
[compile feature_in_stream.o]
[compile feature_index.o]
[compile feature_index_memory.o]
[compile feature_info.o]
[compile feature_node.o]
[compile feature_node_iterator.o]
[compile feature_node_observer.o]
[compile feature_out_stream.o]
[compile feature_stream.o]
[compile feature_visitor.o]
[compile gap_str.o]
[compile genome_node.o]
[compile gff3_escaping.o]
[compile gff3_in_stream.o]
[compile gff3_in_stream_plain.o]
[compile gff3_linesorted_out_stream.o]
[compile gff3_numsorted_out_stream.o]
[compile gff3_out_stream.o]
[compile gff3_output.o]
[compile gff3_parser.o]
[compile gff3_visitor.o]
[compile globalchaining.o]
[compile golomb.o]
[compile gtdatahelp.o]
[compile gtf_in_stream.o]
[compile gtf_out_stream.o]
[compile gtf_parser.o]
[compile gtf_visitor.o]
[compile hcr.o]
[compile hmm.o]
[compile hpol_processor.o]
[compile huffcode.o]
[compile id_to_md5_stream.o]
[compile id_to_md5_visitor.o]
[compile inter_feature_stream.o]
[compile inter_feature_visitor.o]
[compile intset.o]
[compile intset_16.o]
[compile intset_32.o]
[compile intset_8.o]
[compile intset_combined.o]
[compile io_function_pointers.o]
[compile kmer_database.o]
[compile linearalign.o]
[compile linearalign_affinegapcost.o]
[compile linspace_management.o]
[compile load_stream.o]
[compile luahelper.o]
[compile luaserialize.o]
[compile mapping.o]
[compile match.o]
[compile match_blast.o]
[compile match_iterator.o]
[compile match_iterator_blast.o]
[compile match_iterator_last.o]
[compile match_iterator_open.o]
[compile match_iterator_sw.o]
[compile match_last.o]
[compile match_open.o]
[compile match_sw.o]
[compile match_visitor.o]
[compile maxcoordvalue.o]
[compile md5_to_id_stream.o]
[compile md5_to_id_visitor.o]
[compile md5set.o]
[compile merge_feature_stream.o]
[compile merge_feature_visitor.o]
[compile merge_stream.o]
[compile meta_node.o]
[compile multi_sanitizer_visitor.o]
[compile multieoplist.o]
[compile mutate.o]
[compile node_stream.o]
[compile node_visitor.o]
[compile obo_parse_tree.o]
[compile obo_stanza.o]
[compile orf_finder_stream.o]
[compile orf_finder_visitor.o]
[compile orf_iterator.o]
[compile orphanage.o]
[compile permute_words.o]
[compile popcount_tab.o]
[compile priority_queue.o]
[compile ranked_list.o]
[compile rbtree.o]
[compile rcr.o]
[compile rdb.o]
[compile rdb_sqlite.o]
[compile rdb_visitor.o]
[compile reconstructalignment.o]
[compile region_mapping.o]
[compile region_node.o]
[compile region_node_builder.o]
[compile regioncov_visitor.o]
[compile regular_seqid.o]
[compile reverse.o]
[compile rmq.o]
[compile safe_popen.o]
[compile sam_alignment.o]
[compile sam_query_name_iterator.o]
[compile samfile_encseq_mapping.o]
[compile samfile_iterator.o]
[compile sampling.o]
[compile scorehandler.o]
[compile script_filter.o]
[compile script_wrapper_stream.o]
[compile script_wrapper_visitor.o]
[compile select_stream.o]
[compile select_visitor.o]
[compile seqid2file.o]
[compile seqid2seqnum_mapping.o]
[compile seqpos_classifier.o]
[compile sequence_node.o]
[compile sequence_node_add_stream.o]
[compile sequence_node_out_stream.o]
[compile sequence_node_out_visitor.o]
[compile set_source_visitor.o]
[compile shredder.o]
[compile snp_annotator_stream.o]
[compile snp_annotator_visitor.o]
[compile sort_stream.o]
[compile spec_results.o]
[compile spec_visitor.o]
[compile splice_site_info_stream.o]
[compile splice_site_info_visitor.o]
[compile splicedseq.o]
[compile squarealign.o]
[compile sspliced_alignment.o]
[compile sspliced_alignment_parsing.o]
[compile stat_stream.o]
[compile stat_visitor.o]
[compile stream_evaluator.o]
[compile string_matching.o]
[compile swalign.o]
[compile tag_value_map.o]
[compile targetbest_select_stream.o]
[compile tidy_region_node_stream.o]
[compile tidy_region_node_visitor.o]
[compile tir_stream.o]
[compile transcript_bittabs.o]
[compile transcript_counts.o]
[compile transcript_evaluators.o]
[compile transcript_exons.o]
[compile transcript_used_exons.o]
[compile type_checker.o]
[compile type_checker_builtin.o]
[compile type_checker_obo.o]
[compile type_graph.o]
[compile type_node.o]
[compile typecheck_info.o]
[compile uint64hashtable.o]
[compile union_find.o]
[compile uniq_stream.o]
[compile visitor_stream.o]
[compile wtree.o]
[compile wtree_encseq.o]
[compile xrf_abbr_entry.o]
[compile xrf_abbr_parse_tree.o]
[compile xrf_checker.o]
[compile xrfcheck_info.o]
[compile alphabet_lua.o]
[compile annotationsketch_lua.o]
[compile bittab_lua.o]
[compile canvas_lua.o]
[compile cds_stream_lua.o]
[compile csa_stream_lua.o]
[compile diagram_lua.o]
[compile encseq_lua.o]
[compile feature_index_lua.o]
[compile feature_node_iterator_lua.o]
[compile feature_stream_lua.o]
[compile feature_visitor_lua.o]
[compile genome_node_lua.o]
[compile genome_stream_lua.o]
[compile genome_visitor_lua.o]
[compile gt_lua.o]
[compile gtcore_lua.o]
[compile gtext_lua.o]
[compile image_info_lua.o]
[compile layout_lua.o]
[compile mathsupport_lua.o]
[compile range_lua.o]
[compile region_mapping_lua.o]
[compile score_matrix_lua.o]
[compile stream_evaluator_lua.o]
[compile translate_lua.o]
[compile apmeoveridx.o]
[compile asqg_writer.o]
[compile bare-encseq.o]
[compile bcktab.o]
[compile cgr_spacedseed.o]
[compile chain2dim.o]
[compile chainofin.o]
[compile cutendpfx.o]
[compile diagbandseed.o]
[compile dist-short.o]
[compile echoseq.o]
[compile eis-blockcomp-param.o]
[compile eis-blockcomp.o]
[compile eis-bwtseq-construct.o]
[compile eis-bwtseq-context-param.o]
[compile eis-bwtseq-context.o]
[compile eis-bwtseq-extinfo.o]
[compile eis-bwtseq-param.o]
[compile eis-bwtseq-sass.o]
[compile eis-bwtseq.o]
[compile eis-encidxseq-construct.o]
[compile eis-encidxseq-param.o]
[compile eis-encidxseq.o]
[compile eis-mrangealphabet.o]
[compile eis-sa-common.o]
[compile eis-seqblocktranslate.o]
[compile eis-seqranges.o]
[compile eis-sequencemultiread.o]
[compile eis-specialsrank.o]
[compile eis-suffixarray-interface.o]
[compile eis-suffixerator-interface.o]
[compile eis-voiditf.o]
[compile encseq2offset.o]
[compile enum-patt.o]
[compile esa-bottomup.o]
[compile esa-dfs.o]
[compile esa-lcpintervals.o]
[compile esa-map.o]
[compile esa-maxpairs.o]
[compile esa-merge.o]
[compile esa-minunique.o]
[compile esa-mmsearch.o]
[compile esa-scanprj.o]
[compile esa-seqread.o]
[compile esa-shulen.o]
[compile esa-splititv-simple.o]
[compile esa-splititv.o]
[compile esa-spmitvs.o]
[compile esa-spmsk.o]
[compile esa_lcpintervals_visitor.o]
[compile esa_spmitvs_visitor.o]
[compile esa_visitor.o]
[compile firstcodes-accum.o]
[compile firstcodes-cache.o]
[compile firstcodes-insert.o]
[compile firstcodes-psbuf.o]
[compile firstcodes-scan.o]
[compile firstcodes-spacelog.o]
[compile firstcodes-tab.o]
[compile firstcodes.o]
[compile fmi-fwduni.o]
[compile fmi-keyval.o]
[compile fmi-locate.o]
[compile fmi-map.o]
[compile fmi-mapspec.o]
[compile fmi-mkindex.o]
[compile fmi-save.o]
[compile fmi-sufbwtstream.o]
[compile ft-front-generation.o]
[compile ft-front-prune.o]
[compile ft-polish.o]
[compile ft-trimstat.o]
[compile giextract.o]
[compile greedyedist.o]
[compile greedyfwdmat.o]
[compile hashfirstcodes.o]
[compile hlk-version.o]
[compile hplstore.o]
[compile idx-limdfs.o]
[compile idxlocali.o]
[compile idxlocalidp.o]
[compile idxlocalisw.o]
[compile index_options.o]
[compile initbasepower.o]
[compile initeqsvec.o]
[compile iter-window.o]
[compile kmer2string.o]
[compile lua_tools.o]
[compile marksubstring.o]
[compile merger-trie.o]
[compile mssufpat.o]
[compile myersapm.o]
[compile nullcols.o]
[compile optionargmode.o]
[compile pck-count-nodes.o]
[compile pckbucket.o]
[compile pckdfs.o]
[compile prsqualint.o]
[compile pssm.o]
[compile querymatch-align.o]
[compile querymatch.o]
[compile radixsort_str.o]
[compile randomcodes-correct.o]
[compile randomcodes-find-seldom.o]
[compile randomcodes-hpcorrect.o]
[compile randomcodes-insert.o]
[compile randomcodes-sfx-partssuf.o]
[compile randomcodes-tab.o]
[compile randomcodes.o]
[compile rdj-cntlist.o]
[compile rdj-contfind-bottomup.o]
[compile rdj-contfinder.o]
[compile rdj-contigpaths.o]
[compile rdj-contigs-graph.o]
[compile rdj-contigs-writer.o]
[compile rdj-errfind.o]
[compile rdj-ovlfind-bf.o]
[compile rdj-ovlfind-dp.o]
[compile rdj-ovlfind-gusfield.o]
[compile rdj-ovlfind-kmp.o]
[compile rdj-pairwise.o]
[compile rdj-spmfind.o]
[compile rdj-spmlist.o]
[compile rdj-spmproc.o]
[compile rdj-strgraph.o]
[compile rdj-twobitenc-editor.o]
[compile rdj-version.o]
[compile reads2twobit.o]
[compile reads_libraries_table.o]
[compile revcompl.o]
[compile seed-extend-iter.o]
[compile seed-extend.o]
[compile seqabstract.o]
[compile seqnumrelpos.o]
[compile sfx-apfxlen.o]
[compile sfx-bentsedg.o]
[compile sfx-bltrie.o]
[compile sfx-copysort.o]
[compile sfx-diffcov.o]
[compile sfx-enumcodes.o]
[compile sfx-lcpvalues.o]
[compile sfx-linlcp.o]
[compile sfx-lwcheck.o]
[compile sfx-mappedstr.o]
[compile sfx-maprange.o]
[compile sfx-opt.o]
[compile sfx-outprj.o]
[compile sfx-partssuf.o]
[compile sfx-radixsort.o]
[compile sfx-run.o]
[compile sfx-sain.o]
[compile sfx-shortreadsort.o]
[compile sfx-suffixer.o]
[compile sfx-suffixgetset.o]
[compile sfx-suftaborder.o]
[compile shu-dfs.o]
[compile shu-divergence.o]
[compile shu-encseq-gc.o]
[compile shu-genomediff.o]
[compile shu_unitfile.o]
[compile spaced-seeds.o]
[compile specialrank.o]
[compile spmsuftab.o]
[compile squarededist.o]
[compile substriter.o]
[compile tagerator.o]
[compile test-mappedstr.o]
[compile test-maxpairs.o]
[compile test-mergeesa.o]
[compile test-mtrieins.o]
[compile test-pairwise.o]
[compile turnwheels.o]
[compile twobits2kmers.o]
[compile tyr-map.o]
[compile tyr-mersplit.o]
[compile tyr-mkindex.o]
[compile tyr-occratio.o]
[compile tyr-search.o]
[compile xdrop.o]
[compile ags.o]
[compile ags_build.o]
[compile align_dna.o]
[compile align_protein.o]
[compile backtrace_path.o]
[compile bssm_helper.o]
[compile bssm_param.o]
[compile bssm_param_rmsd.o]
[compile bssm_seq_processor.o]
[compile bssm_train_stream.o]
[compile bssm_train_visitor.o]
[compile call_info.o]
[compile chain_collection.o]
[compile chaining.o]
[compile compute_scores.o]
[compile desc_cache.o]
[compile dp_options_core.o]
[compile dp_options_est.o]
[compile dp_options_postpro.o]
[compile dp_param.o]
[compile dp_scores_protein.o]
[compile editoperation.o]
[compile gff3_pgl_visitor.o]
[compile gff3_sa_visitor.o]
[compile gt_gth.o]
[compile gt_gthbssmbuild.o]
[compile gt_gthbssmfileinfo.o]
[compile gt_gthbssmprint.o]
[compile gt_gthbssmrmsd.o]
[compile gt_gthbssmtrain.o]
[compile gt_gthconsensus.o]
[compile gt_gthfilestat.o]
[compile gt_gthmkbssmfiles.o]
[compile gt_gthsplit.o]
[compile gthalignment.o]
[compile gthchain.o]
[compile gthcluster.o]
[compile gthcutoffsminimal.o]
[compile gthcutoffsrelaxed.o]
[compile gthcutoffsstrict.o]
[compile gthmatch.o]
[compile gthorf.o]
[compile gthoutput.o]
[compile gthsadistri.o]
[compile gthsortags.o]
[compile gthsplicesitescr.o]
[compile gthtrans.o]
[compile gthtravalign.o]
[compile gthverbosefunc.o]
[compile gthverbosefuncvm.o]
[compile gthxml.o]
[compile indent.o]
[compile input.o]
[compile intermediate.o]
[compile md5_cache.o]
[compile parse_options.o]
[compile path_matrix.o]
[compile path_walker.o]
[compile pgl.o]
[compile pgl_collection.o]
[compile pgl_visitor.o]
[compile proc_sa_collection.o]
[compile region_factory.o]
[compile run_header.o]
[compile sa.o]
[compile sa_cmp.o]
[compile sa_collection.o]
[compile sa_filter.o]
[compile sa_visitor.o]
[compile seq_con.o]
[compile similarity_filter.o]
[compile splice_site_model.o]
[compile spliced_seq.o]
[compile stat.o]
[compile time.o]
[compile txt_pgl_visitor.o]
[compile txt_sa_visitor.o]
[compile xml_final_sa_visitor.o]
[compile xml_inter_sa_visitor.o]
[compile xml_pgl_visitor.o]
[compile gt_ltrclustering.o]
[compile gt_ltrdigest.o]
[compile gt_ltrharvest.o]
[compile ltr_classify_stream.o]
[compile ltr_cluster_prepare_seq_visitor.o]
[compile ltr_cluster_stream.o]
[compile ltr_four_char_motif.o]
[compile ltr_input_check_visitor.o]
[compile ltr_orf_annotator_stream.o]
[compile ltr_refseq_match_stream.o]
[compile ltrdigest_file_out_stream.o]
[compile ltrdigest_pbs_visitor.o]
[compile ltrdigest_pdom_visitor.o]
[compile ltrdigest_ppt_visitor.o]
[compile ltrdigest_strand_assign_visitor.o]
[compile ltrharvest_fasta_out_stream.o]
[compile ltrharvest_fasta_out_visitor.o]
[compile ltrharvest_stream.o]
[compile ltrharvest_tabout_stream.o]
[compile ltrharvest_tabout_visitor.o]
[compile pdom_model_set.o]
[compile metagenomethreader.o]
[compile mg_codon.o]
[compile mg_combinedscore.o]
[compile mg_compute_gene_prediction.o]
[compile mg_computepath.o]
[compile mg_outputwriter.o]
[compile mg_reverse.o]
[compile mg_xmlparser.o]
[compile block.o]
[compile canvas.o]
[compile canvas_cairo.o]
[compile canvas_cairo_context.o]
[compile canvas_cairo_file.o]
[compile color.o]
[compile coords.o]
[compile custom_track.o]
[compile custom_track_example.o]
[compile custom_track_gc_content.o]
[compile custom_track_script_wrapper.o]
[compile diagram.o]
[compile drawing_range.o]
[compile element.o]
[compile graphics.o]
[compile graphics_cairo.o]
[compile gt_sketch.o]
[compile gt_sketch_page.o]
[compile image_info.o]
[compile layout.o]
[compile line.o]
[compile line_breaker.o]
[compile line_breaker_bases.o]
[compile line_breaker_captions.o]
[compile luastyle.o]
[compile rec_map.o]
[compile style.o]
[compile text_width_calculator.o]
[compile text_width_calculator_cairo.o]
[compile track.o]
[link libgenometools.a]
ar: creating lib/libgenometools.a
[gathering public API symbols to obj/public_symbols.lst]
[link libgenometools.so]
[compile gt.o]
[compile gtr.o]
[compile gtt.o]
[compile interactive.o]
[compile gt_bed_to_gff3.o]
[compile gt_cds.o]
[compile gt_chain2dim.o]
[compile gt_chseqids.o]
[compile gt_clean.o]
[compile gt_compreads.o]
[compile gt_compreads_compress.o]
[compile gt_compreads_decompress.o]
[compile gt_compreads_refcompress.o]
[compile gt_compreads_refdecompress.o]
[compile gt_compressedbits.o]
[compile gt_condenseq.o]
[compile gt_condenseq_blast.o]
[compile gt_condenseq_compress.o]
[compile gt_condenseq_extract.o]
[compile gt_condenseq_hmmsearch.o]
[compile gt_condenseq_info.o]
[compile gt_condenseq_search.o]
[compile gt_congruence.o]
[compile gt_consensus_sa.o]
[compile gt_convertseq.o]
[compile gt_csa.o]
[compile gt_dev.o]
[compile gt_dot.o]
[compile gt_dupfeat.o]
[compile gt_encseq.o]
[compile gt_encseq2spm.o]
[compile gt_encseq_bench.o]
[compile gt_encseq_bitextract.o]
[compile gt_encseq_check.o]
[compile gt_encseq_decode.o]
[compile gt_encseq_encode.o]
[compile gt_encseq_info.o]
[compile gt_encseq_md5.o]
[compile gt_encseq_sample.o]
[compile gt_eval.o]
[compile gt_extractfeat.o]
[compile gt_extractseq.o]
[compile gt_extracttarget.o]
[compile gt_fastq_sample.o]
[compile gt_featureindex.o]
[compile gt_fingerprint.o]
[compile gt_gdiffcalc.o]
[compile gt_genomediff.o]
[compile gt_gff3.o]
[compile gt_gff3_to_gtf.o]
[compile gt_gff3validator.o]
[compile gt_gtf_to_gff3.o]
[compile gt_guessprot.o]
[compile gt_hop.o]
[compile gt_id_to_md5.o]
[compile gt_idxlocali.o]
[compile gt_inlineseq_add.o]
[compile gt_inlineseq_split.o]
[compile gt_interfeat.o]
[compile gt_kmer_database.o]
[compile gt_linspace_align.o]
[compile gt_loccheck.o]
[compile gt_magicmatch.o]
[compile gt_matchtool.o]
[compile gt_matstat.o]
[compile gt_md5_to_id.o]
[compile gt_merge.o]
[compile gt_mergeesa.o]
[compile gt_mergefeat.o]
[compile gt_mgth.o]
[compile gt_mkfeatureindex.o]
[compile gt_mkfmindex.o]
[compile gt_mmapandread.o]
[compile gt_orffinder.o]
[compile gt_packedindex.o]
[compile gt_packedindex_chk_integrity.o]
[compile gt_packedindex_chk_search.o]
[compile gt_packedindex_mkctxmap.o]
[compile gt_packedindex_trsuftab.o]
[compile gt_paircmp.o]
[compile gt_parsexrf.o]
[compile gt_patternmatch.o]
[compile gt_prebwt.o]
[compile gt_readjoiner.o]
[compile gt_readjoiner_asqg.o]
[compile gt_readjoiner_assembly.o]
[compile gt_readjoiner_cgraph.o]
[compile gt_readjoiner_cnttest.o]
[compile gt_readjoiner_correct.o]
[compile gt_readjoiner_graph.o]
[compile gt_readjoiner_overlap.o]
[compile gt_readjoiner_prefilter.o]
[compile gt_readjoiner_spmtest.o]
[compile gt_readreads.o]
[compile gt_regioncov.o]
[compile gt_repfind.o]
[compile gt_sain.o]
[compile gt_sam_interface.o]
[compile gt_script_filter.o]
[compile gt_seed_extend.o]
[compile gt_select.o]
[compile gt_seq.o]
[compile gt_seqcorrect.o]
[compile gt_seqfilter.o]
[compile gt_seqids.o]
[compile gt_seqlensort.o]
[compile gt_seqmutate.o]
[compile gt_seqorder.o]
[compile gt_seqstat.o]
[compile gt_seqtransform.o]
[compile gt_seqtranslate.o]
[compile gt_sequniq.o]
[compile gt_sfxmap.o]
[compile gt_show_seedext.o]
[compile gt_shredder.o]
[compile gt_shulen.o]
[compile gt_simreads.o]
[compile gt_skproto.o]
[compile gt_snpper.o]
[compile gt_sortbench.o]
[compile gt_speck.o]
[compile gt_splicesiteinfo.o]
[compile gt_splitfasta.o]
[compile gt_stat.o]
[compile gt_suffixerator.o]
[compile gt_tagerator.o]
[compile gt_tallymer.o]
[compile gt_template.o]
[compile gt_tir.o]
[compile gt_trieins.o]
[compile gt_uniq.o]
[compile gt_wtree.o]
[compile gt_wtree_bench.o]
[link gt]
[compile custom_stream.o]
[link custom_stream]
[compile gff3sort.o]
[link gff3sort]
[compile gff3validator.o]
[link gff3validator]
[compile noop.o]
[link noop]
[compile sketch_constructed.o]
[link sketch_constructed]
[compile sketch_parsed_with_ctrack.o]
[link sketch_parsed_with_ctrack]
[compile sketch_parsed_with_ordering.o]
[link sketch_parsed_with_ordering]
[compile sketch_parsed.o]
[link sketch_parsed]
bin/gt gtscripts/gtdoc.lua -html /«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 \
          www/genometools.org/htdocs/images/parsed.png \
          testdata/eden.gff3
bin/examples/sketch_parsed \
  www/genometools.org/htdocs/annotationsketch/callbacks.style \
  www/genometools.org/htdocs/images/callbacks.png \
          www/genometools.org/htdocs/annotationsketch/callback_examples_with_score.gff3
bin/examples/sketch_constructed gtdata/sketch/default.style \
  www/genometools.org/htdocs/images/constructed.png
mogrify -format jpg +set date:create +set date:modify \
  -define png:exclude-chunk=time \
  www/genometools.org/htdocs/images/*.png && \
  rm -rf www/genometools.org/htdocs/images/*.png
sed -nf scripts/incl.sed \
  www/genometools.org/htdocs/examples_tmpl.html | \
          sed 'N;N;s/\n//' > /tmp/tmp.sed.$$ && \
sed -f /tmp/tmp.sed.$$ \
  www/genometools.org/htdocs/examples_tmpl.html > \
  www/genometools.org/htdocs/examples.html; rm -f /tmp/tmp.sed.$$
bin/gt gtscripts/gtdoc.lua -tex /«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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Output written on devguide.pdf (29 pages, 257411 bytes).
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chapter 2.

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95 to \OT1/cmtt/m/n/10.95 size\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 size \OT
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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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[]\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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[]\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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[]\OT1/cmtt/m/n/10.95 void gt[]output[]file[]info[]register[]options([]GtOutput
FileInfo

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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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\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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[]\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] [111]
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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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[113]
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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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[114]
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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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[115]
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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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[116]
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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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[117]
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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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[120]
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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
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/ptm/m/n/10.95 the com-mand line \OT1/cmtt/m/n/10.95 gt gtscripts/sketch[]p
arsed.lua <style[]file> <PNG[]file> <GFF3[]file>\OT1/ptm/m/n/10.95 ) 
(../../gtscripts/sketch_parsed.lua [21]) (../../gtruby/sketch_parsed.rb
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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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[]\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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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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[]\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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[]\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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[92]
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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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[93] [94]
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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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[97]
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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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[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] [115]
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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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[116]
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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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[117]
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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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[118]
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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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[119]
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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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[120]
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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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[125] [126] [127] [128]
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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
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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chapter 1.

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arsed.lua <style[]file> <PNG[]file> <GFF3[]file>\OT1/ptm/m/n/10.95 ) 
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(../../gtruby/sketch_constructed.rb [27]) (../../gtpython/sketch_constructed.py
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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
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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 
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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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const char

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[]\OT1/cmtt/m/n/10.95 GtUchar gt[]alphabet[]pretty[]symbol([]const GtAlphabet *
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[]\OT1/cmtt/m/n/10.95 GtFeatureIndex* gt[]anno[]db[]schema[]get[]feature[]index
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95 to \OT1/cmtt/m/n/10.95 size\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 size \OT
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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
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]in[]stream[]new([]GtArray *nodes
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]cds[]stream[]new([]GtNodeStream *in[]st
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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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[56] [57] [58]
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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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[]\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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[81] [82]
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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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[]\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] [115]
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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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[116]
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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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[117]
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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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[118]
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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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[119]
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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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[120]
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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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[121]
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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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[124]
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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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[125] [126] [127] [128]
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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
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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[149] [150]) [151] (./annotationsketch.aux)

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onts/type1/public/amsfonts/cm/cmssbx10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmtt8.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/ut
mb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on annotationsketch.pdf (151 pages, 1171064 bytes).
Transcript written on annotationsketch.log.
mv annotationsketch.aux annotationsketch-pdf.aux
test -e annotationsketch.bbl && mv annotationsketch.bbl annotationsketch-pdf.bbl
make[3]: Leaving directory '/«PKGBUILDDIR»/doc/manuals'
make -C /«PKGBUILDDIR»/doc/manuals
make[3]: Entering directory '/«PKGBUILDDIR»/doc/manuals'
test -e readjoiner-pdf.aux && mv readjoiner-pdf.aux readjoiner.aux
Makefile:39: recipe for target 'readjoiner-pdf.aux' failed
make[3]: [readjoiner-pdf.aux] Error 1 (ignored)
pdflatex readjoiner.tex && rm readjoiner.pdf
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./readjoiner.tex
LaTeX2e <2015/10/01> patch level 2
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)
No file readjoiner.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]

LaTeX Warning: Citation `MYE:2005' on page 1 undefined on input line 55.


LaTeX Warning: Citation `genometools' on page 1 undefined on input line 58.


Overfull \hbox (6.12744pt too wide) in paragraph at lines 63--73
[] 

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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 ,
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1]
Underfull \hbox (badness 4132) in paragraph at lines 183--186
[]\OT1/ptm/m/n/12 a single-end li-brary plus an in-ter-leaved
[2]

LaTeX Warning: Citation `MYE:2005' on page 3 undefined on input line 209.

[3]

LaTeX Warning: Citation `MYE:2005' on page 4 undefined on input line 259.

[4]

LaTeX Warning: Citation `Edena' on page 5 undefined on input line 326.

[5] [6] [7] (./readjoiner.aux)

LaTeX Warning: There were undefined references.


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

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
rw/times/utmri8a.pfb>
Output written on readjoiner.pdf (8 pages, 109483 bytes).
Transcript written on readjoiner.log.
mv readjoiner.aux readjoiner-pdf.aux
test -e readjoiner-pdf.aux && mv readjoiner-pdf.aux readjoiner.aux
bibtex readjoiner
This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
The top-level auxiliary file: readjoiner.aux
I found no \bibdata command---while reading file readjoiner.aux
I found no \bibstyle command---while reading file readjoiner.aux
(There were 2 error messages)
make[3]: [readjoiner-pdf.bbl] Error 2 (ignored)
Makefile:32: recipe for target 'readjoiner-pdf.bbl' failed
test -e readjoiner-pdf.bbl || touch readjoiner-pdf.bbl
diff readjoiner-pdf.bbl readjoiner.bbl || mv readjoiner.bbl readjoiner-pdf.bbl && rm -f readjoiner.bbl
mv readjoiner.aux readjoiner-pdf.aux
test -e readjoiner-pdf.aux && mv readjoiner-pdf.aux readjoiner.aux
test -e readjoiner-pdf.bbl && mv readjoiner-pdf.bbl readjoiner.bbl
pdflatex readjoiner.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./readjoiner.tex
LaTeX2e <2015/10/01> patch level 2
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)
(./readjoiner.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (6.12744pt too wide) in paragraph at lines 63--73
[] 

Overfull \hbox (19.25665pt too wide) in paragraph at lines 78--81
[]\OT1/ptm/m/n/12 The \OT1/ptm/m/it/12 Read-joiner \OT1/ptm/m/n/12 tools are ru
n us-ing the fol-low-ing syn-tax: \OT1/pcr/m/n/12 gt readjoiner <tool> <argumen
ts>\OT1/ptm/m/n/12 ,
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1]
Underfull \hbox (badness 4132) in paragraph at lines 183--186
[]\OT1/ptm/m/n/12 a single-end li-brary plus an in-ter-leaved
[2] [3] [4] [5] [6] [7] (./readjoiner.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
rw/times/utmri8a.pfb>
Output written on readjoiner.pdf (8 pages, 108817 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 2
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)
(./readjoiner.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (6.12744pt too wide) in paragraph at lines 63--73
[] 

Overfull \hbox (19.25665pt too wide) in paragraph at lines 78--81
[]\OT1/ptm/m/n/12 The \OT1/ptm/m/it/12 Read-joiner \OT1/ptm/m/n/12 tools are ru
n us-ing the fol-low-ing syn-tax: \OT1/pcr/m/n/12 gt readjoiner <tool> <argumen
ts>\OT1/ptm/m/n/12 ,
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1]
Underfull \hbox (badness 4132) in paragraph at lines 183--186
[]\OT1/ptm/m/n/12 a single-end li-brary plus an in-ter-leaved
[2] [3] [4] [5] [6] [7] (./readjoiner.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/share/texlive/texmf-dis
t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
rw/times/utmri8a.pfb>
Output written on readjoiner.pdf (8 pages, 108817 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 2
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)
No file hop.aux.
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]

LaTeX Warning: Citation `HOP' on page 1 undefined on input line 40.


LaTeX Warning: Citation `genometools' on page 1 undefined on input line 69.

[1]
Overfull \hbox (37.48308pt too wide) in paragraph at lines 130--138
[]\OT1/ptm/m/n/12 It is usu-ally quite easy to pre-pare the map-ping as re-quir
ed. Say the reads to be cor-rected are \OT1/pcr/m/n/12 f[]reads.fastq

Overfull \hbox (32.30313pt too wide) in paragraph at lines 144--144
[]\OT1/pcr/m/n/10 > bwa sampe cognate.fas -f map.sam f_reads.sai r_reads.sai f_
reads.fastq r_reads.fastq[] 
[2] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)
Overfull \hbox (14.55139pt too wide) in paragraph at lines 206--211
\OT1/ptm/m/n/12 The pre-fix added by HOP (in this case \OT1/pcr/m/n/12 hop\OT1/
ptm/m/n/12 , which is the de-fault) can be changed us-ing the \OT1/pcr/m/n/12 -
outprefix
[3] [4] (./hop.aux)

LaTeX Warning: There were undefined references.


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

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courie
r/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></
usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on hop.pdf (5 pages, 74598 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 2
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)
(./hop.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}] [1]
Overfull \hbox (37.48308pt too wide) in paragraph at lines 130--138
[]\OT1/ptm/m/n/12 It is usu-ally quite easy to pre-pare the map-ping as re-quir
ed. Say the reads to be cor-rected are \OT1/pcr/m/n/12 f[]reads.fastq

Overfull \hbox (32.30313pt too wide) in paragraph at lines 144--144
[]\OT1/pcr/m/n/10 > bwa sampe cognate.fas -f map.sam f_reads.sai r_reads.sai f_
reads.fastq r_reads.fastq[] 
[2] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd)
Overfull \hbox (14.55139pt too wide) in paragraph at lines 206--211
\OT1/ptm/m/n/12 The pre-fix added by HOP (in this case \OT1/pcr/m/n/12 hop\OT1/
ptm/m/n/12 , which is the de-fault) can be changed us-ing the \OT1/pcr/m/n/12 -
outprefix
[3] [4] (./hop.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courie
r/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></
usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on hop.pdf (5 pages, 73999 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 2
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)
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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_
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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
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Output written on hop.pdf (5 pages, 73999 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)
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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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[]\OT1/pcr/m/n/10 $ gt ltrharvest -index chr02.19970727.fsa -seed 30 -xdrop 5 -
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[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
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[9]

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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
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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
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cm/cmmi6.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi
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are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/te
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nts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/t
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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)
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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)
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entering extended mode
(./ltrharvest.tex
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(see the transcript file for additional information){/usr/share/texlive/texmf-d
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pdflatex ltrharvest.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
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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
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/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
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mv ltrharvest.aux ltrharvest-pdf.aux
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make[3]: [ltrdigest-pdf.aux] Error 1 (ignored)
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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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Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
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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/
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\OT1/pcr/m/n/12 -hmms HMM*.hmm -outfileprefix mygenome-ltrs ltrs[]sorted.gff3 g
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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)
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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
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n/12 and \OT1/pcr/m/n/12 HMM3.hmm\OT1/ptm/m/n/12 ,

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pdflatex ltrdigest.tex
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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
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Output written on uniquesub.pdf (3 pages, 98849 bytes).
Transcript written on uniquesub.log.
mv uniquesub.aux uniquesub-pdf.aux
test -e uniquesub-pdf.aux && mv uniquesub-pdf.aux uniquesub.aux
bibtex uniquesub
This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
The top-level auxiliary file: uniquesub.aux
I found no \bibdata command---while reading file uniquesub.aux
I found no \bibstyle command---while reading file uniquesub.aux
(There were 2 error messages)
make[3]: [uniquesub-pdf.bbl] Error 2 (ignored)
Makefile:32: recipe for target 'uniquesub-pdf.bbl' failed
test -e uniquesub-pdf.bbl || touch uniquesub-pdf.bbl
diff uniquesub-pdf.bbl uniquesub.bbl || mv uniquesub.bbl uniquesub-pdf.bbl && rm -f uniquesub.bbl
mv uniquesub.aux uniquesub-pdf.aux
test -e uniquesub-pdf.aux && mv uniquesub-pdf.aux uniquesub.aux
test -e uniquesub-pdf.bbl && mv uniquesub-pdf.bbl uniquesub.bbl
pdflatex uniquesub.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./uniquesub.tex
LaTeX2e <2015/10/01> patch level 2
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)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/tools/xspace.sty)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (./optionman.sty)
(./uniquesub.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omsptm.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (8.18253pt too wide) in paragraph at lines 127--131
\OT1/ptm/m/n/12 loaded from $\OT1/pcr/m/n/12 ftp : / / ftp . ensembl . org / pu
b / current _ fasta / homo _ sapiens _ 47 _ 36i /
[2] [3] (./uniquesub.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti
12.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive
/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/ti
mes/utmri8a.pfb>
Output written on uniquesub.pdf (3 pages, 97841 bytes).
Transcript written on uniquesub.log.
pdflatex uniquesub.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./uniquesub.tex
LaTeX2e <2015/10/01> patch level 2
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)
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (./optionman.sty)
(./uniquesub.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd)
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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] [3] (./uniquesub.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti
12.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive
/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/ti
mes/utmri8a.pfb>
Output written on uniquesub.pdf (3 pages, 97841 bytes).
Transcript written on uniquesub.log.
mv uniquesub.aux uniquesub-pdf.aux
test -e uniquesub.bbl && mv uniquesub.bbl uniquesub-pdf.bbl
test -e matstat-pdf.aux && mv matstat-pdf.aux matstat.aux
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 2
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)
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(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (./optionman.sty)
No file matstat.aux.
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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 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, 92775 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 2
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)
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (./optionman.sty)
(./matstat.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1pcr.fd) [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map}]
Overfull \hbox (8.18253pt too wide) in paragraph at lines 120--124
\OT1/ptm/m/n/12 loaded from $\OT1/pcr/m/n/12 ftp : / / ftp . ensembl . org / pu
b / current _ fasta / homo _ sapiens _ 47 _ 36i /
[2] (./matstat.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti
12.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive
/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/ti
mes/utmri8a.pfb>
Output written on matstat.pdf (2 pages, 92775 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 2
Babel <3.9m> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
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(/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/listings.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (./optionman.sty)
(./matstat.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
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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
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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, 92775 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 2
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(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
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(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
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[6] (./packedindex.aux)

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Output written on packedindex.pdf (7 pages, 157514 bytes).
Transcript written on packedindex.log.
mv packedindex.aux packedindex-pdf.aux
test -e packedindex-pdf.aux && mv packedindex-pdf.aux packedindex.aux
bibtex packedindex
This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
The top-level auxiliary file: packedindex.aux
The style file: unsrt.bst
Database file #1: gtmanuals.bib
test -e packedindex-pdf.bbl || touch packedindex-pdf.bbl
diff packedindex-pdf.bbl packedindex.bbl || mv packedindex.bbl packedindex-pdf.bbl && rm -f packedindex.bbl
0a1,21
> \begin{thebibliography}{1}
> 
> \bibitem{oai:CiteSeerPSU:481302}
> Paolo Ferragina and Giovanni Manzini.
> \newblock Opportunistic data structures with applications, September~03 2000.
> 
> \bibitem{journals/talg/FerraginaMMN07}
> Paolo Ferragina, Giovanni Manzini, Veli M{\"a}kinen, and Gonzalo Navarro.
> \newblock Compressed representations of sequences and full-text indexes.
> \newblock {\em ACM Transactions on Algorithms}, 3(2), 2007.
> 
> \bibitem{genometools}
> Gordon Gremme.
> \newblock The \textsc{GenomeTools} genome analysis system.
> \newblock \url{http://genometools.org}.
> 
> \bibitem{gttestdata}
> \textsc{GenomeTools} test data set.
> \newblock \url{git://genometools.org/gttestdata.git}.
> 
> \end{thebibliography}
mv packedindex.aux packedindex-pdf.aux
test -e packedindex-pdf.aux && mv packedindex-pdf.aux packedindex.aux
test -e packedindex-pdf.bbl && mv packedindex-pdf.bbl packedindex.bbl
pdflatex packedindex.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./packedindex.tex
LaTeX2e <2015/10/01> patch level 2
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Excluding comment 'comment') (./optionman.sty) (./packedindex.aux)
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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/
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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
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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
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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
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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
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test -e repfind-pdf.aux && mv repfind-pdf.aux repfind.aux
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pdflatex repfind.tex && rm repfind.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 Suppose the in-put se-quence $\OML/cmm/m/it/12 S \OT1/cmr/m/n
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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,

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bibtex repfind
This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
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I found no \citation commands---while reading file repfind.aux
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pdflatex repfind.tex
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 Kurtz, S., Choud-huri, J. V., Ohle-busch, E., Schleier-ma-che
r, C., Stoye, J., Giegerich,
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pdflatex repfind.tex
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*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
 -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, 103170 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)
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entering extended mode
(./tallymer-tmp.tex
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(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
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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></
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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
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fb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on tallymer-tmp.pdf (9 pages, 139953 bytes).
Transcript written on tallymer-tmp.log.
pdflatex tallymer-tmp
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
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entering extended mode
(./tallymer-tmp.tex
LaTeX2e <2015/10/01> patch level 2
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(./tallymer-tmp.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)

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[]\OT1/pcr/m/n/12 gt tallymer occratio: error: fopen(): cannot open file 'reads
.prj':
[2] [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) )
(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></
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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
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fb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on tallymer-tmp.pdf (9 pages, 139320 bytes).
Transcript written on tallymer-tmp.log.
mv tallymer-tmp.pdf tallymer.pdf
../../bin/gt packedindex mkindex -dna -dir rev -parts 12 -bsize 10 \
                      -sprank -locfreq 32 -tis -ssp -indexname pck-human\
                      -db ../../testdata/at1MB
cp ../../testdata/Q1.gz Q1.gz
./findemptyoutfiles.sh
./execcommand.pl tagerator.tex > tagerator-tmp.tex
# file output/gt-tagerator--q-Q1.gz--maxocc-10--pck-pck-human.out already exists
# file output/gt-tagerator--q-Q1.gz--pck-pck-human--e-2.out already exists
# file output/gt-tagerator--q-Q1.gz--pck-pck-human--e-1--maxocc-5.out already exists
pdflatex tagerator-tmp
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
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entering extended mode
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[]\OT1/pcr/m/n/8 # computing prefix matches with up to 1 differences and at mos
t 5 occurrences in the subject sequences[] 
[5] (./tagerator-tmp.aux) )
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ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
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m/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.
pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></
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st/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/
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Output written on tagerator-tmp.pdf (5 pages, 112841 bytes).
Transcript written on tagerator-tmp.log.
pdflatex tagerator-tmp
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)
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t 5 occurrences in the subject sequences[] 
[5] (./tagerator-tmp.aux) )
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ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
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st/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/
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mv tagerator-tmp.pdf tagerator.pdf
test -e genomediff-pdf.aux && mv genomediff-pdf.aux genomediff.aux
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fb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></u
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exmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on genomediff.pdf (6 pages, 163631 bytes).
Transcript written on genomediff.log.
mv genomediff.aux genomediff-pdf.aux
test -e genomediff-pdf.aux && mv genomediff-pdf.aux genomediff.aux
bibtex genomediff
This is BibTeX, Version 0.99d (TeX Live 2015/Debian)
The top-level auxiliary file: genomediff.aux
The style file: unsrt.bst
Database file #1: gtmanuals.bib
test -e genomediff-pdf.bbl || touch genomediff-pdf.bbl
diff genomediff-pdf.bbl genomediff.bbl || mv genomediff.bbl genomediff-pdf.bbl && rm -f genomediff.bbl
0a1,25
> \begin{thebibliography}{1}
> 
> \bibitem{HAU:DOM:WIE:2008}
> Bernhard Haubold, Mirjana Domazet-Loso, and Thomas Wiehe.
> \newblock An alignment-free distance measure for closely related genomes.
> \newblock In {\em RECOMB-CG ’08: Proceedings of the international workshop on
>   Comparative Genomics}, pages 87--99, Berlin, Heidelberg, 2008.
>   Springer-Verlag.
> 
> \bibitem{HAU:PFA:DOM:WIE:2009}
> B.~Haubold, P.~Pfaffelhuber, M.~Domazet-Loso, and T.~Wiehe.
> \newblock Estimating mutation distances from unaligned genomes.
> \newblock {\em J. Comput. Biol.}, 16:1487--1500, "Oct" 2009.
> 
> \bibitem{HAU:REE:PFA:2011}
> Bernhard Haubold, Floyd~A. Reed, and Peter Pfaffelhuber.
> \newblock Alignment-free estimation of nucleotide diversity.
> \newblock {\em Bioinformatics}, 27(4):449--455, 2011.
> 
> \bibitem{genometools}
> Gordon Gremme.
> \newblock The \textsc{GenomeTools} genome analysis system.
> \newblock \url{http://genometools.org}.
> 
> \end{thebibliography}
mv genomediff.aux genomediff-pdf.aux
test -e genomediff-pdf.aux && mv genomediff-pdf.aux genomediff.aux
test -e genomediff-pdf.bbl && mv genomediff-pdf.bbl genomediff.bbl
pdflatex genomediff.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./genomediff.tex
LaTeX2e <2015/10/01> patch level 2
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(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
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(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu)
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(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
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(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(./genomediff.aux)
*geometry* driver: auto-detecting
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[Loading MPS to PDF converter (version 2006.09.02).]
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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/
type1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmitt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.pfb></
usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/te
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dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on genomediff.pdf (6 pages, 176742 bytes).
Transcript written on genomediff.log.
pdflatex genomediff.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./genomediff.tex
LaTeX2e <2015/10/01> patch level 2
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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(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
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(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.sty
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(./optionman.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
(/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty)
(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(./genomediff.aux)
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
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[Loading MPS to PDF converter (version 2006.09.02).]
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(./genomediff.bbl) [5] (./genomediff.aux) )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmbxti10.pfb></usr/share/texlive/texmf-dist/fonts/
type1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmitt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.pfb></
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are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/te
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dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on genomediff.pdf (6 pages, 176515 bytes).
Transcript written on genomediff.log.
mv genomediff.aux genomediff-pdf.aux
test -e genomediff.bbl && mv genomediff.bbl genomediff-pdf.bbl
make[3]: Leaving directory '/«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=413764980
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=2040088680
1364: gt sketch short test (unknown output format)                : ok
1362: gt sketch short test                                        : ok
1363: gt sketch short test (stdin)                                : ok
1365: gt sketch short test (unwriteable PNG file)                 : ok
1367: gt sketch short test (nonexistant style file)               : ok
1369: gt sketch prob 1                                            : ok
1368: gt sketch short test (invalid style file)                   : ok
1366: gt sketch short test (unwriteable PDF file)                 : ok
1370: gt sketch prob 2                                            : ok
1372: gt sketch multiline without parent                          : ok
1371: gt sketch track IDs to style file                           : ok
1373: gt sketch pipe                                              : ok
1375: gt sketch -showrecmaps                                      : ok
1376: gt sketch -showrecmaps (normal text size)                   : ok
1377: gt sketch -showrecmaps (narrow image)                       : ok
1378: gt sketch -showrecmaps (large text size)                    : ok
1379: gt sketch for transcript (neg. coords in ruler)             : ok
1381: sketch_constructed (C)                                      : ok
1382: sketch_parsed (C)                                           : ok
1383: sketch_parsed reverse order (C)                             : ok
1384: sketch_constructed (Lua)                                    : ok
1385: sketch_parsed (Lua)                                         : ok
1374: gt sketch streams <-> file output                           : ok
1380: gt sketch runtime Lua failures                              : ok
make[1]: Leaving directory '/«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 \
  x32=no 64bit=no errorcheck=no prefix=/«PKGBUILDDIR»/debian/tmp/usr
	make -j1 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no installmanpages useshared=yes x32=no 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\\" -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DHAVE_MEMMOVE -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN -DLUA_USE_MKSTEMP -DHAVE_SQLITE!' \
  -e 's!@CXX@!g++!' -e 's!@CXXFLAGS@!-g -O2 -fstack-protector-strong -Wformat -Werror=format-security!' \
  -e 's!@LDFLAGS@!-L/«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@!"2016-01-13 06:15:06"!' \
  -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
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
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a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
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a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
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a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
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a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
..............................................................................................
test ! -d /«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/props.py -> build/lib.linux-armv7l-2.7/gt
copying gt/version.py -> build/lib.linux-armv7l-2.7/gt
copying gt/dlload.py -> build/lib.linux-armv7l-2.7/gt
creating build/lib.linux-armv7l-2.7/gt/core
copying gt/core/__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
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/props.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
copying build/lib.linux-armv7l-2.7/gt/version.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
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-1.5.8.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 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-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 liblua5.1-filesystem.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libgenometools0/usr/lib/libgenometools.so.0 was not linked against liblua5.1-des56.so.0 (it uses none of the library's symbols)
   dh_installdeb -a
   dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: Depends field of package libgenometools0-dev: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: Depends field of package genometools-dbg: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
   dh_md5sums -a
   dh_builddeb -a
dpkg-deb: building package 'genometools' in '../genometools_1.5.8-1_armhf.deb'.
dpkg-deb: building package 'libgenometools0-dev' in '../libgenometools0-dev_1.5.8-1_armhf.deb'.
dpkg-deb: building package 'genometools-dbg' in '../genometools-dbg_1.5.8-1_armhf.deb'.
dpkg-deb: building package 'libgenometools0' in '../libgenometools0_1.5.8-1_armhf.deb'.
 dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../genometools_1.5.8-1_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build genometools-1.5.8
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20160113-0643

Finished
────────

I: Built successfully

┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot                                                            │
└──────────────────────────────────────────────────────────────────────────────┘


┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘


genometools_1.5.8-1_armhf.changes:
──────────────────────────────────

Format: 1.8
Date: Thu, 07 Jan 2016 22:18:31 +0000
Source: genometools
Binary: genometools genometools-common libgenometools0 libgenometools0-dev genometools-doc genometools-dbg python-genometools
Architecture: armhf
Version: 1.5.8-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <sascha@steinbiss.name>
Description:
 genometools - versatile genome analysis toolkit
 genometools-common - shared data files for GenomeTools
 genometools-dbg - versatile genome analysis toolkit, with debug symbols
 genometools-doc - documentation for GenomeTools
 libgenometools0 - versatile genome analysis library
 libgenometools0-dev - development files for GenomeTools
 python-genometools - Python bindings for genometools
Changes:
 genometools (1.5.8-1) unstable; urgency=medium
 .
   * New upstream release.
   * Ensure that /usr/share/genometools/* is complete.
   * Fix spelling.
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents                                                             │
└──────────────────────────────────────────────────────────────────────────────┘


genometools-dbg_1.5.8-1_armhf.deb
─────────────────────────────────

 new debian package, version 2.0.
 size 4128586 bytes: control archive=713 bytes.
     623 bytes,    15 lines      control              
     341 bytes,     4 lines      md5sums              
 Package: genometools-dbg
 Source: genometools
 Version: 1.5.8-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 4598
 Depends: genometools (= 1.5.8-1) | libgenometools0 (= 1.5.8-1)
 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: 607fb35530bbf795541a4a68e86789c813030a39

drwxr-xr-x root/root         0 2016-01-13 06:42 ./
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/lib/
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/lib/debug/
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/lib/debug/.build-id/60/
-rw-r--r-- root/root   4683640 2016-01-13 06:42 ./usr/lib/debug/.build-id/60/7fb35530bbf795541a4a68e86789c813030a39.debug
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/share/
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/share/doc/genometools-dbg/
-rw-r--r-- root/root      2410 2016-01-07 22:19 ./usr/share/doc/genometools-dbg/changelog.Debian.gz
-rw-r--r-- root/root      6081 2016-01-07 19:56 ./usr/share/doc/genometools-dbg/changelog.gz
-rw-r--r-- root/root      5077 2014-12-12 20:59 ./usr/share/doc/genometools-dbg/copyright


genometools_1.5.8-1_armhf.deb
─────────────────────────────

 new debian package, version 2.0.
 size 1726618 bytes: control archive=3562 bytes.
     887 bytes,    16 lines      control              
    7249 bytes,   101 lines      md5sums              
 Package: genometools
 Version: 1.5.8-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 5507
 Depends: libbz2-1.0, libc6 (>= 2.15), libcairo2 (>= 1.2.4), libexpat1 (>= 2.0.1), libglib2.0-0 (>= 2.12.0), liblua5.1-0, libpango-1.0-0 (>= 1.14.0), libpangocairo-1.0-0 (>= 1.14.0), libsqlite3-0 (>= 3.5.9), libtre5, lua-filesystem, lua-lpeg, lua-md5, zlib1g (>= 1:1.2.3.3), genometools-common
 Section: science
 Priority: optional
 Homepage: http://genometools.org
 Description: versatile genome analysis toolkit
  The GenomeTools contains a collection of useful tools for biological
  sequence analysis and -presentation combined into a single binary.
  .
  The toolkit contains binaries for sequence and annotation handling, sequence
  compression, index structure generation and access, annotation visualization,
  and much more.

drwxr-xr-x root/root         0 2016-01-13 06:42 ./
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/bin/
-rwxr-xr-x root/root   5472628 2016-01-13 06:42 ./usr/bin/gt
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/share/
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/share/doc/genometools/
-rw-r--r-- root/root       833 2016-01-07 19:56 ./usr/share/doc/genometools/CONTRIBUTORS
-rw-r--r-- root/root      1772 2016-01-07 19:56 ./usr/share/doc/genometools/README
-rw-r--r-- root/root         6 2016-01-07 19:56 ./usr/share/doc/genometools/VERSION
-rw-r--r-- root/root      2410 2016-01-07 22:19 ./usr/share/doc/genometools/changelog.Debian.gz
-rw-r--r-- root/root      6081 2016-01-07 19:56 ./usr/share/doc/genometools/changelog.gz
-rw-r--r-- root/root      5077 2014-12-12 20:59 ./usr/share/doc/genometools/copyright
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/share/man/
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/share/man/man1/
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-rw-r--r-- root/root      1713 2016-01-13 06:42 ./usr/share/man/man1/gt-genomediff.1.gz
-rw-r--r-- root/root      1923 2016-01-13 06:42 ./usr/share/man/man1/gt-gff3.1.gz
-rw-r--r-- root/root       776 2016-01-13 06:42 ./usr/share/man/man1/gt-gff3_to_gtf.1.gz
-rw-r--r-- root/root       992 2016-01-13 06:42 ./usr/share/man/man1/gt-gff3validator.1.gz
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libgenometools0-dev_1.5.8-1_armhf.deb
─────────────────────────────────────

 new debian package, version 2.0.
 size 77460 bytes: control archive=5107 bytes.
     672 bytes,    18 lines      control              
   13509 bytes,   160 lines      md5sums              
 Package: libgenometools0-dev
 Source: genometools
 Version: 1.5.8-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 560
 Depends: libgenometools0 (= 1.5.8-1)
 Section: libdevel
 Priority: optional
 Homepage: http://genometools.org
 Description: development files for GenomeTools
  This package contains the GenomeTools static library and necessary
  header files.
  .
  Besides basic bioinformatics data structures, the library contains components
  for sequence and annotation handling, sequence compression, index structure
  generation and access, efficient matching, annotation visualization and much
  more.

drwxr-xr-x root/root         0 2016-01-13 06:42 ./
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/
drwxr-xr-x root/root         0 2016-01-13 06:15 ./usr/include/
drwxr-xr-x root/root         0 2016-01-13 06:15 ./usr/include/genometools/
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/include/genometools/annotationsketch/
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lrwxrwxrwx root/root         0 2016-01-13 06:42 ./usr/lib/libgenometools.so -> libgenometools.so.0
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drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-01-13 06:42 ./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_1.5.8-1_armhf.deb
─────────────────────────────────

 new debian package, version 2.0.
 size 1600934 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: 1.5.8-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 5368
 Depends: libbz2-1.0, libc6 (>= 2.15), libcairo2 (>= 1.2.4), libexpat1 (>= 2.0.1), libglib2.0-0 (>= 2.12.0), liblua5.1-0, libpango-1.0-0 (>= 1.14.0), libpangocairo-1.0-0 (>= 1.14.0), libsqlite3-0 (>= 3.5.9), libtre5, lua-filesystem, lua-lpeg, lua-md5, zlib1g (>= 1:1.2.3.3), genometools-common
 Section: libs
 Priority: optional
 Homepage: http://genometools.org
 Description: versatile genome analysis library
  This package contains the GenomeTools shared library and header
  files. It offers efficient sequence analysis components, available
  via an object-oriented interface.
  .
  Besides basic bioinformatics data structures, the library contains components
  for sequence and annotation handling, sequence compression, index structure
  generation and access, efficient matching, annotation visualization and much
  more.

drwxr-xr-x root/root         0 2016-01-13 06:42 ./
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/lib/
-rw-r--r-- root/root   5470896 2016-01-13 06:42 ./usr/lib/libgenometools.so.0
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/share/
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-01-13 06:42 ./usr/share/doc/libgenometools0/
-rw-r--r-- root/root      2410 2016-01-07 22:19 ./usr/share/doc/libgenometools0/changelog.Debian.gz
-rw-r--r-- root/root      6081 2016-01-07 19:56 ./usr/share/doc/libgenometools0/changelog.gz
-rw-r--r-- root/root      5077 2014-12-12 20:59 ./usr/share/doc/libgenometools0/copyright


┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build                                                                   │
└──────────────────────────────────────────────────────────────────────────────┘


┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use

┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

Build Architecture: armhf
Build-Space: 265704
Build-Time: 4006
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 1607
Job: genometools_1.5.8-1
Machine Architecture: armhf
Package: genometools
Package-Time: 5665
Source-Version: 1.5.8-1
Space: 265704
Status: successful
Version: 1.5.8-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20160113-0643
Build needed 01:34:25, 265704k disc space
Raspbian Package Auto-Building

Build log for genometools (1.5.8-1) on armhf
