Build log for genometools (1.5.3-1) on armhf

genometools → 1.5.3-1 → armhf → 2014-07-27 07:35:19

sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-04

╔══════════════════════════════════════════════════════════════════════════════╗
║ genometools 1.5.3-1 (armhf)                                27 Jul 2014 05:59 ║
╚══════════════════════════════════════════════════════════════════════════════╝

Package: genometools
Version: 1.5.3-1
Source Version: 1.5.3-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'build/genometools-QFkRzw/genometools-1.5.3' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/genometools-QFkRzw' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-038cab1f-7a49-4e7c-accc-4d126c069a41' with '«CHROOT»'

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

Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [7425 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8413 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 15.8 MB in 29s (544 kB/s)
Reading package lists...

┌──────────────────────────────────────────────────────────────────────────────┐
│ 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 12.4 MB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main genometools 1.5.3-1 (dsc) [2767 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main genometools 1.5.3-1 (tar) [12.3 MB]
Get:3 http://172.17.0.1/private/ jessie-staging/main genometools 1.5.3-1 (diff) [14.6 kB]
Fetched 12.4 MB in 2s (4138 kB/s)
Download complete and in download only mode

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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-q1kFxf/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 38 not upgraded.
Need to get 0 B/818 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11827 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), liblua5.1-0-dev, lua-md5-dev, lua-filesystem-dev, lua-lpeg-dev, libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, libncurses5-dev, libsqlite3-dev, libbam-dev, libpango1.0-dev, libtre-dev, texlive-latex-base, texlive-latex-extra, texlive-fonts-extra, latex-xcolor, texlive-fonts-recommended, python, asciidoc, libxml2-utils, xsltproc, ruby, docbook-xsl
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), liblua5.1-0-dev, lua-md5-dev, lua-filesystem-dev, lua-lpeg-dev, libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, libncurses5-dev, libsqlite3-dev, libbam-dev, libpango1.0-dev, libtre-dev, texlive-latex-base, texlive-latex-extra, texlive-fonts-extra, latex-xcolor, texlive-fonts-recommended, python, asciidoc, libxml2-utils, xsltproc, ruby, docbook-xsl
dpkg-deb: building package `sbuild-build-depends-genometools-dummy' in `/«BUILDDIR»/resolver-erfZz_/apt_archive/sbuild-build-depends-genometools-dummy.deb'.
OK
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
  asciidoc bsdmainutils debhelper docbook-xsl file fontconfig
  fontconfig-config fonts-cabin fonts-comfortaa fonts-dejavu-core
  fonts-dejavu-extra fonts-droid fonts-ebgaramond fonts-ebgaramond-extra
  fonts-font-awesome fonts-freefont-otf fonts-freefont-ttf fonts-gfs-artemisia
  fonts-gfs-complutum fonts-gfs-didot fonts-gfs-neohellenic fonts-gfs-olga
  fonts-gfs-solomos fonts-inconsolata fonts-junicode fonts-lato
  fonts-linuxlibertine fonts-lobster fonts-lobstertwo fonts-oflb-asana-math
  fonts-sil-gentium fonts-sil-gentium-basic fonts-stix gettext gettext-base
  gir1.2-freedesktop gir1.2-glib-2.0 gir1.2-pango-1.0 groff-base
  intltool-debian libasprintf0c2 libavahi-client3 libavahi-common-data
  libavahi-common3 libbam-dev libbz2-dev libcairo-gobject2
  libcairo-script-interpreter2 libcairo2 libcairo2-dev libcroco3 libcups2
  libcupsfilters1 libcupsimage2 libdatrie1 libdrm-dev libdrm-nouveau2
  libdrm-omap1 libdrm-radeon1 libdrm2 libelfg0 libexpat1 libexpat1-dev libffi6
  libfontconfig1 libfontconfig1-dev libfreetype6 libfreetype6-dev libgcrypt11
  libgirepository-1.0-1 libgl1-mesa-dev libgl1-mesa-glx libglapi-mesa
  libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libgnutls-deb0-28
  libgpg-error0 libgraphite2-3 libgs9 libgs9-common libgssapi-krb5-2
  libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b
  libhogweed2 libice-dev libice6 libicu52 libidn11 libijs-0.35 libjasper1
  libjbig0 libjbig2dec0 libjpeg8 libjs-jquery libk5crypto3 libkeyutils1
  libkpathsea6 libkrb5-3 libkrb5support0 liblcms2-2 liblua5.1-0
  liblua5.1-0-dev liblzo2-2 libmagic1 libncurses5-dev libnettle4 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 libpcre3-dev
  libpcrecpp0 libpipeline1 libpixman-1-0 libpixman-1-dev libpng12-0
  libpng12-dev libpoppler46 libpotrace0 libptexenc1 libpthread-stubs0-dev
  libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline-dev
  libreadline6-dev libruby2.1 libsm-dev libsm6 libsqlite3-0 libsqlite3-dev
  libssl1.0.0 libsynctex1 libtasn1-6 libthai-data libthai0 libtiff5
  libtinfo-dev libtre-dev libtre5 libunistring0 libx11-6 libx11-data
  libx11-dev libx11-xcb-dev libx11-xcb1 libxau-dev libxau6 libxaw7
  libxcb-dri2-0 libxcb-dri2-0-dev libxcb-dri3-0 libxcb-dri3-dev libxcb-glx0
  libxcb-glx0-dev libxcb-present-dev libxcb-present0 libxcb-randr0
  libxcb-randr0-dev libxcb-render0 libxcb-render0-dev libxcb-shape0
  libxcb-shape0-dev libxcb-shm0 libxcb-shm0-dev libxcb-sync-dev libxcb-sync1
  libxcb-xfixes0 libxcb-xfixes0-dev libxcb1 libxcb1-dev libxdamage-dev
  libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes-dev
  libxfixes3 libxft-dev libxft2 libxi6 libxml2 libxml2-utils libxmu6 libxpm4
  libxrender-dev libxrender1 libxshmfence-dev libxshmfence1 libxslt1.1 libxt6
  libxxf86vm-dev libxxf86vm1 libyaml-0-2 libzzip-0-13 lua-filesystem
  lua-filesystem-dev lua-lpeg lua-lpeg-dev lua-md5 lua-md5-dev man-db
  mesa-common-dev mime-support pkg-config po-debconf poppler-data
  preview-latex-style python python-minimal python-support python2.7
  python2.7-minimal ruby ruby2.1 rubygems-integration sgml-base 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 ucf x11-common
  x11proto-core-dev x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev
  x11proto-gl-dev x11proto-input-dev x11proto-kb-dev x11proto-render-dev
  x11proto-xext-dev x11proto-xf86vidmode-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 groff libcairo2-doc cups-common
  rng-tools libglib2.0-doc gnutls-bin krb5-doc krb5-user libice-doc
  libjasper-runtime liblcms2-utils ncurses-doc ttf-baekmuk ttf-arphic-gbsn00lp
  ttf-arphic-bsmi00lp ttf-arphic-gkai00mp ttf-arphic-bkai00mp libpango1.0-doc
  imagemagick 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 ruby-dev bundler sgml-base-doc gv
  postscript-viewer perl-tk xpdf-reader pdf-viewer cm-super python-pygments
  libfile-which-perl libtcltk-ruby dot2tex gvfs-bin
Recommended packages:
  dblatex docbook-utils xmlto docbook-xml curl wget lynx-cur autopoint
  libasprintf-dev libgettextpo-dev libgl1-mesa-dri shared-mime-info
  javascript-common krb5-locales libtool libx11-doc libmail-sendmail-perl
  lmodern wish texlive-fonts-extra-doc tex-gyre texlive-fonts-recommended-doc
  tipa texlive-latex-base-doc texlive-latex-extra-doc
  texlive-latex-recommended-doc prosper texlive-pictures-doc prerex
  libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils
  x11-xserver-utils
The following NEW packages will be installed:
  asciidoc bsdmainutils debhelper docbook-xsl file fontconfig
  fontconfig-config fonts-cabin fonts-comfortaa fonts-dejavu-core
  fonts-dejavu-extra fonts-droid fonts-ebgaramond fonts-ebgaramond-extra
  fonts-font-awesome fonts-freefont-otf fonts-freefont-ttf fonts-gfs-artemisia
  fonts-gfs-complutum fonts-gfs-didot fonts-gfs-neohellenic fonts-gfs-olga
  fonts-gfs-solomos fonts-inconsolata fonts-junicode fonts-lato
  fonts-linuxlibertine fonts-lobster fonts-lobstertwo fonts-oflb-asana-math
  fonts-sil-gentium fonts-sil-gentium-basic fonts-stix gettext gettext-base
  gir1.2-freedesktop gir1.2-glib-2.0 gir1.2-pango-1.0 groff-base
  intltool-debian libasprintf0c2 libavahi-client3 libavahi-common-data
  libavahi-common3 libbam-dev libbz2-dev libcairo-gobject2
  libcairo-script-interpreter2 libcairo2 libcairo2-dev libcroco3 libcups2
  libcupsfilters1 libcupsimage2 libdatrie1 libdrm-dev libdrm-nouveau2
  libdrm-omap1 libdrm-radeon1 libdrm2 libelfg0 libexpat1 libexpat1-dev libffi6
  libfontconfig1 libfontconfig1-dev libfreetype6 libfreetype6-dev libgcrypt11
  libgirepository-1.0-1 libgl1-mesa-dev libgl1-mesa-glx libglapi-mesa
  libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libgnutls-deb0-28
  libgpg-error0 libgraphite2-3 libgs9 libgs9-common libgssapi-krb5-2
  libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b
  libhogweed2 libice-dev libice6 libicu52 libidn11 libijs-0.35 libjasper1
  libjbig0 libjbig2dec0 libjpeg8 libjs-jquery libk5crypto3 libkeyutils1
  libkpathsea6 libkrb5-3 libkrb5support0 liblcms2-2 liblua5.1-0
  liblua5.1-0-dev liblzo2-2 libmagic1 libncurses5-dev libnettle4 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 libpcre3-dev
  libpcrecpp0 libpipeline1 libpixman-1-0 libpixman-1-dev libpng12-0
  libpng12-dev libpoppler46 libpotrace0 libptexenc1 libpthread-stubs0-dev
  libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline-dev
  libreadline6-dev libruby2.1 libsm-dev libsm6 libsqlite3-0 libsqlite3-dev
  libssl1.0.0 libsynctex1 libtasn1-6 libthai-data libthai0 libtiff5
  libtinfo-dev libtre-dev libtre5 libunistring0 libx11-6 libx11-data
  libx11-dev libx11-xcb-dev libx11-xcb1 libxau-dev libxau6 libxaw7
  libxcb-dri2-0 libxcb-dri2-0-dev libxcb-dri3-0 libxcb-dri3-dev libxcb-glx0
  libxcb-glx0-dev libxcb-present-dev libxcb-present0 libxcb-randr0
  libxcb-randr0-dev libxcb-render0 libxcb-render0-dev libxcb-shape0
  libxcb-shape0-dev libxcb-shm0 libxcb-shm0-dev libxcb-sync-dev libxcb-sync1
  libxcb-xfixes0 libxcb-xfixes0-dev libxcb1 libxcb1-dev libxdamage-dev
  libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes-dev
  libxfixes3 libxft-dev libxft2 libxi6 libxml2 libxml2-utils libxmu6 libxpm4
  libxrender-dev libxrender1 libxshmfence-dev libxshmfence1 libxslt1.1 libxt6
  libxxf86vm-dev libxxf86vm1 libyaml-0-2 libzzip-0-13 lua-filesystem
  lua-filesystem-dev lua-lpeg lua-lpeg-dev lua-md5 lua-md5-dev man-db
  mesa-common-dev mime-support pkg-config po-debconf poppler-data
  preview-latex-style python python-minimal python-support python2.7
  python2.7-minimal ruby ruby2.1 rubygems-integration
  sbuild-build-depends-genometools-dummy sgml-base 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 ucf x11-common
  x11proto-core-dev x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev
  x11proto-gl-dev x11proto-input-dev x11proto-kb-dev x11proto-render-dev
  x11proto-xext-dev x11proto-xf86vidmode-dev xdg-utils xml-core
  xorg-sgml-doctools xsltproc xtrans-dev zlib1g-dev
0 upgraded, 257 newly installed, 0 to remove and 38 not upgraded.
Need to get 312 MB/312 MB of archives.
After this operation, 970 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.3.0-1 [21.1 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main libssl1.0.0 armhf 1.0.1h-3 [830 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-6 [962 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.7.1-1 [964 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3.2-4 [29.4 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libgpg-error0 armhf 1.13-0.2 [58.2 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libgcrypt11 armhf 1.5.3-4 [233 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libnettle4 armhf 2.7.1-2 [177 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libhogweed2 armhf 2.7.1-2 [116 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.1-2 [18.1 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main libp11-kit0 armhf 0.20.2-5 [66.1 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main libtasn1-6 armhf 4.0-2 [42.0 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main libgnutls-deb0-28 armhf 3.2.15-3 [609 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main libkeyutils1 armhf 1.5.9-4 [10.8 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main libkrb5support0 armhf 1.12.1+dfsg-5 [53.0 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main libk5crypto3 armhf 1.12.1+dfsg-5 [105 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main libkrb5-3 armhf 1.12.1+dfsg-5 [248 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main libgssapi-krb5-2 armhf 1.12.1+dfsg-5 [123 kB]
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Get:24 http://172.17.0.1/private/ jessie-staging/main libpython2.7-minimal armhf 2.7.8-1 [347 kB]
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Get:26 http://172.17.0.1/private/ jessie-staging/main fonts-droid all 1:4.3-3 [3038 kB]
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Get:34 http://172.17.0.1/private/ jessie-staging/main ucf all 3.0030 [69.7 kB]
Get:35 http://172.17.0.1/private/ jessie-staging/main fonts-dejavu-core all 2.34-1 [1047 kB]
Get:36 http://172.17.0.1/private/ jessie-staging/main fontconfig-config all 2.11.0-5 [273 kB]
Get:37 http://172.17.0.1/private/ jessie-staging/main libfontconfig1 armhf 2.11.0-5 [310 kB]
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Get:48 http://172.17.0.1/private/ jessie-staging/main libxcb-glx0 armhf 1.10-3 [23.8 kB]
Get:49 http://172.17.0.1/private/ jessie-staging/main libxcb-present0 armhf 1.10-3 [10.8 kB]
Get:50 http://172.17.0.1/private/ jessie-staging/main libxcb-sync1 armhf 1.10-3 [13.2 kB]
Get:51 http://172.17.0.1/private/ jessie-staging/main libxfixes3 armhf 1:5.0.1-2 [19.6 kB]
Get:52 http://172.17.0.1/private/ jessie-staging/main libxdamage1 armhf 1:1.1.4-2 [13.9 kB]
Get:53 http://172.17.0.1/private/ jessie-staging/main libxext6 armhf 2:1.3.2-1 [51.1 kB]
Get:54 http://172.17.0.1/private/ jessie-staging/main libxshmfence1 armhf 1.1-2 [6736 B]
Get:55 http://172.17.0.1/private/ jessie-staging/main libxxf86vm1 armhf 1:1.1.3-1 [20.0 kB]
Get:56 http://172.17.0.1/private/ jessie-staging/main libgl1-mesa-glx armhf 10.2.4-1 [136 kB]
Get:57 http://172.17.0.1/private/ jessie-staging/main libpixman-1-0 armhf 0.32.6-1 [422 kB]
Get:58 http://172.17.0.1/private/ jessie-staging/main libxcb-render0 armhf 1.10-3 [16.0 kB]
Get:59 http://172.17.0.1/private/ jessie-staging/main libxcb-shm0 armhf 1.10-3 [11.0 kB]
Get:60 http://172.17.0.1/private/ jessie-staging/main libxrender1 armhf 1:0.9.8-1 [30.4 kB]
Get:61 http://172.17.0.1/private/ jessie-staging/main libcairo2 armhf 1.12.16-2+rpi1 [894 kB]
Get:62 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.40.0-3 [2247 kB]
Get:63 http://172.17.0.1/private/ jessie-staging/main libcairo-gobject2 armhf 1.12.16-2+rpi1 [537 kB]
Get:64 http://172.17.0.1/private/ jessie-staging/main liblzo2-2 armhf 2.08-1 [46.9 kB]
Get:65 http://172.17.0.1/private/ jessie-staging/main libcairo-script-interpreter2 armhf 1.12.16-2+rpi1 [564 kB]
Get:66 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
Get:67 http://172.17.0.1/private/ jessie-staging/main libcups2 armhf 1.7.4-1 [250 kB]
Get:68 http://172.17.0.1/private/ jessie-staging/main libcupsimage2 armhf 1.7.4-1 [113 kB]
Get:69 http://172.17.0.1/private/ jessie-staging/main libjpeg8 armhf 8d1-1 [108 kB]
Get:70 http://172.17.0.1/private/ jessie-staging/main libjbig0 armhf 2.0-2.1 [26.8 kB]
Get:71 http://172.17.0.1/private/ jessie-staging/main libtiff5 armhf 4.0.3-9 [191 kB]
Get:72 http://172.17.0.1/private/ jessie-staging/main libcupsfilters1 armhf 1.0.54-3+b1 [93.1 kB]
Get:73 http://172.17.0.1/private/ jessie-staging/main libdatrie1 armhf 0.2.8-1 [29.1 kB]
Get:74 http://172.17.0.1/private/ jessie-staging/main libdrm-nouveau2 armhf 2.4.54-1 [21.1 kB]
Get:75 http://172.17.0.1/private/ jessie-staging/main libdrm-omap1 armhf 2.4.54-1 [13.5 kB]
Get:76 http://172.17.0.1/private/ jessie-staging/main libdrm-radeon1 armhf 2.4.54-1 [28.0 kB]
Get:77 http://172.17.0.1/private/ jessie-staging/main libelfg0 armhf 0.8.13-5 [55.7 kB]
Get:78 http://172.17.0.1/private/ jessie-staging/main libgraphite2-3 armhf 1.2.4-3 [48.2 kB]
Get:79 http://172.17.0.1/private/ jessie-staging/main libharfbuzz0b armhf 0.9.29-1 [435 kB]
Get:80 http://172.17.0.1/private/ jessie-staging/main libharfbuzz-gobject0 armhf 0.9.29-1 [340 kB]
Get:81 http://172.17.0.1/private/ jessie-staging/main libicu52 armhf 52.1-4 [6522 kB]
Get:82 http://172.17.0.1/private/ jessie-staging/main libharfbuzz-icu0 armhf 0.9.29-1 [336 kB]
Get:83 http://172.17.0.1/private/ jessie-staging/main x11-common all 1:7.7+7 [287 kB]
Get:84 http://172.17.0.1/private/ jessie-staging/main libice6 armhf 2:1.0.9-1 [51.2 kB]
Get:85 http://172.17.0.1/private/ jessie-staging/main libijs-0.35 armhf 0.35-10 [18.5 kB]
Get:86 http://172.17.0.1/private/ jessie-staging/main libjasper1 armhf 1.900.1-debian1-2 [109 kB]
Get:87 http://172.17.0.1/private/ jessie-staging/main liblcms2-2 armhf 2.6-3 [113 kB]
Get:88 http://172.17.0.1/private/ jessie-staging/main liblua5.1-0 armhf 5.1.5-5 [146 kB]
Get:89 http://172.17.0.1/private/ jessie-staging/main libthai-data all 0.1.20-3 [157 kB]
Get:90 http://172.17.0.1/private/ jessie-staging/main libthai0 armhf 0.1.20-3 [41.6 kB]
Get:91 http://172.17.0.1/private/ jessie-staging/main fontconfig armhf 2.11.0-5 [401 kB]
Get:92 http://172.17.0.1/private/ jessie-staging/main libpango-1.0-0 armhf 1.36.3-1 [265 kB]
Get:93 http://172.17.0.1/private/ jessie-staging/main libpangoft2-1.0-0 armhf 1.36.3-1 [199 kB]
Get:94 http://172.17.0.1/private/ jessie-staging/main libpangocairo-1.0-0 armhf 1.36.3-1 [189 kB]
Get:95 http://172.17.0.1/private/ jessie-staging/main libxft2 armhf 2.3.2-1 [48.3 kB]
Get:96 http://172.17.0.1/private/ jessie-staging/main libpangoxft-1.0-0 armhf 1.36.3-1 [185 kB]
Get:97 http://172.17.0.1/private/ jessie-staging/main libpaper1 armhf 1.1.24+nmu3 [20.7 kB]
Get:98 http://172.17.0.1/private/ jessie-staging/main libpcrecpp0 armhf 1:8.31-5 [124 kB]
Get:99 http://172.17.0.1/private/ jessie-staging/main libopenjpeg5 armhf 1.5.2-2 [93.5 kB]
Get:100 http://172.17.0.1/private/ jessie-staging/main libpoppler46 armhf 0.26.3-1 [1075 kB]
Get:101 http://172.17.0.1/private/ jessie-staging/main libsm6 armhf 2:1.2.2-1 [31.2 kB]
Get:102 http://172.17.0.1/private/ jessie-staging/main libtre5 armhf 0.8.0-4 [51.3 kB]
Get:103 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:104 http://172.17.0.1/private/ jessie-staging/main libxt6 armhf 1:1.1.4-1 [183 kB]
Get:105 http://172.17.0.1/private/ jessie-staging/main libxmu6 armhf 2:1.1.2-1 [50.8 kB]
Get:106 http://172.17.0.1/private/ jessie-staging/main libxpm4 armhf 1:3.5.11-1 [41.7 kB]
Get:107 http://172.17.0.1/private/ jessie-staging/main libxaw7 armhf 2:1.0.12-2 [159 kB]
Get:108 http://172.17.0.1/private/ jessie-staging/main libxcb-randr0 armhf 1.10-3 [18.7 kB]
Get:109 http://172.17.0.1/private/ jessie-staging/main libxcb-shape0 armhf 1.10-3 [11.0 kB]
Get:110 http://172.17.0.1/private/ jessie-staging/main libxcb-xfixes0 armhf 1.10-3 [13.8 kB]
Get:111 http://172.17.0.1/private/ jessie-staging/main libxi6 armhf 2:1.7.2-1 [76.8 kB]
Get:112 http://172.17.0.1/private/ jessie-staging/main libxslt1.1 armhf 1.1.28-2 [243 kB]
Get:113 http://172.17.0.1/private/ jessie-staging/main libyaml-0-2 armhf 0.1.4-3.2 [38.4 kB]
Get:114 http://172.17.0.1/private/ jessie-staging/main libzzip-0-13 armhf 0.13.62-2 [51.0 kB]
Get:115 http://172.17.0.1/private/ jessie-staging/main lua-filesystem armhf 1.6.2-1 [11.8 kB]
Get:116 http://172.17.0.1/private/ jessie-staging/main lua-filesystem-dev armhf 1.6.2-1 [25.6 kB]
Get:117 http://172.17.0.1/private/ jessie-staging/main lua-lpeg armhf 0.12-1 [38.8 kB]
Get:118 http://172.17.0.1/private/ jessie-staging/main lua-lpeg-dev armhf 0.12-1 [61.5 kB]
Get:119 http://172.17.0.1/private/ jessie-staging/main lua-md5 armhf 1.2+git+1+8d87fee-1 [14.6 kB]
Get:120 http://172.17.0.1/private/ jessie-staging/main lua-md5-dev armhf 1.2+git+1+8d87fee-1 [22.3 kB]
Get:121 http://172.17.0.1/private/ jessie-staging/main poppler-data all 0.4.6-5 [1489 kB]
Get:122 http://172.17.0.1/private/ jessie-staging/main sgml-base all 1.26+nmu4 [14.6 kB]
Get:123 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.19-1 [57.7 kB]
Get:124 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.3.2-4 [111 kB]
Get:125 http://172.17.0.1/private/ jessie-staging/main mime-support all 3.56 [35.5 kB]
Get:126 http://172.17.0.1/private/ jessie-staging/main libpython2.7-stdlib armhf 2.7.8-1 [1834 kB]
Get:127 http://172.17.0.1/private/ jessie-staging/main python2.7 armhf 2.7.8-1 [243 kB]
Get:128 http://172.17.0.1/private/ jessie-staging/main python-minimal armhf 2.7.8-1 [39.8 kB]
Get:129 http://172.17.0.1/private/ jessie-staging/main libpython-stdlib armhf 2.7.8-1 [19.2 kB]
Get:130 http://172.17.0.1/private/ jessie-staging/main python armhf 2.7.8-1 [150 kB]
Get:131 http://172.17.0.1/private/ jessie-staging/main python-support all 1.0.15 [33.6 kB]
Get:132 http://172.17.0.1/private/ jessie-staging/main asciidoc all 8.6.9-2 [814 kB]
Get:133 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.3.2-4 [1134 kB]
Get:134 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:135 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu3 [220 kB]
Get:136 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20140613 [692 kB]
Get:137 http://172.17.0.1/private/ jessie-staging/main xml-core all 0.13+nmu2 [24.2 kB]
Get:138 http://172.17.0.1/private/ jessie-staging/main docbook-xsl all 1.78.1+dfsg-1 [2339 kB]
Get:139 http://172.17.0.1/private/ jessie-staging/main fonts-cabin all 1.5-2 [139 kB]
Get:140 http://172.17.0.1/private/ jessie-staging/main fonts-comfortaa all 2.003-1 [133 kB]
Get:141 http://172.17.0.1/private/ jessie-staging/main fonts-dejavu-extra all 2.34-1 [1771 kB]
Get:142 http://172.17.0.1/private/ jessie-staging/main fonts-ebgaramond all 0.015+git20130628-3 [415 kB]
Get:143 http://172.17.0.1/private/ jessie-staging/main fonts-ebgaramond-extra all 0.015+git20130628-3 [680 kB]
Get:144 http://172.17.0.1/private/ jessie-staging/main fonts-font-awesome all 4.1.0~dfsg-1 [375 kB]
Get:145 http://172.17.0.1/private/ jessie-staging/main fonts-freefont-otf all 20120503-4 [3186 kB]
Get:146 http://172.17.0.1/private/ jessie-staging/main fonts-freefont-ttf all 20120503-4 [4262 kB]
Get:147 http://172.17.0.1/private/ jessie-staging/main fonts-gfs-artemisia all 1.1-5 [259 kB]
Get:148 http://172.17.0.1/private/ jessie-staging/main fonts-gfs-complutum all 1.1-6 [41.6 kB]
Get:149 http://172.17.0.1/private/ jessie-staging/main fonts-gfs-didot all 1.1-6 [278 kB]
Get:150 http://172.17.0.1/private/ jessie-staging/main fonts-gfs-neohellenic all 1.1-6 [215 kB]
Get:151 http://172.17.0.1/private/ jessie-staging/main fonts-gfs-olga all 1.1-5 [33.2 kB]
Get:152 http://172.17.0.1/private/ jessie-staging/main fonts-gfs-solomos all 1.1-5 [40.6 kB]
Get:153 http://172.17.0.1/private/ jessie-staging/main fonts-inconsolata all 001.010-5 [61.6 kB]
Get:154 http://172.17.0.1/private/ jessie-staging/main fonts-junicode all 0.7.8-2 [643 kB]
Get:155 http://172.17.0.1/private/ jessie-staging/main fonts-linuxlibertine all 5.3.0-2 [1713 kB]
Get:156 http://172.17.0.1/private/ jessie-staging/main fonts-lobster all 2.0-2 [39.5 kB]
Get:157 http://172.17.0.1/private/ jessie-staging/main fonts-lobstertwo all 2.0-2 [94.0 kB]
Get:158 http://172.17.0.1/private/ jessie-staging/main fonts-oflb-asana-math all 000.907-6 [245 kB]
Get:159 http://172.17.0.1/private/ jessie-staging/main fonts-sil-gentium all 20081126:1.02-13 [241 kB]
Get:160 http://172.17.0.1/private/ jessie-staging/main fonts-sil-gentium-basic all 1.1-7 [382 kB]
Get:161 http://172.17.0.1/private/ jessie-staging/main libgirepository-1.0-1 armhf 1.40.0-2 [80.0 kB]
Get:162 http://172.17.0.1/private/ jessie-staging/main gir1.2-glib-2.0 armhf 1.40.0-2 [138 kB]
Get:163 http://172.17.0.1/private/ jessie-staging/main gir1.2-freedesktop armhf 1.40.0-2 [20.2 kB]
Get:164 http://172.17.0.1/private/ jessie-staging/main gir1.2-pango-1.0 armhf 1.36.3-1 [191 kB]
Get:165 http://172.17.0.1/private/ jessie-staging/main libbam-dev armhf 0.1.19-1 [110 kB]
Get:166 http://172.17.0.1/private/ jessie-staging/main libbz2-dev armhf 1.0.6-5 [33.8 kB]
Get:167 http://172.17.0.1/private/ jessie-staging/main libexpat1-dev armhf 2.1.0-6 [117 kB]
Get:168 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-1+rpi1 [192 kB]
Get:169 http://172.17.0.1/private/ jessie-staging/main libpng12-dev armhf 1.2.50-1 [260 kB]
Get:170 http://172.17.0.1/private/ jessie-staging/main libfreetype6-dev armhf 2.5.2-1 [575 kB]
Get:171 http://172.17.0.1/private/ jessie-staging/main pkg-config armhf 0.28-1 [55.1 kB]
Get:172 http://172.17.0.1/private/ jessie-staging/main libfontconfig1-dev armhf 2.11.0-5 [873 kB]
Get:173 http://172.17.0.1/private/ jessie-staging/main xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:174 http://172.17.0.1/private/ jessie-staging/main x11proto-core-dev all 7.0.26-1 [729 kB]
Get:175 http://172.17.0.1/private/ jessie-staging/main libxau-dev armhf 1:1.0.8-1 [23.0 kB]
Get:176 http://172.17.0.1/private/ jessie-staging/main libxdmcp-dev armhf 1:1.1.1-1 [40.8 kB]
Get:177 http://172.17.0.1/private/ jessie-staging/main x11proto-input-dev all 2.3.1-1 [157 kB]
Get:178 http://172.17.0.1/private/ jessie-staging/main x11proto-kb-dev all 1.0.6-2 [269 kB]
Get:179 http://172.17.0.1/private/ jessie-staging/main xtrans-dev all 1.3.4-1 [99.3 kB]
Get:180 http://172.17.0.1/private/ jessie-staging/main libpthread-stubs0-dev armhf 0.3-4 [4042 B]
Get:181 http://172.17.0.1/private/ jessie-staging/main libxcb1-dev armhf 1.10-3 [78.1 kB]
Get:182 http://172.17.0.1/private/ jessie-staging/main libx11-dev armhf 2:1.6.2-2 [728 kB]
Get:183 http://172.17.0.1/private/ jessie-staging/main x11proto-render-dev all 2:0.11.1-2 [20.8 kB]
Get:184 http://172.17.0.1/private/ jessie-staging/main libxrender-dev armhf 1:0.9.8-1 [38.8 kB]
Get:185 http://172.17.0.1/private/ jessie-staging/main x11proto-xext-dev all 7.3.0-1 [212 kB]
Get:186 http://172.17.0.1/private/ jessie-staging/main libxext-dev armhf 2:1.3.2-1 [110 kB]
Get:187 http://172.17.0.1/private/ jessie-staging/main libice-dev armhf 2:1.0.9-1 [58.1 kB]
Get:188 http://172.17.0.1/private/ jessie-staging/main libsm-dev armhf 2:1.2.2-1 [33.5 kB]
Get:189 http://172.17.0.1/private/ jessie-staging/main libpixman-1-dev armhf 0.32.6-1 [440 kB]
Get:190 http://172.17.0.1/private/ jessie-staging/main libxcb-render0-dev armhf 1.10-3 [21.7 kB]
Get:191 http://172.17.0.1/private/ jessie-staging/main libxcb-shm0-dev armhf 1.10-3 [12.4 kB]
Get:192 http://172.17.0.1/private/ jessie-staging/main libdrm-dev armhf 2.4.54-1 [118 kB]
Get:193 http://172.17.0.1/private/ jessie-staging/main mesa-common-dev armhf 10.2.4-1 [298 kB]
Get:194 http://172.17.0.1/private/ jessie-staging/main libx11-xcb-dev armhf 2:1.6.2-2 [165 kB]
Get:195 http://172.17.0.1/private/ jessie-staging/main libxcb-dri3-dev armhf 1.10-3 [11.4 kB]
Get:196 http://172.17.0.1/private/ jessie-staging/main libxcb-randr0-dev armhf 1.10-3 [25.6 kB]
Get:197 http://172.17.0.1/private/ jessie-staging/main libxcb-shape0-dev armhf 1.10-3 [12.6 kB]
Get:198 http://172.17.0.1/private/ jessie-staging/main libxcb-xfixes0-dev armhf 1.10-3 [17.1 kB]
Get:199 http://172.17.0.1/private/ jessie-staging/main libxcb-sync-dev armhf 1.10-3 [15.8 kB]
Get:200 http://172.17.0.1/private/ jessie-staging/main libxcb-present-dev armhf 1.10-3 [12.4 kB]
Get:201 http://172.17.0.1/private/ jessie-staging/main libxshmfence-dev armhf 1.1-2 [6172 B]
Get:202 http://172.17.0.1/private/ jessie-staging/main libxcb-dri2-0-dev armhf 1.10-3 [14.3 kB]
Get:203 http://172.17.0.1/private/ jessie-staging/main libxcb-glx0-dev armhf 1.10-3 [35.2 kB]
Get:204 http://172.17.0.1/private/ jessie-staging/main x11proto-fixes-dev all 1:5.0-2 [19.2 kB]
Get:205 http://172.17.0.1/private/ jessie-staging/main libxfixes-dev armhf 1:5.0.1-2 [21.5 kB]
Get:206 http://172.17.0.1/private/ jessie-staging/main x11proto-damage-dev all 1:1.2.1-2 [11.8 kB]
Get:207 http://172.17.0.1/private/ jessie-staging/main libxdamage-dev armhf 1:1.1.4-2 [13.7 kB]
Get:208 http://172.17.0.1/private/ jessie-staging/main x11proto-xf86vidmode-dev all 2.3.1-2 [6114 B]
Get:209 http://172.17.0.1/private/ jessie-staging/main libxxf86vm-dev armhf 1:1.1.3-1 [25.5 kB]
Get:210 http://172.17.0.1/private/ jessie-staging/main x11proto-dri2-dev all 2.8-2 [18.2 kB]
Get:211 http://172.17.0.1/private/ jessie-staging/main x11proto-gl-dev all 1.4.17-1 [28.0 kB]
Get:212 http://172.17.0.1/private/ jessie-staging/main libgl1-mesa-dev armhf 10.2.4-1 [37.3 kB]
Get:213 http://172.17.0.1/private/ jessie-staging/main libglib2.0-data all 2.40.0-3 [2183 kB]
Get:214 http://172.17.0.1/private/ jessie-staging/main libglib2.0-bin armhf 2.40.0-3 [1359 kB]
Get:215 http://172.17.0.1/private/ jessie-staging/main libpcre3-dev armhf 1:8.31-5 [357 kB]
Get:216 http://172.17.0.1/private/ jessie-staging/main libglib2.0-dev armhf 2.40.0-3 [2471 kB]
Get:217 http://172.17.0.1/private/ jessie-staging/main libcairo2-dev armhf 1.12.16-2+rpi1 [1028 kB]
Get:218 http://172.17.0.1/private/ jessie-staging/main libjbig2dec0 armhf 0.11+20120125-1 [46.4 kB]
Get:219 http://172.17.0.1/private/ jessie-staging/main libgs9-common all 9.05~dfsg-8.1 [1981 kB]
Get:220 http://172.17.0.1/private/ jessie-staging/main libgs9 armhf 9.05~dfsg-8.1 [1564 kB]
Get:221 http://172.17.0.1/private/ jessie-staging/main libharfbuzz-dev armhf 0.9.29-1 [360 kB]
Get:222 http://172.17.0.1/private/ jessie-staging/main libjs-jquery all 1.7.2+dfsg-3 [96.9 kB]
Get:223 http://172.17.0.1/private/ jessie-staging/main libkpathsea6 armhf 2014.20140528.34243-4 [143 kB]
Get:224 http://172.17.0.1/private/ jessie-staging/main libtinfo-dev armhf 5.9+20140118-1 [64.8 kB]
Get:225 http://172.17.0.1/private/ jessie-staging/main libreadline6-dev armhf 6.3-6 [194 kB]
Get:226 http://172.17.0.1/private/ jessie-staging/main libreadline-dev armhf 6.3-6 [994 B]
Get:227 http://172.17.0.1/private/ jessie-staging/main liblua5.1-0-dev armhf 5.1.5-5 [202 kB]
Get:228 http://172.17.0.1/private/ jessie-staging/main libncurses5-dev armhf 5.9+20140118-1 [152 kB]
Get:229 http://172.17.0.1/private/ jessie-staging/main libxft-dev armhf 2.3.2-1 [59.1 kB]
Get:230 http://172.17.0.1/private/ jessie-staging/main libpango1.0-dev armhf 1.36.3-1 [422 kB]
Get:231 http://172.17.0.1/private/ jessie-staging/main libpaper-utils armhf 1.1.24+nmu3 [17.0 kB]
Get:232 http://172.17.0.1/private/ jessie-staging/main libpotrace0 armhf 1.11-2 [22.6 kB]
Get:233 http://172.17.0.1/private/ jessie-staging/main libptexenc1 armhf 2014.20140528.34243-4 [51.3 kB]
Get:234 http://172.17.0.1/private/ jessie-staging/main libsqlite3-dev armhf 3.8.5-2 [464 kB]
Get:235 http://172.17.0.1/private/ jessie-staging/main libsynctex1 armhf 2014.20140528.34243-4 [53.9 kB]
Get:236 http://172.17.0.1/private/ jessie-staging/main libtre-dev armhf 0.8.0-4 [27.1 kB]
Get:237 http://172.17.0.1/private/ jessie-staging/main libxml2-utils armhf 2.9.1+dfsg1-4 [89.1 kB]
Get:238 http://172.17.0.1/private/ jessie-staging/main tex-common all 5.02 [625 kB]
Get:239 http://172.17.0.1/private/ jessie-staging/main preview-latex-style all 11.87-1 [317 kB]
Get:240 http://172.17.0.1/private/ jessie-staging/main rubygems-integration all 1.7 [4286 B]
Get:241 http://172.17.0.1/private/ jessie-staging/main libruby2.1 armhf 2.1.2-2 [2988 kB]
Get:242 http://172.17.0.1/private/ jessie-staging/main ruby2.1 armhf 2.1.2-2 [257 kB]
Get:243 http://172.17.0.1/private/ jessie-staging/main ruby all 1:2.1.0.1 [8760 B]
Get:244 http://172.17.0.1/private/ jessie-staging/main xdg-utils all 1.1.0~rc1+git20111210-7.1 [64.6 kB]
Get:245 http://172.17.0.1/private/ jessie-staging/main texlive-binaries armhf 2014.20140528.34243-4 [5261 kB]
Get:246 http://172.17.0.1/private/ jessie-staging/main texlive-base all 2014.20140717-01 [17.7 MB]
Get:247 http://172.17.0.1/private/ jessie-staging/main ttf-adf-accanthis all 0.20090423-2 [401 kB]
Get:248 http://172.17.0.1/private/ jessie-staging/main ttf-adf-gillius all 0.20090423-2 [400 kB]
Get:249 http://172.17.0.1/private/ jessie-staging/main fonts-stix all 1.1.1-1 [588 kB]
Get:250 http://172.17.0.1/private/ jessie-staging/main texlive-fonts-extra all 2014.20140717-1 [181 MB]
Get:251 http://172.17.0.1/private/ jessie-staging/main texlive-fonts-recommended all 2014.20140717-01 [5710 kB]
Get:252 http://172.17.0.1/private/ jessie-staging/main texlive-latex-base all 2014.20140717-01 [858 kB]
Get:253 http://172.17.0.1/private/ jessie-staging/main texlive-latex-recommended all 2014.20140717-01 [7547 kB]
Get:254 http://172.17.0.1/private/ jessie-staging/main texlive-pictures all 2014.20140717-01 [3000 kB]
Get:255 http://172.17.0.1/private/ jessie-staging/main texlive-latex-extra all 2014.20140717-1 [7362 kB]
Get:256 http://172.17.0.1/private/ jessie-staging/main xsltproc armhf 1.1.28-2 [119 kB]
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Setting up ruby (1:2.1.0.1) ...
Setting up texlive-binaries (2014.20140528.34243-4) ...
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
Building format(s) --refresh.
	This may take some time... done.
Setting up texlive-base (2014.20140717-01) ...
/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.
Running mktexlsr. This may take some time... done.
Building format(s) --all.
	This may take some time... done.
Setting up libruby2.1:armhf (2.1.2-2) ...
Processing triggers for tex-common (5.02) ...
Running mktexlsr. This may take some time... done.
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Setting up texlive-latex-base (2014.20140717-01) ...
Running mktexlsr. This may take some time... done.
Building format(s) --all --cnffile /etc/texmf/fmt.d/10texlive-latex-base.cnf.
	This may take some time... done.
Setting up texlive-fonts-extra (2014.20140717-1) ...
Setting up texlive-fonts-recommended (2014.20140717-01) ...
Processing triggers for tex-common (5.02) ...
Running mktexlsr. This may take some time... done.
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Setting up texlive-latex-recommended (2014.20140717-01) ...
Processing triggers for tex-common (5.02) ...
Running mktexlsr. This may take some time... done.
Setting up texlive-pictures (2014.20140717-01) ...
Processing triggers for tex-common (5.02) ...
Running mktexlsr. This may take some time... done.
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Setting up texlive-latex-extra (2014.20140717-1) ...
Processing triggers for tex-common (5.02) ...
Running mktexlsr. This may take some time... done.
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Setting up sbuild-build-depends-genometools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-7) ...
Processing triggers for python-support (1.0.15) ...

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

Kernel: Linux 3.15-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24.51.20140617-1 dpkg-dev_1.17.10 g++-4.9_4.9.0-7 gcc-4.8_4.8.3-4 gcc-4.9_4.9.0-7 libc6-dev_2.19-7 libstdc++-4.9-dev_4.9.0-7 libstdc++6_4.9.0-7 linux-libc-dev_3.14.4-1+rpi1
Package versions: apt_1.0.6 asciidoc_8.6.9-2 base-files_7.3+rpi1 base-passwd_3.5.28 bash_4.3-7 binutils_2.24.51.20140617-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.6 bzip2_1.0.6-5 coreutils_8.21-1.2 cpio_2.11+dfsg-2 cpp_4:4.9.0-4 cpp-4.8_4.8.3-4 cpp-4.9_4.9.0-7 dash_0.5.7-4 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-1.2 debhelper_9.20140613 debianutils_4.4 diffutils_1:3.3-1 docbook-xsl_1.78.1+dfsg-1 dpkg_1.17.10 dpkg-dev_1.17.10 e2fslibs_1.42.10-1.1 e2fsprogs_1.42.10-1.1 fakeroot_1.18.4-2 file_1:5.19-1 findutils_4.4.2-9 fontconfig_2.11.0-5 fontconfig-config_2.11.0-5 fonts-cabin_1.5-2 fonts-comfortaa_2.003-1 fonts-dejavu-core_2.34-1 fonts-dejavu-extra_2.34-1 fonts-droid_1:4.3-3 fonts-ebgaramond_0.015+git20130628-3 fonts-ebgaramond-extra_0.015+git20130628-3 fonts-font-awesome_4.1.0~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_1.104-4 fonts-linuxlibertine_5.3.0-2 fonts-lobster_2.0-2 fonts-lobstertwo_2.0-2 fonts-oflb-asana-math_000.907-6 fonts-sil-gentium_20081126:1.02-13 fonts-sil-gentium-basic_1.1-7 fonts-stix_1.1.1-1 g++_4:4.9.0-4 g++-4.9_4.9.0-7 gcc_4:4.9.0-4 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8_4.8.3-4 gcc-4.8-base_4.8.3-4 gcc-4.9_4.9.0-7 gcc-4.9-base_4.9.0-7 gettext_0.18.3.2-4 gettext-base_0.18.3.2-4 gir1.2-freedesktop_1.40.0-2 gir1.2-glib-2.0_1.40.0-2 gir1.2-pango-1.0_1.36.3-1 gnupg_1.4.18-2 gpgv_1.4.18-2 grep_2.18-2 groff-base_1.22.2-6 gzip_1.6-3 hostname_3.15 init-system-helpers_1.19 initramfs-tools_0.115 initscripts_2.88dsf-53.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.3-1+rpi1 kmod_16-2 libacl1_2.2.52-1 libapt-pkg4.12_1.0.6 libasan0_4.8.3-4 libasan1_4.9.0-7 libasprintf0c2_0.18.3.2-4 libatomic1_4.9.0-7 libattr1_1:2.4.47-1 libaudit-common_1:2.3.7-1 libaudit1_1:2.3.7-1 libavahi-client3_0.6.31-4 libavahi-common-data_0.6.31-4 libavahi-common3_0.6.31-4 libbam-dev_0.1.19-1 libblkid1_2.20.1-5.8 libbz2-1.0_1.0.6-5 libbz2-dev_1.0.6-5 libc-bin_2.19-7 libc-dev-bin_2.19-7 libc6_2.19-7 libc6-dev_2.19-7 libcairo-gobject2_1.12.16-2+rpi1 libcairo-script-interpreter2_1.12.16-2+rpi1 libcairo2_1.12.16-2+rpi1 libcairo2-dev_1.12.16-2+rpi1 libcap2_1:2.22-1.2 libcloog-isl4_0.18.2-1 libcomerr2_1.42.10-1.1 libcroco3_0.6.8-2 libcups2_1.7.4-1 libcupsfilters1_1.0.54-3+b1 libcupsimage2_1.7.4-1 libdatrie1_0.2.8-1 libdb5.1_5.1.29-6 libdb5.3_5.3.28-5 libdbus-1-3_1.8.6-1 libdpkg-perl_1.17.10 libdrm-dev_2.4.54-1 libdrm-nouveau2_2.4.54-1 libdrm-omap1_2.4.54-1 libdrm-radeon1_2.4.54-1 libdrm2_2.4.54-1 libelfg0_0.8.13-5 libexpat1_2.1.0-6 libexpat1-dev_2.1.0-6 libffi6_3.1-2 libfontconfig1_2.11.0-5 libfontconfig1-dev_2.11.0-5 libfreetype6_2.5.2-1 libfreetype6-dev_2.5.2-1 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.3-4 libgcc-4.9-dev_4.9.0-7 libgcc1_1:4.9.0-7 libgcrypt11_1.5.3-4 libgdbm3_1.8.3-12 libgirepository-1.0-1_1.40.0-2 libgl1-mesa-dev_10.2.4-1 libgl1-mesa-glx_10.2.4-1 libglapi-mesa_10.2.4-1 libglib2.0-0_2.40.0-3 libglib2.0-bin_2.40.0-3 libglib2.0-data_2.40.0-3 libglib2.0-dev_2.40.0-3 libgmp10_2:6.0.0+dfsg-4+rpi1 libgnutls-deb0-28_3.2.15-3 libgomp1_4.9.0-7 libgpg-error0_1.13-0.2 libgraphite2-3_1.2.4-3 libgs9_9.05~dfsg-8.1 libgs9-common_9.05~dfsg-8.1 libgssapi-krb5-2_1.12.1+dfsg-5 libharfbuzz-dev_0.9.29-1 libharfbuzz-gobject0_0.9.29-1 libharfbuzz-icu0_0.9.29-1 libharfbuzz0b_0.9.29-1 libhogweed2_2.7.1-2 libice-dev_2:1.0.9-1 libice6_2:1.0.9-1 libicu52_52.1-4 libidn11_1.28-2 libijs-0.35_0.35-10 libisl10_0.12.2-2 libjasper1_1.900.1-debian1-2 libjbig0_2.0-2.1 libjbig2dec0_0.11+20120125-1 libjpeg8_8d1-1 libjs-jquery_1.7.2+dfsg-3 libk5crypto3_1.12.1+dfsg-5 libkeyutils1_1.5.9-4 libklibc_2.0.3-1+rpi1 libkmod2_16-2 libkpathsea6_2014.20140528.34243-4 libkrb5-3_1.12.1+dfsg-5 libkrb5support0_1.12.1+dfsg-5 liblcms2-2_2.6-3 liblocale-gettext-perl_1.05-8 liblua5.1-0_5.1.5-5 liblua5.1-0-dev_5.1.5-5 liblzma5_5.1.1alpha+20120614-2 liblzo2-2_2.08-1 libmagic1_1:5.19-1 libmount1_2.20.1-5.8 libmpc3_1.0.2-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1 libncurses5-dev_5.9+20140118-1 libncursesw5_5.9+20140118-1 libnettle4_2.7.1-2 libopenjpeg5_1.5.2-2 libp11-kit0_0.20.2-5 libpam-modules_1.1.8-3 libpam-modules-bin_1.1.8-3 libpam-runtime_1.1.8-3 libpam0g_1.1.8-3 libpango-1.0-0_1.36.3-1 libpango1.0-dev_1.36.3-1 libpangocairo-1.0-0_1.36.3-1 libpangoft2-1.0-0_1.36.3-1 libpangoxft-1.0-0_1.36.3-1 libpaper-utils_1.1.24+nmu3 libpaper1_1.1.24+nmu3 libpcre3_1:8.31-5 libpcre3-dev_1:8.31-5 libpcrecpp0_1:8.31-5 libpipeline1_1.3.0-1 libpixman-1-0_0.32.6-1 libpixman-1-dev_0.32.6-1 libpng12-0_1.2.50-1 libpng12-dev_1.2.50-1 libpoppler46_0.26.3-1 libpotrace0_1.11-2 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-5 libptexenc1_2014.20140528.34243-4 libpthread-stubs0-dev_0.3-4 libpython-stdlib_2.7.8-1 libpython2.7-minimal_2.7.8-1 libpython2.7-stdlib_2.7.8-1 libreadline-dev_6.3-6 libreadline6_6.3-6 libreadline6-dev_6.3-6 libruby2.1_2.1.2-2 libselinux1_2.3-1 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-1 libslang2_2.2.4-17 libsm-dev_2:1.2.2-1 libsm6_2:1.2.2-1 libsqlite3-0_3.8.5-2 libsqlite3-dev_3.8.5-2 libss2_1.42.10-1.1 libssl1.0.0_1.0.1h-3 libstdc++-4.9-dev_4.9.0-7 libstdc++6_4.9.0-7 libsynctex1_2014.20140528.34243-4 libtasn1-6_4.0-2 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b3 libtext-wrapi18n-perl_0.06-7 libthai-data_0.1.20-3 libthai0_0.1.20-3 libtiff5_4.0.3-9 libtimedate-perl_2.3000-2 libtinfo-dev_5.9+20140118-1 libtinfo5_5.9+20140118-1 libtre-dev_0.8.0-4 libtre5_0.8.0-4 libubsan0_4.9.0-7 libudev1_204-14 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-24 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.8 libx11-6_2:1.6.2-2 libx11-data_2:1.6.2-2 libx11-dev_2:1.6.2-2 libx11-xcb-dev_2:1.6.2-2 libx11-xcb1_2:1.6.2-2 libxau-dev_1:1.0.8-1 libxau6_1:1.0.8-1 libxaw7_2:1.0.12-2 libxcb-dri2-0_1.10-3 libxcb-dri2-0-dev_1.10-3 libxcb-dri3-0_1.10-3 libxcb-dri3-dev_1.10-3 libxcb-glx0_1.10-3 libxcb-glx0-dev_1.10-3 libxcb-present-dev_1.10-3 libxcb-present0_1.10-3 libxcb-randr0_1.10-3 libxcb-randr0-dev_1.10-3 libxcb-render0_1.10-3 libxcb-render0-dev_1.10-3 libxcb-shape0_1.10-3 libxcb-shape0-dev_1.10-3 libxcb-shm0_1.10-3 libxcb-shm0-dev_1.10-3 libxcb-sync-dev_1.10-3 libxcb-sync1_1.10-3 libxcb-xfixes0_1.10-3 libxcb-xfixes0-dev_1.10-3 libxcb1_1.10-3 libxcb1-dev_1.10-3 libxdamage-dev_1:1.1.4-2 libxdamage1_1:1.1.4-2 libxdmcp-dev_1:1.1.1-1 libxdmcp6_1:1.1.1-1 libxext-dev_2:1.3.2-1 libxext6_2:1.3.2-1 libxfixes-dev_1:5.0.1-2 libxfixes3_1:5.0.1-2 libxft-dev_2.3.2-1 libxft2_2.3.2-1 libxi6_2:1.7.2-1 libxml2_2.9.1+dfsg1-4 libxml2-utils_2.9.1+dfsg1-4 libxmu6_2:1.1.2-1 libxpm4_1:3.5.11-1 libxrender-dev_1:0.9.8-1 libxrender1_1:0.9.8-1 libxshmfence-dev_1.1-2 libxshmfence1_1.1-2 libxslt1.1_1.1.28-2 libxt6_1:1.1.4-1 libxxf86vm-dev_1:1.1.3-1 libxxf86vm1_1:1.1.3-1 libyaml-0-2_0.1.4-3.2 libzzip-0-13_0.13.62-2 linux-libc-dev_3.14.4-1+rpi1 login_1:4.2-2 lsb-base_4.1+Debian13+rpi1 lua-filesystem_1.6.2-1 lua-filesystem-dev_1.6.2-1 lua-lpeg_0.12-1 lua-lpeg-dev_0.12-1 lua-md5_1.2+git+1+8d87fee-1 lua-md5-dev_1.2+git+1+8d87fee-1 make_4.0-8 makedev_2.3.1-93 man-db_2.6.7.1-1 mawk_1.3.3-17 mesa-common-dev_10.2.4-1 mime-support_3.56 mount_2.20.1-5.8 multiarch-support_2.19-7 nano_2.2.6-1.1 ncurses-base_5.9+20140118-1 ncurses-bin_5.9+20140118-1 passwd_1:4.2-2 patch_2.7.1-5 perl_5.18.2-6 perl-base_5.18.2-6 perl-modules_5.18.2-6 pkg-config_0.28-1 plymouth_0.9.0-4 po-debconf_1.0.16+nmu3 poppler-data_0.4.6-5 preview-latex-style_11.87-1 procps_1:3.3.9-5 python_2.7.8-1 python-minimal_2.7.8-1 python-support_1.0.15 python2.7_2.7.8-1 python2.7-minimal_2.7.8-1 raspbian-archive-keyring_20120528.2 readline-common_6.3-6 ruby_1:2.1.0.1 ruby2.1_2.1.2-2 rubygems-integration_1.7 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-genometools-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 sgml-base_1.26+nmu4 startpar_0.59-3 sysv-rc_2.88dsf-53.2 sysvinit_2.88dsf-53.2 sysvinit-core_2.88dsf-53.2 sysvinit-utils_2.88dsf-53.2 tar_1.27.1-2 tex-common_5.02 texlive-base_2014.20140717-01 texlive-binaries_2014.20140528.34243-4 texlive-fonts-extra_2014.20140717-1 texlive-fonts-recommended_2014.20140717-01 texlive-latex-base_2014.20140717-01 texlive-latex-extra_2014.20140717-1 texlive-latex-recommended_2014.20140717-01 texlive-pictures_2014.20140717-01 ttf-adf-accanthis_0.20090423-2 ttf-adf-gillius_0.20090423-2 tzdata_2014e-1 ucf_3.0030 udev_204-14 util-linux_2.20.1-5.8 x11-common_1:7.7+7 x11proto-core-dev_7.0.26-1 x11proto-damage-dev_1:1.2.1-2 x11proto-dri2-dev_2.8-2 x11proto-fixes-dev_1:5.0-2 x11proto-gl-dev_1.4.17-1 x11proto-input-dev_2.3.1-1 x11proto-kb-dev_1.0.6-2 x11proto-render-dev_2:0.11.1-2 x11proto-xext-dev_7.3.0-1 x11proto-xf86vidmode-dev_2.3.1-2 xdg-utils_1.1.0~rc1+git20111210-7.1 xml-core_0.13+nmu2 xorg-sgml-doctools_1:1.11-1 xsltproc_1.1.28-2 xtrans-dev_1.3.4-1 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1+rpi1 zlib1g-dev_1:1.2.8.dfsg-1+rpi1

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


Unpack source
─────────────

gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Wed Jul 16 20:47:36 2014 UTC using RSA key ID 04A3610B
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./genometools_1.5.3-1.dsc
dpkg-source: info: extracting genometools in genometools-1.5.3
dpkg-source: info: unpacking genometools_1.5.3.orig.tar.gz
dpkg-source: info: unpacking genometools_1.5.3-1.debian.tar.xz
dpkg-source: info: applying adding_soname
dpkg-source: info: applying libbam-fix
dpkg-source: info: applying remove-gitignores
dpkg-source: info: applying fix-exports
dpkg-source: info: applying split-manuals

Check disc space
────────────────

Sufficient free space for build

User Environment
────────────────

APT_CONFIG=/var/lib/sbuild/apt.conf
COLUMNS=80
CONSOLE=/dev/console
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INIT_VERSION=sysvinit-2.88
LC_ALL=POSIX
LINES=24
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PREVLEVEL=N
PWD=/
RUNLEVEL=2
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-038cab1f-7a49-4e7c-accc-4d126c069a41
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
init=/sbin/init
previous=N
rootmnt=/root
runlevel=2

dpkg-buildpackage
─────────────────

dpkg-buildpackage: source package genometools
dpkg-buildpackage: source version 1.5.3-1
dpkg-buildpackage: source distribution unstable
 dpkg-source --before-build genometools-1.5.3
dpkg-buildpackage: host architecture armhf
 fakeroot debian/rules clean
dh clean --parallel --with python2
   dh_testdir -O--parallel
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/«PKGBUILDDIR»'
/usr/bin/make cleanup
make[2]: Entering directory '/«PKGBUILDDIR»'
rm -rf obj lib
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
rm -rf bin
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; make cleanup
make[2]: Entering directory '/«PKGBUILDDIR»/doc/manuals'
rm -f *.aux  *.log *.bbl  *.blg *.dvi *.mer *.mct *.mbd comment.cut
rm -f *.out *.toc
rm -f U89959.fna read[12].fna 
rm -f reads.al1 reads.esq reads.lcp reads.llv reads.prj reads.suf
rm -f tallymer-tmp.tex
rm -f tagerator-tmp.tex Q1.gz pck-human.*
rm -f readjoiner.pdf hop.pdf ltrharvest.pdf ltrdigest.pdf uniquesub.pdf matstat.pdf mgth.pdf packedindex.pdf repfind.pdf tallymer.pdf tagerator.pdf genomediff.pdf
make[2]: Leaving directory '/«PKGBUILDDIR»/doc/manuals'
# should be deleted inside doc/manuals/Makefile
rm -f doc/manuals/annotationsketch.out \
      doc/manuals/api_reference.tex    \
      doc/manuals/gtscript_reference.tex
find doc . -name "*.toc" -delete
find testdata \( -name '*.ois' -or -name '*.sds' -or -name '*.esq' -or \
      -name '*.ssp' -or -name '*.des' -or -name "*.md5"  \) -and \( -not \
      -name '*foo.32.*' -not -name '*foo.64.*' \) -delete
rm -f www/genometools.org/htdocs/images/callbacks.png \
      www/genometools.org/htdocs/images/parsed.png    \
      www/genometools.org/htdocs/images/constructed.png \
      doc/manuals/annotationsketch.pdf
rm -f www/genometools.org/htdocs/docs.html \
      www/genometools.org/htdocs/examples.html \
      www/genometools.org/htdocs/libgenometools.html \
      www/genometools.org/htdocs/tools/gt.html
rm -rf gtpython/build
make[1]: Leaving directory '/«PKGBUILDDIR»'
   dh_clean -O--parallel
 debian/rules build-arch
dh build-arch --parallel --with python2
   dh_testdir -a -O--parallel
   dh_auto_configure -a -O--parallel
   debian/rules override_dh_auto_build
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_build --parallel -- useshared=yes 64bit=no errorcheck=no all docs manuals
make[2]: Entering directory '/«PKGBUILDDIR»'
[create obj/gt_config.h]
[compile str_cache.o]
[compile interval_tree.o]
[compile bitpackstringop32.o]
[compile strcmp.o]
[compile version.o]
[compile spacepeak.o]
[compile array2dim_sparse.o]
[compile complement.o]
[compile checkbitpackstring8.o]
[compile encseq_ptr.o]
[compile msort.o]
[compile ma.o]
[compile output_file.o]
[compile multithread.o]
[compile fileutils.o]
[compile checkbitpackarray.o]
[compile range.o]
[compile timer.o]
[compile gtdatapath.o]
[compile checkbitpackstring64.o]
[compile combinatorics.o]
[compile thread.o]
[compile bitpackstringop.o]
[compile toolbox.o]
[compile encseq_col.o]
[compile basename.o]
[compile bioseq.o]
[compile example_a.o]
[compile fasta_reader.o]
[compile score_function.o]
[compile encseq_options.o]
[compile init.o]
[compile sequence_buffer_embl.o]
[compile fa.o]
[compile safearith.o]
[compile seq_iterator.o]
[compile dlist.o]
[compile gc_content.o]
[compile password_entry.o]
[compile seq.o]
[compile splitter.o]
[compile encseq_metadata.o]
[compile process.o]
[compile mapspec.o]
[compile dynalloc.o]
[compile str.o]
[compile seq_iterator_sequence_buffer.o]
[compile bsearch.o]
[compile queue.o]
[compile mathsupport.o]
[compile sequence_buffer_fastq.o]
[compile codon_iterator.o]
[compile cstr_table.o]
[compile grep.o]
[compile byte_select.o]
[compile bittab.o]
[compile eansi.o]
[compile phase.o]
[compile disc_distri.o]
[compile sequence_buffer_fasta.o]
[compile yarandom.o]
[compile endianess.o]
[compile symbol.o]
[compile array.o]
[compile bitpackstringop8.o]
[compile checkbitpackstring16.o]
[compile seq_col.o]
[compile encseq_access_type.o]
[compile cstr.o]
[compile seq_iterator_fastq.o]
[compile hashmap.o]
[compile md5_encoder.o]
[compile desc_buffer.o]
[compile array3dim.o]
[compile colorspace.o]
[compile xbsd.o]
[compile md5_seqid.o]
[compile io.o]
[compile tooldriver.o]
[compile checkbitpackstring-int.o]
[compile strand.o]
[compile bioseq_iterator.o]
[compile tokenizer.o]
[compile progressbar.o]
[compile fastq.o]
[compile fasta.o]
[compile class_alloc_lock.o]
[compile example.o]
[compile codon_iterator_encseq.o]
[compile countingsort.o]
[compile bitpackstringop16.o]
[compile orf.o]
[compile radix_sort.o]
[compile sequence_buffer.o]
[compile sequence_buffer_plain.o]
[compile bool_matrix.o]
[compile dyn_bittab.o]
[compile bitbuffer.o]
[compile encseq.o]
[compile str_array.o]
[compile class_alloc.o]
[compile md5_tab.o]
[compile ezlib.o]
[compile sequence_buffer_gb.o]
[compile parseutils.o]
[compile bioseq_col.o]
[compile trans_table.o]
[compile md5_fingerprint.o]
[compile qsort_r.o]
[compile showtime.o]
[compile xansi.o]
[compile compact_ulong_store.o]
[compile fasta_reader_fsm.o]
[compile error.o]
[compile log.o]
[compile translator.o]
[compile xzlib.o]
[compile bitpackstringop64.o]
[compile sig.o]
[compile logger.o]
[compile warning.o]
[compile seq_info_cache.o]
[compile option.o]
[compile string_distri.o]
[compile compat.o]
[compile example_b.o]
[compile tool_iterator.o]
[compile alphabet.o]
[compile score_matrix.o]
[compile file.o]
[compile fasta_reader_seqit.o]
[compile tool.o]
[compile versionfunc.o]
[compile ebzlib.o]
[compile array2dim.o]
[compile xbzlib.o]
[compile hashtable.o]
[compile codon_iterator_simple.o]
[compile readmode.o]
[compile checkbitpackstring32.o]
[compile checkbitpackstring.o]
[compile quality.o]
[compile xposix.o]
[compile unit_testing.o]
[compile byte_popcount.o]
[compile fasta_reader_rec.o]
[compile cstr_array.o]
[compile qsort-ulong.o]
[compile match_iterator.o]
[compile hpol_processor.o]
[compile rmq.o]
[compile tidy_region_node_stream.o]
[compile bed_parser.o]
[compile type_checker.o]
[compile select_stream.o]
[compile id_to_md5_stream.o]
[compile rdb_sqlite.o]
[compile transcript_evaluators.o]
[compile affinealign.o]
[compile gtf_visitor.o]
[compile gtf_parser.o]
[compile node_stream.o]
[compile gff3_parser.o]
[compile rdb.o]
[compile splicedseq.o]
[compile globalchaining.o]
[compile regular_seqid.o]
[compile type_checker_builtin.o]
[compile feature_info.o]
[compile gff3_in_stream_plain.o]
[compile dice_hmm.o]
[compile splice_site_info_stream.o]
[compile clustered_set.o]
[compile gff3_out_stream.o]
[compile tag_value_map.o]
[compile region_node_builder.o]
[compile match_last.o]
[compile rbtree.o]
[compile csa_splice_form.o]
[compile type_node.o]
[compile samfile_encseq_mapping.o]
[compile permute_words.o]
[compile seqpos_classifier.o]
[compile transcript_exons.o]
[compile gtf_in_stream.o]
[compile seqid2seqnum_mapping.o]
[compile luahelper.o]
[compile type_graph.o]
[compile match_iterator_blast.o]
[compile aligned_segments_pile.o]
[compile xrf_abbr_parse_tree.o]
[compile array_out_stream.o]
[compile feature_out_stream.o]
[compile consensus_sa.o]
[compile md5_to_id_stream.o]
[compile buffer_stream.o]
[compile genome_node.o]
[compile cds_stream.o]
[compile xrf_abbr_entry.o]
[compile meta_node.o]
[compile encdesc.o]
[compile dot_visitor.o]
[compile region_node.o]
[compile regioncov_visitor.o]
[compile coin_hmm.o]
[compile visitor_stream.o]
[compile dup_feature_visitor.o]
[compile inter_feature_visitor.o]
[compile script_wrapper_stream.o]
[compile multieoplist.o]
[compile intset_8.o]
[compile fasta_header_iterator.o]
[compile sampling.o]
[compile merge_feature_stream.o]
[compile match_sw.o]
[compile hmm.o]
[compile snp_annotator_visitor.o]
[compile xrfcheck_info.o]
[compile elias_gamma.o]
[compile match_open.o]
[compile feature_node_observer.o]
[compile tidy_region_node_visitor.o]
[compile comment_node.o]
[compile orf_finder_stream.o]
[compile load_stream.o]
[compile intset_16.o]
[compile match_iterator_last.o]
[compile intset_combined.o]
[compile feature_index_memory.o]
[compile dup_feature_stream.o]
[compile inter_feature_stream.o]
[compile mutate.o]
[compile sam_alignment.o]
[compile merge_stream.o]
[compile sort_stream.o]
[compile gtdatahelp.o]
[compile feature_index.o]
[compile snp_annotator_stream.o]
[compile merge_feature_visitor.o]
[compile chain.o]
[compile encdesc_header_io.o]
[compile sam_query_name_iterator.o]
[compile wtree_encseq.o]
[compile gff3_visitor.o]
[compile typecheck_info.o]
[compile sspliced_alignment.o]
[compile obo_stanza.o]
[compile splice_site_info_visitor.o]
[compile gff3_in_stream.o]
[compile golomb.o]
[compile csa_stream.o]
[compile extract_feature_visitor.o]
[compile match_visitor.o]
[compile md5set.o]
[compile region_mapping.o]
[compile feature_node.o]
[compile stream_evaluator.o]
[compile assembly_stats_calculator.o]
[compile cds_check_stream.o]
[compile bed_in_stream.o]
[compile select_visitor.o]
[compile orf_iterator.o]
[compile match.o]
[compile type_checker_obo.o]
[compile stat_stream.o]
[compile shredder.o]
[compile feature_visitor.o]
[compile sequence_node.o]
[compile rdb_visitor.o]
[compile stat_visitor.o]
[compile swalign.o]
[compile transcript_bittabs.o]
[compile luaserialize.o]
[compile uniq_stream.o]
[compile evaluator.o]
[compile xrf_checker.o]
[compile intset.o]
[compile add_introns_stream.o]
[compile multi_sanitizer_visitor.o]
[compile bitoutstream.o]
[compile mapping.o]
[compile set_source_visitor.o]
[compile gff3_output.o]
[compile ranked_list.o]
[compile extract_feature_stream.o]
[compile match_iterator_sw.o]
[compile obo_parse_tree.o]
[compile add_ids_visitor.o]
[compile huffcode.o]
[compile csa_visitor.o]
[compile script_wrapper_visitor.o]
[compile match_iterator_open.o]
[compile check_boundaries_visitor.o]
[compile collect_ids_visitor.o]
[compile seqid2file.o]
[compile popcount_tab.o]
[compile md5_to_id_visitor.o]
[compile compressed_bitsequence.o]
[compile spec_results.o]
[compile gff3_escaping.o]
[compile orphanage.o]
[compile bitinstream.o]
[compile array_in_stream.o]
[compile uint64hashtable.o]
[compile eof_node.o]
[compile orf_finder_visitor.o]
[compile node_visitor.o]
[compile anno_db_schema.o]
[compile cds_check_visitor.o]
[compile gap_str.o]
[compile id_to_md5_visitor.o]
[compile script_filter.o]
[compile reverse.o]
[compile rcr.o]
[compile targetbest_select_stream.o]
[compile linearedist.o]
[compile sspliced_alignment_parsing.o]
[compile transcript_counts.o]
[compile n_r_encseq.o]
[compile editscript.o]
[compile extract_feature_sequence.o]
[compile clustered_set_uf.o]
[compile hcr.o]
[compile io_function_pointers.o]
[compile add_ids_stream.o]
[compile alignment.o]
[compile priority_queue.o]
[compile samfile_iterator.o]
[compile anno_db_gfflike.o]
[compile dot_out_stream.o]
[compile gtf_out_stream.o]
[compile intset_32.o]
[compile feature_node_iterator.o]
[compile spec_visitor.o]
[compile cds_visitor.o]
[compile wtree.o]
[compile cstr_iterator.o]
[compile aligned_segment.o]
[compile csa_variable_strands.o]
[compile tir_stream.o]
[compile transcript_used_exons.o]
[compile csa_gene.o]
[compile string_matching.o]
[compile chseqids_stream.o]
[compile match_blast.o]
[compile feature_stream.o]
[compile feature_in_stream.o]
[compile union_find.o]
[compile bittab_lua.o]
[compile canvas_lua.o]
[compile gtext_lua.o]
[compile encseq_lua.o]
[compile genome_stream_lua.o]
[compile feature_stream_lua.o]
[compile annotationsketch_lua.o]
[compile feature_index_lua.o]
[compile gtcore_lua.o]
[compile layout_lua.o]
[compile feature_visitor_lua.o]
[compile csa_stream_lua.o]
[compile image_info_lua.o]
[compile diagram_lua.o]
[compile translate_lua.o]
[compile feature_node_iterator_lua.o]
[compile genome_node_lua.o]
[compile region_mapping_lua.o]
[compile genome_visitor_lua.o]
[compile cds_stream_lua.o]
[compile alphabet_lua.o]
[compile score_matrix_lua.o]
[compile gt_lua.o]
[compile stream_evaluator_lua.o]
[compile mathsupport_lua.o]
[compile range_lua.o]
[compile rdj-contigs-writer.o]
[compile sfx-mappedstr.o]
[compile eis-bwtseq-extinfo.o]
[compile esa-dfs.o]
[compile idxlocali.o]
[compile echoseq.o]
[compile spaced-seeds.o]
[compile pckbucket.o]
[compile seqnumrelpos.o]
[compile sfx-lcpvalues.o]
[compile esa-mmsearch.o]
[compile chain2dim.o]
[compile eis-blockcomp-param.o]
[compile eis-bwtseq-param.o]
[compile rdj-errfind.o]
[compile eis-voiditf.o]
[compile shu-dfs.o]
[compile apmeoveridx.o]
[compile rdj-spmproc.o]
[compile test-mergeesa.o]
[compile encseq2offset.o]
[compile sfx-outprj.o]
[compile sfx-copysort.o]
[compile test-mappedstr.o]
[compile enum-patt.o]
[compile tyr-mkindex.o]
[compile fmi-keyval.o]
[compile tyr-search.o]
[compile radixsort_str.o]
[compile sfx-lwcheck.o]
[compile sfx-linlcp.o]
[compile rdj-contigs-graph.o]
[compile nullcols.o]
[compile rdj-contigpaths.o]
[compile eis-bwtseq-context.o]
[compile twobits2kmers.o]
[compile rdj-pairwise.o]
[compile xdrop.o]
[compile randomcodes-sfx-partssuf.o]
[compile esa-maxpairs.o]
[compile sfx-suffixer.o]
[compile asqg_writer.o]
[compile pckdfs.o]
[compile merger-trie.o]
[compile greedyfwdmat.o]
[compile rdj-strgraph.o]
[compile firstcodes-scan.o]
[compile fmi-mkindex.o]
[compile fmi-mapspec.o]
[compile randomcodes-tab.o]
[compile seqabstract.o]
[compile randomcodes-correct.o]
[compile spmsuftab.o]
[compile rdj-version.o]
[compile sfx-shortreadsort.o]
[compile rdj-contfind-bottomup.o]
[compile pck-count-nodes.o]
[compile optionargmode.o]
[compile chainofin.o]
[compile fmi-locate.o]
[compile squarededist.o]
[compile test-pairwise.o]
[compile fmi-fwduni.o]
[compile sfx-opt.o]
[compile bcktab.o]
[compile eis-bwtseq-sass.o]
[compile esa-map.o]
[compile idxlocalidp.o]
[compile tyr-occratio.o]
[compile prsqualint.o]
[compile shu-encseq-gc.o]
[compile firstcodes.o]
[compile eis-mrangealphabet.o]
[compile revcompl.o]
[compile esa_spmitvs_visitor.o]
[compile initeqsvec.o]
[compile esa-splititv.o]
[compile esa-scanprj.o]
[compile sfx-suffixgetset.o]
[compile randomcodes-insert.o]
[compile rdj-ovlfind-dp.o]
[compile mssufpat.o]
[compile rdj-ovlfind-bf.o]
[compile eis-bwtseq-context-param.o]
[compile reads_libraries_table.o]
[compile shu-genomediff.o]
[compile sfx-radixsort.o]
[compile rdj-cntlist.o]
[compile querymatch.o]
[compile bare-encseq.o]
[compile firstcodes-tab.o]
[compile sfx-sain.o]
[compile sfx-apfxlen.o]
[compile firstcodes-cache.o]
[compile eis-suffixerator-interface.o]
[compile randomcodes-hpcorrect.o]
[compile sfx-bltrie.o]
[compile eis-encidxseq-construct.o]
[compile sfx-suftaborder.o]
[compile dist-short.o]
[compile lua_tools.o]
[compile sfx-run.o]
[compile randomcodes.o]
[compile tyr-mersplit.o]
[compile randomcodes-find-seldom.o]
[compile shu-divergence.o]
[compile sfx-enumcodes.o]
[compile eis-suffixarray-interface.o]
[compile idxlocalisw.o]
[compile firstcodes-psbuf.o]
[compile esa-lcpintervals.o]
[compile idx-limdfs.o]
[compile cgr_spacedseed.o]
[compile rdj-ovlfind-gusfield.o]
[compile giextract.o]
[compile myersapm.o]
[compile eis-seqranges.o]
[compile eis-sequencemultiread.o]
[compile iter-window.o]
[compile sfx-diffcov.o]
[compile esa-seqread.o]
[compile firstcodes-accum.o]
[compile cutendpfx.o]
[compile rdj-spmlist.o]
[compile reads2twobit.o]
[compile esa_visitor.o]
[compile fmi-sufbwtstream.o]
[compile esa-minunique.o]
[compile esa-splititv-simple.o]
[compile rdj-contfinder.o]
[compile test-mtrieins.o]
[compile sfx-maprange.o]
[compile sfx-partssuf.o]
[compile turnwheels.o]
[compile eis-seqblocktranslate.o]
[compile esa-spmsk.o]
[compile fmi-save.o]
[compile eis-encidxseq.o]
[compile eis-encidxseq-param.o]
[compile index_options.o]
[compile test-maxpairs.o]
[compile fmi-map.o]
[compile eis-blockcomp.o]
[compile specialrank.o]
[compile eis-bwtseq.o]
[compile rdj-ovlfind-kmp.o]
[compile kmer2string.o]
[compile eis-specialsrank.o]
[compile esa-spmitvs.o]
[compile eis-bwtseq-construct.o]
[compile hlk-version.o]
[compile esa-merge.o]
[compile firstcodes-insert.o]
[compile tyr-map.o]
[compile pssm.o]
[compile esa_lcpintervals_visitor.o]
[compile firstcodes-spacelog.o]
[compile rdj-twobitenc-editor.o]
[compile esa-bottomup.o]
[compile hashfirstcodes.o]
[compile eis-sa-common.o]
[compile marksubstring.o]
[compile esa-shulen.o]
[compile hplstore.o]
[compile shu_unitfile.o]
[compile substriter.o]
[compile tagerator.o]
[compile rdj-spmfind.o]
[compile initbasepower.o]
[compile sfx-bentsedg.o]
[compile greedyedist.o]
[compile xml_pgl_visitor.o]
[compile gthmatch.o]
[compile gt_gthbssmrmsd.o]
[compile gthsadistri.o]
[compile gt_gthconsensus.o]
[compile backtrace_path.o]
[compile gthcutoffsstrict.o]
[compile sa.o]
[compile editoperation.o]
[compile compute_scores.o]
[compile gthverbosefunc.o]
[compile indent.o]
[compile time.o]
[compile chaining.o]
[compile pgl_visitor.o]
[compile input.o]
[compile pgl_collection.o]
[compile sa_collection.o]
[compile gt_gthbssmprint.o]
[compile txt_pgl_visitor.o]
[compile gthorf.o]
[compile gthcutoffsminimal.o]
[compile dp_scores_protein.o]
[compile gff3_sa_visitor.o]
[compile chain_collection.o]
[compile gt_gthbssmfileinfo.o]
[compile gt_gthmkbssmfiles.o]
[compile gthverbosefuncvm.o]
[compile splice_site_model.o]
[compile spliced_seq.o]
[compile seq_con.o]
[compile intermediate.o]
[compile region_factory.o]
[compile gthchain.o]
[compile dp_options_postpro.o]
[compile dp_options_est.o]
[compile sa_filter.o]
[compile proc_sa_collection.o]
[compile txt_sa_visitor.o]
[compile gthxml.o]
[compile gt_gthsplit.o]
[compile gthoutput.o]
[compile bssm_param_rmsd.o]
[compile gt_gth.o]
[compile gt_gthbssmbuild.o]
[compile xml_inter_sa_visitor.o]
[compile path_walker.o]
[compile gthtravalign.o]
[compile bssm_param.o]
[compile bssm_train_stream.o]
[compile align_dna.o]
[compile sa_cmp.o]
[compile bssm_train_visitor.o]
[compile call_info.o]
[compile pgl.o]
[compile gthalignment.o]
[compile bssm_seq_processor.o]
[compile sa_visitor.o]
[compile dp_options_core.o]
[compile ags_build.o]
[compile bssm_helper.o]
[compile gt_gthfilestat.o]
[compile run_header.o]
[compile xml_final_sa_visitor.o]
[compile gthsortags.o]
[compile gt_gthbssmtrain.o]
[compile path_matrix.o]
[compile gthsplicesitescr.o]
[compile gff3_pgl_visitor.o]
[compile parse_options.o]
[compile gthcluster.o]
[compile stat.o]
[compile similarity_filter.o]
[compile md5_cache.o]
[compile gthtrans.o]
[compile align_protein.o]
[compile dp_param.o]
[compile desc_cache.o]
[compile gthcutoffsrelaxed.o]
[compile ags.o]
[compile ltrharvest_fasta_out_visitor.o]
[compile pdom_model_set.o]
[compile ltrdigest_pdom_visitor.o]
[compile ltr_four_char_motif.o]
[compile ltrharvest_stream.o]
[compile ltrdigest_ppt_visitor.o]
[compile gt_ltrclustering.o]
[compile ltr_refseq_match_stream.o]
[compile gt_ltrharvest.o]
[compile ltrdigest_pbs_visitor.o]
[compile ltrharvest_tabout_visitor.o]
[compile ltrdigest_file_out_stream.o]
[compile ltrharvest_fasta_out_stream.o]
[compile gt_ltrdigest.o]
[compile ltrdigest_strand_assign_visitor.o]
[compile ltr_cluster_prepare_seq_visitor.o]
[compile ltr_cluster_stream.o]
[compile ltr_classify_stream.o]
[compile ltrharvest_tabout_stream.o]
[compile ltr_orf_annotator_stream.o]
[compile mg_compute_gene_prediction.o]
[compile metagenomethreader.o]
[compile mg_outputwriter.o]
[compile mg_combinedscore.o]
[compile mg_codon.o]
[compile mg_xmlparser.o]
[compile mg_reverse.o]
[compile mg_computepath.o]
[compile style.o]
[compile image_info.o]
[compile luastyle.o]
[compile custom_track_example.o]
[compile canvas_cairo.o]
[compile line_breaker_bases.o]
[compile custom_track_script_wrapper.o]
[compile element.o]
[compile coords.o]
[compile block.o]
[compile text_width_calculator_cairo.o]
[compile canvas_cairo_context.o]
[compile gt_sketch_page.o]
[compile custom_track.o]
[compile line_breaker.o]
[compile layout.o]
[compile canvas_cairo_file.o]
[compile track.o]
[compile custom_track_gc_content.o]
[compile diagram.o]
[compile line_breaker_captions.o]
[compile graphics_cairo.o]
[compile text_width_calculator.o]
[compile graphics.o]
[compile line.o]
[compile gt_sketch.o]
[compile color.o]
[compile canvas.o]
[compile drawing_range.o]
[compile rec_map.o]
[gathering public API symbols to obj/public_symbols.lst]
[compile gt.o]
[compile gtt.o]
[compile gtr.o]
[compile interactive.o]
[compile gt_seqtranslate.o]
[compile gt_packedindex_mkctxmap.o]
[compile gt_compreads_refcompress.o]
[compile gt_convertseq.o]
[compile gt_packedindex.o]
[compile gt_uniq.o]
[compile gt_orffinder.o]
[compile gt_fastq_sample.o]
[compile gt_readjoiner_asqg.o]
[compile gt_speck.o]
[compile gt_mkfeatureindex.o]
[compile gt_compressedbits.o]
[compile gt_seqmutate.o]
[compile gt_matstat.o]
[compile gt_packedindex_chk_search.o]
[compile gt_dupfeat.o]
[compile gt_shredder.o]
[compile gt_shulen.o]
[compile gt_extractfeat.o]
[compile gt_packedindex_trsuftab.o]
[compile gt_gff3_to_gtf.o]
[compile gt_readreads.o]
[compile gt_readjoiner_prefilter.o]
[compile gt_suffixerator.o]
[compile gt_packedindex_chk_integrity.o]
[compile gt_sortbench.o]
[compile gt_encseq_encode.o]
[compile gt_seqtransform.o]
[compile gt_trieins.o]
[compile gt_featureindex.o]
[compile gt_readjoiner_graph.o]
[compile gt_cds.o]
[compile gt_fingerprint.o]
[compile gt_template.o]
[compile gt_congruence.o]
[compile gt_encseq_bitextract.o]
[compile gt_wtree_bench.o]
[compile gt_select.o]
[compile gt_patternmatch.o]
[compile gt_magicmatch.o]
[compile gt_splitfasta.o]
[compile gt_extracttarget.o]
[compile gt_compreads_decompress.o]
[compile gt_seq.o]
[compile gt_consensus_sa.o]
[compile gt_skproto.o]
[compile gt_chseqids.o]
[compile gt_genomediff.o]
[compile gt_matchtool.o]
[compile gt_condenser_extract.o]
[compile gt_readjoiner_correct.o]
[compile gt_seqstat.o]
[compile gt_encseq_decode.o]
[compile gt_gff3.o]
[compile gt_bed_to_gff3.o]
[compile gt_readjoiner.o]
[compile gt_condenser_compress.o]
[compile gt_condenser_compsearch.o]
[compile gt_sain.o]
[compile gt_readjoiner_cnttest.o]
[compile gt_seqids.o]
[compile gt_md5_to_id.o]
[compile gt_mergeesa.o]
[compile gt_encseq_bench.o]
[compile gt_condenser.o]
[compile gt_tagerator.o]
[compile gt_loccheck.o]
[compile gt_encseq_check.o]
[compile gt_prebwt.o]
[compile gt_dev.o]
[compile gt_mmapandread.o]
[compile gt_tallymer.o]
[compile gt_chain2dim.o]
[compile gt_tir.o]
[compile gt_encseq.o]
[compile gt_compreads_refdecompress.o]
[compile gt_sam_interface.o]
[compile gt_compreads_compress.o]
[compile gt_stat.o]
[compile gt_script_filter.o]
[compile gt_hop.o]
[compile gt_regioncov.o]
[compile gt_eval.o]
[compile gt_snpper.o]
[compile gt_seqorder.o]
[compile gt_compreads.o]
[compile gt_encseq_sample.o]
[compile gt_readjoiner_assembly.o]
[compile gt_encseq2spm.o]
[compile gt_parsexrf.o]
[compile gt_readjoiner_cgraph.o]
[compile gt_clean.o]
[compile gt_id_to_md5.o]
[compile gt_condenser_info.o]
[compile gt_readjoiner_overlap.o]
[compile gt_seqfilter.o]
[compile gt_guessprot.o]
[compile gt_paircmp.o]
[compile gt_mkfmindex.o]
[compile gt_extractseq.o]
[compile gt_merge.o]
[compile gt_encseq_info.o]
[compile gt_interfeat.o]
[compile gt_gdiffcalc.o]
[compile gt_repfind.o]
[compile gt_mergefeat.o]
[compile gt_readjoiner_spmtest.o]
[compile gt_csa.o]
[compile gt_sfxmap.o]
[compile gt_mgth.o]
[compile gt_seqlensort.o]
[compile gt_simreads.o]
[compile gt_encseq_md5.o]
[compile gt_dot.o]
[compile gt_gtf_to_gff3.o]
[compile gt_idxlocali.o]
[compile gt_splicesiteinfo.o]
[compile gt_sequniq.o]
[compile gt_seqcorrect.o]
[compile gt_wtree.o]
[compile gt_gff3validator.o]
[compile custom_stream.o]
[compile gff3sort.o]
[compile gff3validator.o]
[compile noop.o]
[compile sketch_constructed.o]
[compile sketch_parsed_with_ctrack.o]
[compile sketch_parsed_with_ordering.o]
[compile sketch_parsed.o]
[link libgenometools.a]
ar: creating lib/libgenometools.a
[link libgenometools.so]
[link gt]
[link custom_stream]
[link gff3sort]
[link gff3validator]
[link noop]
[link sketch_constructed]
[link sketch_parsed_with_ctrack]
[link sketch_parsed_with_ordering]
[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
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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(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
(../../src/examples/sketch_parsed.c [15 <../../www/genometools.org/htdocs/image
s/example_ct2.png>] [16 <../../www/genometools.org/htdocs/images/parsed.png>])
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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 [17]) (../../gtruby/sketch_parsed.rb
[18]) (../../gtpython/sketch_parsed.py [19])

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<../../www/genometools.org/htdocs/images/constructed.png, id=515, 602.25pt x 14
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images/constructed.png>] [21])
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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 [22])
(../../gtruby/sketch_constructed.rb [23]) (../../gtpython/sketch_constructed.py
[24]) (./api_reference.tex [25]
Chapter 2.

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[28]

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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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[41]
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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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[42]
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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 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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[67] [68] [69] [70]
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[]\OT1/cmtt/m/n/10.95 GtFeatureNodeIterator* gt[]feature[]node[]iterator[]new([
]const GtFeatureNode

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

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

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

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

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\OT1/cmtt/m/n/10.95 fi\OT1/ptm/m/n/10.95 . Note: The \OT1/cmtt/m/n/10.95 GtFeat
ureStream \OT1/ptm/m/n/10.95 class is now dep-re-cated. Please use the

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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[]\OT1/ptm/m/n/10.95 Compare \OT1/cmtt/m/n/10.95 genome[]node[]a \OT1/ptm/m/n/1
0.95 with \OT1/cmtt/m/n/10.95 genome[]node[]b \OT1/ptm/m/n/10.95 and re-turn th
e re-sult (sim-i-lar to

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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[]\OT1/ptm/m/n/10.95 Iterate over \OT1/cmtt/m/n/10.95 hashmap \OT1/ptm/m/n/10.9
5 in ei-ther al-pha-bet-i-cal or-der (if \OT1/cmtt/m/n/10.95 GtHashType \OT1/pt
m/m/n/10.95 was spec-i-

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\OT1/ptm/m/n/10.95 fied as \OT1/cmtt/m/n/10.95 GT[]HASH[]STRING\OT1/ptm/m/n/10.
95 ) or nu-mer-i-cal or-der (if \OT1/cmtt/m/n/10.95 GtHashType \OT1/ptm/m/n/10.
95 was spec-i-fied as

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

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

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\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. A \OT1/cmtt/m/n/10.95 GtInterFeatureStream \OT1/ptm/m/n/10.
95 in-serts new fea-ture nodes

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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[89]
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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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[90]
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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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[95]
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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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[96]
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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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[]\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 the \OT1/cmtt/m/n/10.95 minimum \OT1/ptm/m/n/10.95 and
 \OT1/cmtt/m/n/10.95 maximum \OT1/ptm/m/n/10.95 num-ber of ad-di-tional com-man
d line ar-gu-ments

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

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

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

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

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[106]
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[]\OT1/cmtt/m/n/10.95 int gt[]rdb[]visitor[]visit[]sqlite([]GtRDBVisitor *rdbv,
 GtRDBSqlite *rdbs,

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

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

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

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\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
[108]
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[]\OT1/cmtt/m/n/10.95 GtRecMap* gt[]rec[]map[]new([]double nw[]x, double nw[]y,
 double se[]x, double

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

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtRegionMapping \OT1/ptm/
m/n/10.95 ob-ject for the map-ping file with the given

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

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtRegionMapping \OT1/ptm/
m/n/10.95 ob-ject for the se-quence files given in

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\OT1/cmtt/m/n/10.95 sequence[]filenames\OT1/ptm/m/n/10.95 . If \OT1/cmtt/m/n/10
.95 matchdesc \OT1/ptm/m/n/10.95 is \OT1/cmtt/m/n/10.95 true\OT1/ptm/m/n/10.95 
, the se-quence de-scrip-tions from

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

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

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

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

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

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

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

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[110]
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\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtGenomeNode \OT1/ptm/m/n
/10.95 in-ter-face. Re-gion nodes cor-re-spond to the \OT1/cmtt/m/n/10.95 ##seq
uence-region

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

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

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

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

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

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[]\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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[112]
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[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]set[]symbolmap([]GtSeqIterator*, 
const GtUchar

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

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

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

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

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

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

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

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

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[]\OT1/ptm/m/n/10.95 Create a new \OT1/cmtt/m/n/10.95 GtSequenceNode* \OT1/ptm/
m/n/10.95 rep-re-sent-ing a FASTA en-try with the given

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

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

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

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[115]
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\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeVisitor \OT1/ptm/m/
n/10.95 in-ter-face. Used with the \OT1/cmtt/m/n/10.95 GtVisitorStream \OT1/ptm
/m/n/10.95 class, a \OT1/cmtt/m/n/10.95 GtSetSourceVisitor

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

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[116]
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\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. A \OT1/cmtt/m/n/10.95 GtStatStream \OT1/ptm/m/n/10.95 gath-
ers statis-tics about the \OT1/cmtt/m/n/10.95 GtGenomeNode

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

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

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

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

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\OT1/ptm/m/n/10.95 ment equals \OT1/cmtt/m/n/10.95 true\OT1/ptm/m/n/10.95 : \OT
1/cmtt/m/n/10.95 gene[]length[]distribution\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/n/1
0.95 gene[]score[]distribution\OT1/ptm/m/n/10.95 ,

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

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[]\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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[117] [118]
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[]\OT1/cmtt/m/n/10.95 void gt[]str[]array[]add[]cstr[]nt([]GtStrArray *str[]arr
ay, const char *cstr,

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

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

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[]\OT1/ptm/m/n/10.95 Set the size of \OT1/cmtt/m/n/10.95 str[]array \OT1/ptm/m/
n/10.95 to \OT1/cmtt/m/n/10.95 size\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 siz
e \OT1/ptm/m/n/10.95 must be smaller or equal than

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[119]
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\OT1/ptm/m/n/10.95 This enum type de-fines the pos-si-ble strands. The fol-low-
ing strands are de-fined: \OT1/cmtt/m/n/10.95 GT[]STRAND[]FORWARD\OT1/ptm/m/n/1
0.95 ,

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[]\OT1/ptm/m/n/10.95 Map \OT1/cmtt/m/n/10.95 strand[]char \OT1/ptm/m/n/10.95 to
 the cor-re-spond-ing strand enum type. Re-turns

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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[120] [121] [122]
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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/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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Chapter 2.
[30] [31] [32] [33] [34]
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[]\OT1/cmtt/m/n/10.95 void gt[]alphabet[]echo[]pretty[]symbol([]const GtAlphabe
t *alphabet, FILE

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

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

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

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

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

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[]\OT1/ptm/m/n/10.95 Set the size of \OT1/cmtt/m/n/10.95 array \OT1/ptm/m/n/10.
95 to \OT1/cmtt/m/n/10.95 size\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 size \OT
1/ptm/m/n/10.95 must be smaller or equal than

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

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

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\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. \OT1/cmtt/m/n/10.95 GtArrayOutStream \OT1/ptm/m/n/10.95 tak
es an ar-ray of \OT1/cmtt/m/n/10.95 GtGenomeNodes

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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\OT1/cmtt/m/n/10.95 fi\OT1/ptm/m/n/10.95 . Note: The \OT1/cmtt/m/n/10.95 GtFeat
ureStream \OT1/ptm/m/n/10.95 class is now dep-re-cated. Please use the

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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[]\OT1/ptm/m/n/10.95 Compare \OT1/cmtt/m/n/10.95 genome[]node[]a \OT1/ptm/m/n/1
0.95 with \OT1/cmtt/m/n/10.95 genome[]node[]b \OT1/ptm/m/n/10.95 and re-turn th
e re-sult (sim-i-lar to

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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[]\OT1/ptm/m/n/10.95 Iterate over \OT1/cmtt/m/n/10.95 hashmap \OT1/ptm/m/n/10.9
5 in ei-ther al-pha-bet-i-cal or-der (if \OT1/cmtt/m/n/10.95 GtHashType \OT1/pt
m/m/n/10.95 was spec-i-

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\OT1/ptm/m/n/10.95 fied as \OT1/cmtt/m/n/10.95 GT[]HASH[]STRING\OT1/ptm/m/n/10.
95 ) or nu-mer-i-cal or-der (if \OT1/cmtt/m/n/10.95 GtHashType \OT1/ptm/m/n/10.
95 was spec-i-fied as

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

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

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\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. A \OT1/cmtt/m/n/10.95 GtInterFeatureStream \OT1/ptm/m/n/10.
95 in-serts new fea-ture nodes

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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[]\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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[100]
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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 the \OT1/cmtt/m/n/10.95 minimum \OT1/ptm/m/n/10.95 and
 \OT1/cmtt/m/n/10.95 maximum \OT1/ptm/m/n/10.95 num-ber of ad-di-tional com-man
d line 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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[]\OT1/cmtt/m/n/10.95 GtRDB* gt[]rdb[]mysql[]new([]const char *server, unsigned
 int port, const char

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[110]
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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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\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
[112]
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[]\OT1/cmtt/m/n/10.95 GtRecMap* gt[]rec[]map[]new([]double nw[]x, double nw[]y,
 double se[]x, double

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

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtRegionMapping \OT1/ptm/
m/n/10.95 ob-ject for the map-ping file with the given

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

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtRegionMapping \OT1/ptm/
m/n/10.95 ob-ject for the se-quence files given in

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\OT1/cmtt/m/n/10.95 sequence[]filenames\OT1/ptm/m/n/10.95 . If \OT1/cmtt/m/n/10
.95 matchdesc \OT1/ptm/m/n/10.95 is \OT1/cmtt/m/n/10.95 true\OT1/ptm/m/n/10.95 
, the se-quence de-scrip-tions from

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

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

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

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

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

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

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

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[114]
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\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtGenomeNode \OT1/ptm/m/n
/10.95 in-ter-face. Re-gion nodes cor-re-spond to the \OT1/cmtt/m/n/10.95 ##seq
uence-region

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

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[115]
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]script[]wrapper[]stream[]new([]GtScript
WrapperStreamNextFunc,

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

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

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

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[]\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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[116]
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[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]set[]symbolmap([]GtSeqIterator*, 
const GtUchar

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

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

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

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[117]
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[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]fastq[]new([]const GtSt
rArray *filenametab,

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

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

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

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

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[]\OT1/ptm/m/n/10.95 Create a new \OT1/cmtt/m/n/10.95 GtSequenceNode* \OT1/ptm/
m/n/10.95 rep-re-sent-ing a FASTA en-try with the given

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

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

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

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[119]
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\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeVisitor \OT1/ptm/m/
n/10.95 in-ter-face. Used with the \OT1/cmtt/m/n/10.95 GtVisitorStream \OT1/ptm
/m/n/10.95 class, a \OT1/cmtt/m/n/10.95 GtSetSourceVisitor

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

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[120]
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\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. A \OT1/cmtt/m/n/10.95 GtStatStream \OT1/ptm/m/n/10.95 gath-
ers statis-tics about the \OT1/cmtt/m/n/10.95 GtGenomeNode

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

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

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

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

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\OT1/ptm/m/n/10.95 ment equals \OT1/cmtt/m/n/10.95 true\OT1/ptm/m/n/10.95 : \OT
1/cmtt/m/n/10.95 gene[]length[]distribution\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/n/1
0.95 gene[]score[]distribution\OT1/ptm/m/n/10.95 ,

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

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[]\OT1/ptm/m/n/10.95 Set length of \OT1/cmtt/m/n/10.95 str \OT1/ptm/m/n/10.95 t
o \OT1/cmtt/m/n/10.95 length\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 length \OT
1/ptm/m/n/10.95 must be smaller or equal than

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

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

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

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[]\OT1/ptm/m/n/10.95 Set the size of \OT1/cmtt/m/n/10.95 str[]array \OT1/ptm/m/
n/10.95 to \OT1/cmtt/m/n/10.95 size\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 siz
e \OT1/ptm/m/n/10.95 must be smaller or equal than

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\OT1/ptm/m/n/10.95 This enum type de-fines the pos-si-ble strands. The fol-low-
ing strands are de-fined: \OT1/cmtt/m/n/10.95 GT[]STRAND[]FORWARD\OT1/ptm/m/n/1
0.95 ,

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[]\OT1/ptm/m/n/10.95 Map \OT1/cmtt/m/n/10.95 strand[]char \OT1/ptm/m/n/10.95 to
 the cor-re-spond-ing strand enum type. Re-turns

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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\OT1/cmtt/m/n/10.95 cairo[]t \OT1/ptm/m/n/10.95 and which should be used later 
via a \OT1/cmtt/m/n/10.95 GtCanvasCairoContext\OT1/ptm/m/n/10.95 , cre-ate a \O
T1/cmtt/m/n/10.95 GtTextWidthCalculatorCairo

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

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[]\OT1/ptm/m/n/10.95 Output the cur-rent state of \OT1/cmtt/m/n/10.95 timer \OT
1/ptm/m/n/10.95 in the for-mat ""GT[]WD".pointer \OT1/cmtt/m/n/10.95 fp \OT1/pt
m/m/n/10.95 (see

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[]\OT1/ptm/m/n/10.95 Output the cur-rent state of \OT1/cmtt/m/n/10.95 timer \OT
1/ptm/m/n/10.95 on \OT1/cmtt/m/n/10.95 fp \OT1/ptm/m/n/10.95 since the last cal
l of

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\OT1/cmtt/m/n/10.95 gt[]timer[]show[]progress() \OT1/ptm/m/n/10.95 or the last 
start of \OT1/cmtt/m/n/10.95 timer\OT1/ptm/m/n/10.95 , along with the cur-rent

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

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

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

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

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

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

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

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

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

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[]\OT1/ptm/m/n/10.95 Returns a \OT1/cmtt/m/n/10.95 GtStrArray \OT1/ptm/m/n/10.9
5 of trans-la-tion scheme de-scrip-tions, each of the for-mat

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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[]\OT1/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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Chapter 2.
[30] [31] [32] [33] [34]
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[]\OT1/cmtt/m/n/10.95 GtAlphabet* gt[]alphabet[]new[]from[]string([]const char 
*alphadef, GtUword

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

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

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

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

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

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

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

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

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

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

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[]\OT1/ptm/m/n/10.95 Set the size of \OT1/cmtt/m/n/10.95 array \OT1/ptm/m/n/10.
95 to \OT1/cmtt/m/n/10.95 size\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 size \OT
1/ptm/m/n/10.95 must be smaller or equal than

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

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

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\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. \OT1/cmtt/m/n/10.95 GtArrayOutStream \OT1/ptm/m/n/10.95 tak
es an ar-ray of \OT1/cmtt/m/n/10.95 GtGenomeNodes

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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[]\OT1/cmtt/m/n/10.95 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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[]\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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[]\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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[96]
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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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[98]
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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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[100]
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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 the \OT1/cmtt/m/n/10.95 minimum \OT1/ptm/m/n/10.95 and
 \OT1/cmtt/m/n/10.95 maximum \OT1/ptm/m/n/10.95 num-ber of ad-di-tional com-man
d line 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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[]\OT1/cmtt/m/n/10.95 GtRDB* gt[]rdb[]mysql[]new([]const char *server, unsigned
 int port, const char

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[110]
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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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\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
[112]
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[]\OT1/cmtt/m/n/10.95 GtRecMap* gt[]rec[]map[]new([]double nw[]x, double nw[]y,
 double se[]x, double

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

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtRegionMapping \OT1/ptm/
m/n/10.95 ob-ject for the map-ping file with the given

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

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[]\OT1/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtRegionMapping \OT1/ptm/
m/n/10.95 ob-ject for the se-quence files given in

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\OT1/cmtt/m/n/10.95 sequence[]filenames\OT1/ptm/m/n/10.95 . If \OT1/cmtt/m/n/10
.95 matchdesc \OT1/ptm/m/n/10.95 is \OT1/cmtt/m/n/10.95 true\OT1/ptm/m/n/10.95 
, the se-quence de-scrip-tions from

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

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

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

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

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

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

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

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[114]
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\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtGenomeNode \OT1/ptm/m/n
/10.95 in-ter-face. Re-gion nodes cor-re-spond to the \OT1/cmtt/m/n/10.95 ##seq
uence-region

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

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[115]
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]script[]wrapper[]stream[]new([]GtScript
WrapperStreamNextFunc,

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

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

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

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[]\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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[116]
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[]\OT1/cmtt/m/n/10.95 void gt[]seq[]iterator[]set[]symbolmap([]GtSeqIterator*, 
const GtUchar

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

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

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

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[117]
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[]\OT1/cmtt/m/n/10.95 GtSeqIterator* gt[]seq[]iterator[]fastq[]new([]const GtSt
rArray *filenametab,

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

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

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

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

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[]\OT1/ptm/m/n/10.95 Create a new \OT1/cmtt/m/n/10.95 GtSequenceNode* \OT1/ptm/
m/n/10.95 rep-re-sent-ing a FASTA en-try with the given

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

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

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

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[119]
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\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeVisitor \OT1/ptm/m/
n/10.95 in-ter-face. Used with the \OT1/cmtt/m/n/10.95 GtVisitorStream \OT1/ptm
/m/n/10.95 class, a \OT1/cmtt/m/n/10.95 GtSetSourceVisitor

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

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[120]
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\OT1/ptm/m/n/10.95 Implements the \OT1/cmtt/m/n/10.95 GtNodeStream \OT1/ptm/m/n
/10.95 in-ter-face. A \OT1/cmtt/m/n/10.95 GtStatStream \OT1/ptm/m/n/10.95 gath-
ers statis-tics about the \OT1/cmtt/m/n/10.95 GtGenomeNode

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

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

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

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

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\OT1/ptm/m/n/10.95 ment equals \OT1/cmtt/m/n/10.95 true\OT1/ptm/m/n/10.95 : \OT
1/cmtt/m/n/10.95 gene[]length[]distribution\OT1/ptm/m/n/10.95 , \OT1/cmtt/m/n/1
0.95 gene[]score[]distribution\OT1/ptm/m/n/10.95 ,

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

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[]\OT1/ptm/m/n/10.95 Set length of \OT1/cmtt/m/n/10.95 str \OT1/ptm/m/n/10.95 t
o \OT1/cmtt/m/n/10.95 length\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 length \OT
1/ptm/m/n/10.95 must be smaller or equal than

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

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

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

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[]\OT1/ptm/m/n/10.95 Set the size of \OT1/cmtt/m/n/10.95 str[]array \OT1/ptm/m/
n/10.95 to \OT1/cmtt/m/n/10.95 size\OT1/ptm/m/n/10.95 . \OT1/cmtt/m/n/10.95 siz
e \OT1/ptm/m/n/10.95 must be smaller or equal than

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\OT1/ptm/m/n/10.95 This enum type de-fines the pos-si-ble strands. The fol-low-
ing strands are de-fined: \OT1/cmtt/m/n/10.95 GT[]STRAND[]FORWARD\OT1/ptm/m/n/1
0.95 ,

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[]\OT1/ptm/m/n/10.95 Map \OT1/cmtt/m/n/10.95 strand[]char \OT1/ptm/m/n/10.95 to
 the cor-re-spond-ing strand enum type. Re-turns

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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\OT1/cmtt/m/n/10.95 cairo[]t \OT1/ptm/m/n/10.95 and which should be used later 
via a \OT1/cmtt/m/n/10.95 GtCanvasCairoContext\OT1/ptm/m/n/10.95 , cre-ate a \O
T1/cmtt/m/n/10.95 GtTextWidthCalculatorCairo

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

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[]\OT1/ptm/m/n/10.95 Output the cur-rent state of \OT1/cmtt/m/n/10.95 timer \OT
1/ptm/m/n/10.95 in the for-mat ""GT[]WD".pointer \OT1/cmtt/m/n/10.95 fp \OT1/pt
m/m/n/10.95 (see

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[]\OT1/ptm/m/n/10.95 Output the cur-rent state of \OT1/cmtt/m/n/10.95 timer \OT
1/ptm/m/n/10.95 on \OT1/cmtt/m/n/10.95 fp \OT1/ptm/m/n/10.95 since the last cal
l of

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\OT1/cmtt/m/n/10.95 gt[]timer[]show[]progress() \OT1/ptm/m/n/10.95 or the last 
start of \OT1/cmtt/m/n/10.95 timer\OT1/ptm/m/n/10.95 , along with the cur-rent

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

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

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

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

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

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

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

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

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

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[]\OT1/ptm/m/n/10.95 Returns a \OT1/cmtt/m/n/10.95 GtStrArray \OT1/ptm/m/n/10.9
5 of trans-la-tion scheme de-scrip-tions, each of the for-mat

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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[]\OT1/ptm/m/n/10.95 Find \OT1/cmtt/m/n/10.95 file \OT1/ptm/m/n/10.95 in $\OML/
ztmcm/m/it/10.95 PATH; ifithasnodirname\OT1/ztmcm/m/n/10.95 ; \OML/ztmcm/m/it/1
0.95 set[]todirnameotherwise:Sets[]totheemptystringif[]couldnotbefoundin$\OT1/p
tm/m/n/10.95 PATH. 

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

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[]\OT1/ptm/m/n/10.95 Find \OT1/cmtt/m/n/10.95 file \OT1/ptm/m/n/10.95 in the ':
'-separated di-rec-tory list (on Win-

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[]\OML/ztmcm/m/it/10.95 ; ifithasnodirname\OT1/ztmcm/m/n/10.95 ; \OML/ztmcm/m/i
t/10.95 set[]todirnameotherwise:Sets[]totheemptystringif[]couldnotbefoundin$\OT
1/cmtt/m/n/10.95 env\OT1/ptm/m/n/10.95 . 

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[]\OT1/ptm/m/n/10.95 Return the (es-ti-mated) to-tal size of all files given in
 \OT1/cmtt/m/n/10.95 filenames\OT1/ptm/m/n/10.95 . Uses

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

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[]\OT1/ptm/m/n/10.95 Find reg-u-lar ex-e-cutable \OT1/cmtt/m/n/10.95 file \OT1/
ptm/m/n/10.95 in $\OML/ztmcm/m/it/10.95 PATH; ifithasnodirname\OT1/ztmcm/m/n/10
.95 ; \OML/ztmcm/m/it/10.95 set[]todirnameotherwise:Sets[]totheemptystringifreg
ularexecutable[]couldnotbefoundin$\OT1/ptm/m/n/10.95 PATH. 

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

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[]\OT1/ptm/m/n/10.95 Prints the log mes-sage ob-tained from for-mat and fol-low
-ing pa-ram-e-ter ac-cord-

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\OT1/ptm/m/n/10.95 ing to if log-ging is en-abled ana-log to\OT1/cmtt/m/n/10.95
 gt[]log[]log()\OT1/ptm/m/n/10.95 . But in con-trast to

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[]\OT1/cmtt/m/n/10.95 void gt[]msort[]r([]void *base, size[]t nmemb, size[]t si
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
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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
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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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[147] [148]) [149] (./annotationsketch.aux)

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[]$\OT1/pcr/m/n/14.4 http : / / nar . oxfordjournals . org / cgi / content /
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[]\OT1/ptm/m/n/12 The \OT1/ptm/m/it/12 Read-joiner \OT1/ptm/m/n/12 tools are ru
n us-ing the fol-low-ing syn-tax: \OT1/pcr/m/n/12 gt readjoiner <tool> <argumen
ts>\OT1/ptm/m/n/12 ,
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[]\OT1/ptm/m/n/12 a single-end li-brary plus an in-ter-leaved
[2

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[]\OT1/ptm/m/n/12 It is usu-ally quite easy to pre-pare the map-ping as re-quir
ed. Say the reads to be cor-rected are \OT1/pcr/m/n/12 f[]reads.fastq

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[]\OT1/pcr/m/n/10 > bwa sampe cognate.fas -f map.sam f_reads.sai r_reads.sai f_
reads.fastq r_reads.fastq[] 
[2

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\OT1/ptm/m/n/12 se-quence fea-tures of LTR retro-trans-posons in pre-dicted can
-di-dates, like those re-ported by\OT1/ptm/m/it/12 LTRharvest \OT1/ptm/m/n/12 [
[]].
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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]]

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[2] [3>]>

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[]\OT1/pcr/m/n/10 # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) s(rLTR) e(rLTR
) l(rLTR) sim(LTRs) seq-nr[] 

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) l(rLTR) sim(LTRs) seq-nr[] 

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[]\OT1/pcr/m/n/10 $ gt ltrharvest -index chr02.19970727.fsa -seed 30 -xdrop 5 -
mat 2 -mis -2 -ins -3 
[8
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\OT1/ptm/m/n/12 trans-po-son it-self (\OT1/pcr/m/n/12 LTR[]retrotransposon \OT1
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at

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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/ptm/m/sc/12 GFF3\OT1/ptm/m/n/12 , tab de-lim-ited file for-mat for genom
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</usr/share/texlive/texmf-dist/fonts/type1/publ
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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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enome.fas
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(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty</usr/
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ts/type1/urw/times/utmr8a.pfb
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty>)</usr/share/texlive
/texmf-dist/fonts/type1/urw/times/utmb8a.pfb>)</usr/share/texlive/texmf-dist/fonts/type1/urw/ti
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ts/type1/urw/times/utmr8a.pfb>>
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mes/utmri8a.pfb)
Output written on uniquesub.pdf (3 pages, 98698 bytes).
Transcript written on uniquesub.log.
>mv uniquesub.aux uniquesub-pdf.aux
test -e repfind-pdf.aux && mv repfind-pdf.aux repfind.aux

make[3]: [repfind-pdf.aux] Error 1 (ignored)
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.mapMakefile:39: recipe for target 'repfind-pdf.aux' failed
pdflatex repfind.tex && rm repfind.pdf

Output written on matstat.pdf (2 pages, 92627 bytes).
Transcript written on matstat.log.
mv matstat.aux matstat-pdf.aux
head -n 6999 ../../testdata/at1MB > read1.fna
echo ">" > read2.fna
tail -n 6945 ../../testdata/at1MB >> read2.fna
cp ../../testdata/U89959_genomic.fas U89959.fna
../../bin/gt packedindex mkindex -dna -dir rev -parts 12 -bsize 10 \
                      -sprank -locfreq 32 -tis -ssp -indexname pck-human\
                      -db ../../testdata/at1MB
}]

LaTeX Warning: Citation `oai:CiteSeerPSU:481302' on page 1 undefined on input l
ine 49.


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nput line 51.


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 [1]}]

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(./repfind.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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 line 276.

[3]

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\OT1/ptm/m/it/12 Tools \OT1/ptm/m/n/12 (see [[]] for in-stal-la-tion in-struc-t
ions). There are two dif-fer-ent in-stal-la-tion op-tions for the \OT1/ptm/m/it
/12 Genome-
[1)
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[4])
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[]\OT1/pcr/m/n/10.95 BLAST-Filename \OT1/ptm/m/n/12 de-notes the XML for-mat-te
d BLAST-hit file, \OT1/pcr/m/n/10.95 Metagenome-Filename \OT1/ptm/m/n/12 the FA
STA
[2)
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[]\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 (./optionman.sty}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb)
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[]\OT1/ptm/m/n/12 . If this op-

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[3>
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[]\OT1/ptm/m/n/10.95 tataaaatagccaaatctgagcctaaaagcccttggatatccatgatttagaacgaac
catcccctcttattcaggagaagttttctgaactcttcaacatcctcga...| 

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[] 
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LEDYIRATA...| 

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[][] 

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[][]| 

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r/ucrro8a.pfb [7] (./mgth.aux)

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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/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmbi8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi7.pfb>></usr/share/tex
live/texmf-dist/fonts/type1/urw/times/utmr8a.pfb</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr1
2.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist
/fonts/type1/urw/times/utmri8a.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfb>></usr/s
hare/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/
texmf-dist/fonts/type1/urw/times/utmb8a.pfb
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></usr/share/texlive/texmf-dist/font
s/type1/urw/times/utmbi8a.pfbmv packedindex.aux packedindex-pdf.aux
cp ../../testdata/Q1.gz Q1.gz
></usr/share/texlive/texmf-dist/fonts/type1/urw/ti
mes/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb
test -e genomediff-pdf.aux && mv genomediff-pdf.aux genomediff.aux
make[3]: [genomediff-pdf.aux] Error 1 (ignored)
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pdflatex genomediff.tex && rm genomediff.pdf
>}
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mv mgth.aux mgth-pdf.aux
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]bibtex readjoiner
 [2]
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[]\OT1/ptm/m/n/12 Suppose the in-put se-quence $\OML/cmm/m/it/12 S \OT1/cmr/m/n
/12 = \OML/cmm/m/it/12 gagctcgagcgctgct$ \OT1/ptm/m/n/12 is con-tained in the f
ile \OT1/pcr/m/n/12 Repfind-example.fna\OT1/ptm/m/n/12 .

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[]\OT1/pcr/m/n/10 gt suffixerator -db repfinf-sample.seq -indexname repidx -dna
 -suf -tis -lcp -ssp -pl 
[3]
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[]\OT1/ptm/m/n/12 Kurtz, S., Choud-huri, J. V., Ohle-busch, E., Schleier-ma-che
r, C., Stoye, J., Giegerich,

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[4] (./repfind.aux)

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(see the transcript file for additional information){/usr/share/texlive/texmf-d
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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.pfbThis is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2014/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
>This is BibTeX, Version 0.99d (TeX Live 2014/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)
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test -e readjoiner-pdf.bbl || touch readjoiner-pdf.bbl

Output written on repfind.pdf (4 pages, 103838 bytes).
Transcript written on repfind.log.
diff readjoiner-pdf.bbl readjoiner.bbl || mv readjoiner.bbl readjoiner-pdf.bbl && rm -f readjoiner.bbl
mv repfind.aux repfind-pdf.aux
mv readjoiner.aux readjoiner-pdf.aux
test -e hop-pdf.aux && mv hop-pdf.aux hop.aux
test -e ltrharvest-pdf.aux && mv ltrharvest-pdf.aux ltrharvest.aux
bibtex hop
bibtex ltrharvest
entering extended mode
(./genomediff.tex
LaTeX2e <2014/05/01>
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(/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/lstmisc.styThis is BibTeX, Version 0.99d (TeX Live 2014/Debian)
The top-level auxiliary file: hop.aux
I found no \bibdata command---while reading file hop.aux
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(There were 2 error messages)
This is BibTeX, Version 0.99d (TeX Live 2014/Debian)
The top-level auxiliary file: ltrharvest.aux
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(There were 2 error messages)
make[3]: [hop-pdf.bbl] Error 2 (ignored)
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test -e hop-pdf.bbl || touch hop-pdf.bbl
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test -e ltrharvest-pdf.bbl || touch ltrharvest-pdf.bbl
diff ltrharvest-pdf.bbl ltrharvest.bbl || mv ltrharvest.bbl ltrharvest-pdf.bbl && rm -f ltrharvest.bbl
diff hop-pdf.bbl hop.bbl || mv hop.bbl hop-pdf.bbl && rm -f hop.bbl
mv ltrharvest.aux ltrharvest-pdf.aux
mv hop.aux hop-pdf.aux
test -e ltrdigest-pdf.aux && mv ltrdigest-pdf.aux ltrdigest.aux
test -e uniquesub-pdf.aux && mv uniquesub-pdf.aux uniquesub.aux
bibtex ltrdigest
bibtex uniquesub
)
(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(./optionman.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
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(/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.styThis is BibTeX, Version 0.99d (TeX Live 2014/Debian)
The top-level auxiliary file: uniquesub.aux
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(There were 2 error messages)
make[3]: [uniquesub-pdf.bbl] Error 2 (ignored)
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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 matstat-pdf.aux && mv matstat-pdf.aux matstat.aux
bibtex matstat
This is BibTeX, Version 0.99d (TeX Live 2014/Debian)
The top-level auxiliary file: ltrdigest.aux
The style file: unsrt.bst
I found no \bibdata command---while reading file ltrdigest.aux
Warning--I didn't find a database entry for "EKW07"
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(There was 1 error message)
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diff ltrdigest-pdf.bbl ltrdigest.bbl || mv ltrdigest.bbl ltrdigest-pdf.bbl && rm -f ltrdigest.bbl
0a1,3
> \begin{thebibliography}{}
> 
> \end{thebibliography}
mv ltrdigest.aux ltrdigest-pdf.aux
)test -e mgth-pdf.aux && mv mgth-pdf.aux mgth.aux
bibtex mgth

No file genomediff.aux.
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
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[Loading MPS to PDF converter (version 2006.09.02).]
) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.mapThis is BibTeX, Version 0.99d (TeX Live 2014/Debian)
The top-level auxiliary file: matstat.aux
I found no \citation commands---while reading file matstat.aux
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(There were 3 error messages)
make[3]: [matstat-pdf.bbl] Error 2 (ignored)
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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 packedindex-pdf.aux && mv packedindex-pdf.aux packedindex.aux
bibtex packedindex
This is BibTeX, Version 0.99d (TeX Live 2014/Debian)
The top-level auxiliary file: mgth.aux
I found no \bibdata command---while reading file mgth.aux
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(There were 2 error messages)
make[3]: [mgth-pdf.bbl] Error 2 (ignored)
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diff mgth-pdf.bbl mgth.bbl || mv mgth.bbl mgth-pdf.bbl && rm -f mgth.bbl
mv mgth.aux mgth-pdf.aux
test -e repfind-pdf.aux && mv repfind-pdf.aux repfind.aux
bibtex repfind
}]
(/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd)This is BibTeX, Version 0.99d (TeX Live 2014/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}
This is BibTeX, Version 0.99d (TeX Live 2014/Debian)
The top-level auxiliary file: repfind.aux
I found no \citation commands---while reading file repfind.aux
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I found no \bibstyle command---while reading file repfind.aux
(There were 3 error messages)
make[3]: [repfind-pdf.bbl] Error 2 (ignored)
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./findemptyoutfiles.sh
mv repfind.aux repfind-pdf.aux
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# 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
[1]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


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[2]

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[] 

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[]\OT1/ptm/m/n/12 The \OT1/ptm/m/it/12 Read-joiner \OT1/ptm/m/n/12 tools are ru
n us-ing the fol-low-ing syn-tax: \OT1/pcr/m/n/12 gt readjoiner <tool> <argumen
ts>\OT1/ptm/m/n/12 ,
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[]\OT1/ptm/m/n/12 It is usu-ally quite easy to pre-pare the map-ping as re-quir
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[]\OT1/pcr/m/n/10 > bwa sampe cognate.fas -f map.sam f_reads.sai r_reads.sai f_
reads.fastq r_reads.fastq[] 
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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
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Output written on hop.pdf (5 pages, 73997 bytes).
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>pdflatex hop.tex

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[]\OT1/pcr/m/n/10 # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) s(rLTR) e(rLTR
) l(rLTR) sim(LTRs) seq-nr[] 

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[]\OT1/pcr/m/n/10 $ gt ltrharvest -index chr02.19970727.fsa -seed 30 -xdrop 5 -
mat 2 -mis -2 -ins -3 
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[]\OT1/pcr/m/n/10 # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) TSD l(TSD) m(l
LTR) s(rLTR) e(rLTR) l(rLTR) TSD l(TSD) m(rLTR) sim(LTRs) seq-nr[] 

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[]\OT1/pcr/m/n/10 $ gt ltrharvest -index chrAll.19971001.fsa -seed 100 -minlenl
tr 100 -maxlenltr 1000 
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[]\OT1/ptm/m/sc/12 GFF3\OT1/ptm/m/n/12 , tab de-lim-ited file for-mat for genom
e an-no-ta-tion. $\OT1/pcr/m/n/12 http : / / www .

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[]\OT1/ptm/m/n/12 The \OT1/ptm/m/it/12 Read-joiner \OT1/ptm/m/n/12 tools are ru
n us-ing the fol-low-ing syn-tax: \OT1/pcr/m/n/12 gt readjoiner <tool> <argumen
ts>\OT1/ptm/m/n/12 ,
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[]\OT1/ptm/m/n/12 It is usu-ally quite easy to pre-pare the map-ping as re-quir
ed. Say the reads to be cor-rected are \OT1/pcr/m/n/12 f[]reads.fastq

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[]\OT1/pcr/m/n/10 > bwa sampe cognate.fas -f map.sam f_reads.sai r_reads.sai f_
reads.fastq r_reads.fastq[] 
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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 [3]] [4 [4test -e ltrdigest-pdf.aux && mv ltrdigest-pdf.aux ltrdigest.aux
] (./hop.aux) )
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ic/amsfonts/cm/cmsy10.pfb]pdflatex ltrdigest.tex
></usr/share/texlive/texmf-dist/fonts/type1/urw/courie
r/ucrr8a.pfb [5>]</usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></
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ve/texmf-dist/fonts/type1/urw/times/utmri8a.pfb) )
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[]$\OT1/pcr/m/n/14.4 http : / / nar . oxfordjournals . org / cgi / content /
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\OT1/ptm/m/n/12 se-quence fea-tures of LTR retro-trans-posons in pre-dicted can
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[]\OT1/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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[]\OT1/ptm/m/n/12 We will also as-sume that the HMM files to be used are called
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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/ptm/m/n/12 Kurtz, S., Choud-huri, J. V., Ohle-busch, E., Schleier-ma-che
r, C., Stoye, J., Giegerich,
[4
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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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m/cmr8.pfb))]
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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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\OT1/ptm/m/it/12 Tools \OT1/ptm/m/n/12 (see [[]] for in-stal-la-tion in-struc-t
ions). There are two dif-fer-ent in-stal-la-tion op-tions for the \OT1/ptm/m/it
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[]\OT1/pcr/m/n/10.95 BLAST-Filename \OT1/ptm/m/n/12 de-notes the XML for-mat-te
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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,
[4] (./repfind.aux) )
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test -e genomediff-pdf.aux && mv genomediff-pdf.aux genomediff.aux
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}]
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> \begin{thebibliography}{1}
> 
> \bibitem{HAU:DOM:WIE:2008}
> Bernhard Haubold, Mirjana Domazet-Loso, and Thomas Wiehe.
> \newblock An alignment-free distance measure for closely related genomes.
> \newblock In {\em RECOMB-CG ’08: Proceedings of the international workshop on
>   Comparative Genomics}, pages 87--99, Berlin, Heidelberg, 2008.
>   Springer-Verlag.
> 
> \bibitem{HAU:PFA:DOM:WIE:2009}
> B.~Haubold, P.~Pfaffelhuber, M.~Domazet-Loso, and T.~Wiehe.
> \newblock Estimating mutation distances from unaligned genomes.
> \newblock {\em J. Comput. Biol.}, 16:1487--1500, "Oct" 2009.
> 
> \bibitem{HAU:REE:PFA:2011}
> Bernhard Haubold, Floyd~A. Reed, and Peter Pfaffelhuber.
> \newblock Alignment-free estimation of nucleotide diversity.
> \newblock {\em Bioinformatics}, 27(4):449--455, 2011.
> 
> \bibitem{genometools}
> Gordon Gremme.
> \newblock The \textsc{GenomeTools} genome analysis system.
> \newblock \url{http://genometools.org}.
> 
> \end{thebibliography}
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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
line class...ok
mathsupport module...ok
memory allocator module...ok
memory feature index class...ok
n_r_encseq...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
uint64hashtable...ok
xdrop...ok
cd testsuite; ./testsuite.rb -keywords 'gt_sketch and not gt_python and not gt_ruby' -threads 3
seed=1385059208
1240: gt sketch short test (unknown output format)                : ok
1239: gt sketch short test (stdin)                                : ok
1238: gt sketch short test                                        : ok
1241: gt sketch short test (unwriteable PNG file)                 : ok
1243: gt sketch short test (nonexistant style file)               : ok
1245: gt sketch prob 1                                            : ok
1244: gt sketch short test (invalid style file)                   : ok
1242: gt sketch short test (unwriteable PDF file)                 : ok
1246: gt sketch prob 2                                            : ok
1248: gt sketch multiline without parent                          : ok
1247: gt sketch track IDs to style file                           : ok
1249: gt sketch pipe                                              : ok
1251: gt sketch -showrecmaps                                      : ok
1252: gt sketch -showrecmaps (normal text size)                   : ok
1253: gt sketch -showrecmaps (narrow image)                       : ok
1254: gt sketch -showrecmaps (large text size)                    : ok
1256: sketch_constructed (C)                                      : ok
1257: sketch_parsed (C)                                           : ok
1258: sketch_parsed reverse order (C)                             : ok
1259: sketch_constructed (Lua)                                    : ok
1260: sketch_parsed (Lua)                                         : ok
1250: gt sketch streams <-> file output                           : ok
1255: gt sketch runtime Lua failures                              : ok
make[1]: Leaving directory '/«PKGBUILDDIR»'
 fakeroot debian/rules binary-arch
dh binary-arch --parallel --with python2
   dh_testroot -a -O--parallel
   dh_prep -a -O--parallel
   debian/rules override_dh_auto_install
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_install -- installmanpages useshared=yes 64bit=no opt=no errorcheck=no prefix=/«PKGBUILDDIR»/debian/tmp/usr
make[2]: Entering directory '/«PKGBUILDDIR»'
[link libgenometools.so]
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
.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 --param=ssp-buffer-size=4 -Wformat -Werror=format-security!' \
  -e 's!@CPPFLAGS@!-I\\"/«PKGBUILDDIR»/debian/tmp/usr/include\\" -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DHAVE_MEMMOVE -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN -DLUA_USE_MKSTEMP -DHAVE_SQLITE!' \
  -e 's!@CXX@!g++!' -e 's!@CXXFLAGS@!-g -O2 -fstack-protector --param=ssp-buffer-size=4 -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@!"2014-07-27 06:43:04"!' \
  -e 's!@SYSTEM@!Linux!' <src/genometools-config.in \
  >/«PKGBUILDDIR»/debian/tmp/usr/bin/genometools-config
chmod 755 /«PKGBUILDDIR»/debian/tmp/usr/bin/genometools-config
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
a2x: WARNING: --destination-dir option is only applicable to HTML based outputs
..........................................................................................
test ! -d /«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
running install
running build
running build_py
creating build
creating build/lib.linux-armv7l-2.7
creating build/lib.linux-armv7l-2.7/gt
copying gt/__init__.py -> build/lib.linux-armv7l-2.7/gt
copying gt/dlload.py -> build/lib.linux-armv7l-2.7/gt
copying gt/props.py -> build/lib.linux-armv7l-2.7/gt
creating build/lib.linux-armv7l-2.7/gt/core
copying gt/core/__init__.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/alphabet.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/array.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/encseq.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/error.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/gtrange.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/gtstr.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/readmode.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/str_array.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/warning.py -> build/lib.linux-armv7l-2.7/gt/core
creating build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/__init__.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/block.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/canvas.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/color.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/custom_track.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/custom_track_example.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/diagram.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/feature_index.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/feature_stream.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/graphics.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/image_info.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/layout.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/rec_map.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/style.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
creating build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/__init__.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/add_introns_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/anno_db.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/comment_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/custom_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/custom_stream_example.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/custom_visitor.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/custom_visitor_example.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/dup_feature_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/eof_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/feature_index.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/feature_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/feature_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/genome_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/genome_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/gff3_in_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/gff3_out_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/gff3_visitor.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/inter_feature_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/merge_feature_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/meta_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/node_visitor.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/rdb.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/region_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/sequence_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/strand.py -> build/lib.linux-armv7l-2.7/gt/extended
running install_lib
creating /«PKGBUILDDIR»/debian/python-genometools/usr
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
copying build/lib.linux-armv7l-2.7/gt/__init__.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
copying build/lib.linux-armv7l-2.7/gt/dlload.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
copying build/lib.linux-armv7l-2.7/gt/props.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/__init__.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/alphabet.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/array.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/encseq.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/error.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/gtrange.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/gtstr.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/readmode.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/str_array.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/warning.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/__init__.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/block.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/canvas.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/color.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/custom_track.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/custom_track_example.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/diagram.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/feature_index.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/feature_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/graphics.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/image_info.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/layout.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/rec_map.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/style.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/__init__.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/add_introns_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/anno_db.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/comment_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_stream_example.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_visitor.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_visitor_example.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/dup_feature_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/eof_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/feature_index.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/feature_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/feature_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/genome_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/genome_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/gff3_in_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/gff3_out_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/gff3_visitor.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/inter_feature_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/merge_feature_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/meta_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/node_visitor.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/rdb.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/region_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/sequence_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/strand.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
running install_egg_info
Writing /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/GenomeTools-0.1.egg-info
make[1]: Leaving directory '/«PKGBUILDDIR»'
   dh_install -a -O--parallel
   dh_installdocs -a -O--parallel
   dh_installchangelogs -a -O--parallel
   dh_installman -a -O--parallel
   dh_python2 -a -O--parallel
   dh_perl -a -O--parallel
   dh_link -a -O--parallel
   dh_compress -a -O--parallel
   dh_fixperms -a -O--parallel
   debian/rules override_dh_strip
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_strip --dbg-package=genometools-dbg
make[1]: Leaving directory '/«PKGBUILDDIR»'
   dh_makeshlibs -a -O--parallel
   dh_shlibdeps -a -O--parallel
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/genometools/usr/bin/gt was not linked against libglib-2.0.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/genometools/usr/bin/gt was not linked against libdl.so.2 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libgenometools0/usr/lib/libgenometools.so.0 was not linked against 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-des56.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libgenometools0/usr/lib/libgenometools.so.0 was not linked against libglib-2.0.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libgenometools0/usr/lib/libgenometools.so.0 was not linked against liblua5.1-filesystem.so.0 (it uses none of the library's symbols)
   dh_installdeb -a -O--parallel
   dh_gencontrol -a -O--parallel
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: Depends field of package libgenometools0-dev: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: Depends field of package genometools-dbg: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: Depends field of package python-genometools: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package python-genometools: unused substitution variable ${python:Provides}
dpkg-gencontrol: warning: package python-genometools: unused substitution variable ${python:Versions}
   dh_md5sums -a -O--parallel
   dh_builddeb -a -O--parallel
dpkg-deb: building package `libgenometools0' in `../libgenometools0_1.5.3-1_armhf.deb'.
dpkg-deb: building package `genometools-dbg' in `../genometools-dbg_1.5.3-1_armhf.deb'.
dpkg-deb: building package `genometools' in `../genometools_1.5.3-1_armhf.deb'.
dpkg-deb: building package `libgenometools0-dev' in `../libgenometools0-dev_1.5.3-1_armhf.deb'.
dpkg-deb: building package `python-genometools' in `../python-genometools_1.5.3-1_armhf.deb'.
 dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../genometools_1.5.3-1_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
 dpkg-source --after-build genometools-1.5.3
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140727-0734

Finished
────────

I: Built successfully

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


genometools_1.5.3-1_armhf.changes:
──────────────────────────────────

Format: 1.8
Date: Wed, 16 Jul 2014 20:32:19 +0100
Source: genometools
Binary: genometools genometools-common libgenometools0 libgenometools0-dev genometools-doc genometools-dbg python-genometools
Architecture: armhf
Version: 1.5.3-1
Distribution: jessie-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <sascha@steinbiss.name>
Description:
 genometools - versatile genome analysis toolkit
 genometools-common - shared data files for GenomeTools
 genometools-dbg - versatile genome analysis toolkit, with debug symbols
 genometools-doc - documentation for GenomeTools
 libgenometools0 - versatile genome analysis library
 libgenometools0-dev - development files for GenomeTools
 python-genometools - Python bindings for genometools
Changes:
 genometools (1.5.3-1) unstable; urgency=low
 .
   * New upstream release.
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 a8c85689c87c719ff7abb28f96d00e0205ea56d6 75390 libgenometools0-dev_1.5.3-1_armhf.deb
 c73cb2fd27c00be92e4ecfa9bceffb41da144a24 3989530 genometools-dbg_1.5.3-1_armhf.deb
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Checksums-Sha256:
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Files:
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 4294f5948d7ac872a84bc74d5612bffe 28956 python optional python-genometools_1.5.3-1_armhf.deb

┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents                                                             │
└──────────────────────────────────────────────────────────────────────────────┘


genometools_1.5.3-1_armhf.deb
─────────────────────────────

 new debian package, version 2.0.
 size 1590372 bytes: control archive=3680 bytes.
     887 bytes,    16 lines      control              
    7024 bytes,    98 lines      md5sums              
 Package: genometools
 Version: 1.5.3-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 5098
 Depends: libbz2-1.0, libc6 (>= 2.11), 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 2014-07-27 07:33 ./
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/bin/
-rwxr-xr-x root/root   5103700 2014-07-27 07:33 ./usr/bin/gt
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/share/
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/share/doc/
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/share/doc/genometools/
-rw-r--r-- root/root      1772 2014-06-12 20:33 ./usr/share/doc/genometools/README
-rw-r--r-- root/root       816 2014-06-12 20:33 ./usr/share/doc/genometools/CONTRIBUTORS
-rw-r--r-- root/root         6 2014-06-12 20:33 ./usr/share/doc/genometools/VERSION
-rw-r--r-- root/root      6607 2013-03-04 14:48 ./usr/share/doc/genometools/copyright
-rw-r--r-- root/root      1759 2014-07-16 20:03 ./usr/share/doc/genometools/changelog.Debian.gz
-rw-r--r-- root/root      5324 2014-06-12 20:33 ./usr/share/doc/genometools/changelog.gz
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/share/man/
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/share/man/man1/
-rw-r--r-- root/root       833 2014-07-27 07:33 ./usr/share/man/man1/gt-bed_to_gff3.1.gz
-rw-r--r-- root/root      1620 2014-07-27 07:33 ./usr/share/man/man1/gt-cds.1.gz
-rw-r--r-- root/root      1249 2014-07-27 07:33 ./usr/share/man/man1/gt-chain2dim.1.gz
-rw-r--r-- root/root      1069 2014-07-27 07:33 ./usr/share/man/man1/gt-chseqids.1.gz
-rw-r--r-- root/root       666 2014-07-27 07:33 ./usr/share/man/man1/gt-clean.1.gz
-rw-r--r-- root/root      1036 2014-07-27 07:33 ./usr/share/man/man1/gt-compreads-compress.1.gz
-rw-r--r-- root/root       925 2014-07-27 07:33 ./usr/share/man/man1/gt-compreads-decompress.1.gz
-rw-r--r-- root/root      1078 2014-07-27 07:33 ./usr/share/man/man1/gt-compreads-refcompress.1.gz
-rw-r--r-- root/root       875 2014-07-27 07:33 ./usr/share/man/man1/gt-compreads-refdecompress.1.gz
-rw-r--r-- root/root       737 2014-07-27 07:33 ./usr/share/man/man1/gt-compreads.1.gz
-rw-r--r-- root/root       775 2014-07-27 07:33 ./usr/share/man/man1/gt-condenser.1.gz
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-rw-r--r-- root/root       789 2014-07-27 07:33 ./usr/share/man/man1/gt-congruence.1.gz
-rw-r--r-- root/root       936 2014-07-27 07:33 ./usr/share/man/man1/gt-convertseq.1.gz
-rw-r--r-- root/root      1410 2014-07-27 07:33 ./usr/share/man/man1/gt-csa.1.gz
-rw-r--r-- root/root       647 2014-07-27 07:33 ./usr/share/man/man1/gt-dot.1.gz
-rw-r--r-- root/root       812 2014-07-27 07:33 ./usr/share/man/man1/gt-dupfeat.1.gz
-rw-r--r-- root/root       786 2014-07-27 07:33 ./usr/share/man/man1/gt-encseq-bench.1.gz
-rw-r--r-- root/root       839 2014-07-27 07:33 ./usr/share/man/man1/gt-encseq-bitextract.1.gz
-rw-r--r-- root/root       823 2014-07-27 07:33 ./usr/share/man/man1/gt-encseq-check.1.gz
-rw-r--r-- root/root      1051 2014-07-27 07:33 ./usr/share/man/man1/gt-encseq-decode.1.gz
-rw-r--r-- root/root      1045 2014-07-27 07:33 ./usr/share/man/man1/gt-encseq-encode.1.gz
-rw-r--r-- root/root       938 2014-07-27 07:33 ./usr/share/man/man1/gt-encseq-info.1.gz
-rw-r--r-- root/root       800 2014-07-27 07:33 ./usr/share/man/man1/gt-encseq-md5.1.gz
-rw-r--r-- root/root      1028 2014-07-27 07:33 ./usr/share/man/man1/gt-encseq-sample.1.gz
-rw-r--r-- root/root       783 2014-07-27 07:33 ./usr/share/man/man1/gt-encseq.1.gz
-rw-r--r-- root/root       912 2014-07-27 07:33 ./usr/share/man/man1/gt-encseq2spm.1.gz
-rw-r--r-- root/root      1173 2014-07-27 07:33 ./usr/share/man/man1/gt-eval.1.gz
-rw-r--r-- root/root      1667 2014-07-27 07:33 ./usr/share/man/man1/gt-extractfeat.1.gz
-rw-r--r-- root/root      2123 2014-07-27 07:33 ./usr/share/man/man1/gt-extractseq.1.gz
-rw-r--r-- root/root       803 2014-07-27 07:33 ./usr/share/man/man1/gt-fastq_sample.1.gz
-rw-r--r-- root/root       868 2014-07-27 07:33 ./usr/share/man/man1/gt-featureindex.1.gz
-rw-r--r-- root/root      1519 2014-07-27 07:33 ./usr/share/man/man1/gt-fingerprint.1.gz
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-rw-r--r-- root/root      1775 2014-07-27 07:33 ./usr/share/man/man1/gt-gff3.1.gz
-rw-r--r-- root/root       774 2014-07-27 07:33 ./usr/share/man/man1/gt-gff3_to_gtf.1.gz
-rw-r--r-- root/root      1009 2014-07-27 07:33 ./usr/share/man/man1/gt-gff3validator.1.gz
-rw-r--r-- root/root       802 2014-07-27 07:33 ./usr/share/man/man1/gt-gtf_to_gff3.1.gz
-rw-r--r-- root/root      2424 2014-07-27 07:33 ./usr/share/man/man1/gt-hop.1.gz
-rw-r--r-- root/root      1527 2014-07-27 07:33 ./usr/share/man/man1/gt-id_to_md5.1.gz
-rw-r--r-- root/root       827 2014-07-27 07:33 ./usr/share/man/man1/gt-interfeat.1.gz
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-rw-r--r-- root/root       876 2014-07-27 07:33 ./usr/share/man/man1/gt-ltrclustering.1.gz
-rw-r--r-- root/root      2150 2014-07-27 07:33 ./usr/share/man/man1/gt-ltrdigest.1.gz
-rw-r--r-- root/root      1563 2014-07-27 07:33 ./usr/share/man/man1/gt-ltrharvest.1.gz
-rw-r--r-- root/root       937 2014-07-27 07:33 ./usr/share/man/man1/gt-matchtool.1.gz
-rw-r--r-- root/root       891 2014-07-27 07:33 ./usr/share/man/man1/gt-matstat.1.gz
-rw-r--r-- root/root       829 2014-07-27 07:33 ./usr/share/man/man1/gt-md5_to_id.1.gz
-rw-r--r-- root/root       884 2014-07-27 07:33 ./usr/share/man/man1/gt-merge.1.gz
-rw-r--r-- root/root       801 2014-07-27 07:33 ./usr/share/man/man1/gt-mergefeat.1.gz
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-rw-r--r-- root/root       665 2014-07-27 07:33 ./usr/share/man/man1/gt-mmapandread.1.gz
-rw-r--r-- root/root      1292 2014-07-27 07:33 ./usr/share/man/man1/gt-orffinder.1.gz
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-rw-r--r-- root/root       741 2014-07-27 07:33 ./usr/share/man/man1/gt-prebwt.1.gz
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-rw-r--r-- root/root       908 2014-07-27 07:33 ./usr/share/man/man1/gt-readjoiner-overlap.1.gz
-rw-r--r-- root/root      1265 2014-07-27 07:33 ./usr/share/man/man1/gt-readjoiner-prefilter.1.gz
-rw-r--r-- root/root       850 2014-07-27 07:33 ./usr/share/man/man1/gt-readjoiner.1.gz
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libgenometools0_1.5.3-1_armhf.deb
─────────────────────────────────

 new debian package, version 2.0.
 size 1494834 bytes: control archive=1633 bytes.
    1006 bytes,    19 lines      control              
     297 bytes,     4 lines      md5sums              
     976 bytes,    42 lines   *  postinst             #!/bin/sh
     963 bytes,    43 lines   *  postrm               #!/bin/sh
      33 bytes,     1 lines      shlibs               
 Package: libgenometools0
 Source: genometools
 Version: 1.5.3-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 5058
 Depends: libbz2-1.0, libc6 (>= 2.11), 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 2014-07-27 07:33 ./
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/lib/
-rw-r--r-- root/root   5163492 2014-07-27 07:33 ./usr/lib/libgenometools.so.0
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/share/
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/share/doc/
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/share/doc/libgenometools0/
-rw-r--r-- root/root      6607 2013-03-04 14:48 ./usr/share/doc/libgenometools0/copyright
-rw-r--r-- root/root      1759 2014-07-16 20:03 ./usr/share/doc/libgenometools0/changelog.Debian.gz
-rw-r--r-- root/root      5324 2014-06-12 20:33 ./usr/share/doc/libgenometools0/changelog.gz


libgenometools0-dev_1.5.3-1_armhf.deb
─────────────────────────────────────

 new debian package, version 2.0.
 size 75390 bytes: control archive=5445 bytes.
     672 bytes,    18 lines      control              
   13429 bytes,   159 lines      md5sums              
 Package: libgenometools0-dev
 Source: genometools
 Version: 1.5.3-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 459
 Depends: libgenometools0 (= 1.5.3-1)
 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.

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drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/include/genometools/ltr/
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-rw-r--r-- root/root      1821 2014-07-27 06:43 ./usr/include/genometools/ltr/ltr_orf_annotator_stream_api.h
-rw-r--r-- root/root      2642 2014-07-27 06:43 ./usr/include/genometools/ltr/ltr_refseq_match_stream_api.h
-rw-r--r-- root/root      2002 2014-07-27 06:43 ./usr/include/genometools/gt_config.h
-rw-r--r-- root/root      6539 2014-07-27 06:43 ./usr/include/genometools/genometools.h
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/share/
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/share/doc/
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/share/doc/libgenometools0-dev/
-rw-r--r-- root/root      6607 2013-03-04 14:48 ./usr/share/doc/libgenometools0-dev/copyright
-rw-r--r-- root/root      1759 2014-07-16 20:03 ./usr/share/doc/libgenometools0-dev/changelog.Debian.gz
-rw-r--r-- root/root      5324 2014-06-12 20:33 ./usr/share/doc/libgenometools0-dev/changelog.gz
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/lib/
lrwxrwxrwx root/root         0 2014-07-27 07:33 ./usr/lib/libgenometools.so -> libgenometools.so.0


genometools-dbg_1.5.3-1_armhf.deb
─────────────────────────────────

 new debian package, version 2.0.
 size 3989530 bytes: control archive=758 bytes.
     571 bytes,    14 lines      control              
     341 bytes,     4 lines      md5sums              
 Package: genometools-dbg
 Source: genometools
 Version: 1.5.3-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 4414
 Depends: genometools (= 1.5.3-1) | libgenometools0 (= 1.5.3-1)
 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.

drwxr-xr-x root/root         0 2014-07-27 07:33 ./
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/share/
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/share/doc/
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/share/doc/genometools-dbg/
-rw-r--r-- root/root      6607 2013-03-04 14:48 ./usr/share/doc/genometools-dbg/copyright
-rw-r--r-- root/root      1759 2014-07-16 20:03 ./usr/share/doc/genometools-dbg/changelog.Debian.gz
-rw-r--r-- root/root      5324 2014-06-12 20:33 ./usr/share/doc/genometools-dbg/changelog.gz
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/lib/
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/lib/debug/
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/lib/debug/.build-id/
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-rw-r--r-- root/root   4505365 2014-07-27 07:33 ./usr/lib/debug/.build-id/4c/6f7ed5ab852357e9e98265692ebceb786f6180.debug


python-genometools_1.5.3-1_armhf.deb
────────────────────────────────────

 new debian package, version 2.0.
 size 28956 bytes: control archive=2692 bytes.
     672 bytes,    15 lines      control              
    5278 bytes,    57 lines      md5sums              
     168 bytes,     9 lines   *  postinst             #!/bin/sh
     273 bytes,    14 lines   *  prerm                #!/bin/sh
 Package: python-genometools
 Source: genometools
 Version: 1.5.3-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 170
 Depends: python (>= 2.7), python (<< 2.8), python-ctypes, libgenometools0
 Section: python
 Priority: optional
 Homepage: http://genometools.org
 Description: Python bindings for genometools
  Partial Python2 bindings for the GenomeTools library. Besides basic
  bioinformatics data structures, the library contains components for sequence
  and annotation handling, sequence compression, index structure generation and
  access, efficient matching, annotation visualization and much more.

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-rw-r--r-- root/root      1378 2014-06-12 20:33 ./usr/lib/python2.7/dist-packages/gt/extended/eof_node.py
-rw-r--r-- root/root      5813 2014-06-12 20:33 ./usr/lib/python2.7/dist-packages/gt/extended/feature_index.py
-rw-r--r-- root/root      8909 2014-06-12 20:33 ./usr/lib/python2.7/dist-packages/gt/extended/feature_node.py
-rw-r--r-- root/root      1699 2014-06-12 20:33 ./usr/lib/python2.7/dist-packages/gt/extended/feature_stream.py
-rw-r--r-- root/root      4547 2014-06-12 20:33 ./usr/lib/python2.7/dist-packages/gt/extended/genome_node.py
-rw-r--r-- root/root      2078 2014-06-12 20:33 ./usr/lib/python2.7/dist-packages/gt/extended/genome_stream.py
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-rw-r--r-- root/root      2334 2014-06-12 20:33 ./usr/lib/python2.7/dist-packages/gt/extended/sequence_node.py
-rw-r--r-- root/root       933 2014-06-12 20:33 ./usr/lib/python2.7/dist-packages/gt/extended/strand.py
-rw-r--r-- root/root       257 2014-07-27 07:33 ./usr/lib/python2.7/dist-packages/GenomeTools-0.1.egg-info
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drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/share/doc/
drwxr-xr-x root/root         0 2014-07-27 07:33 ./usr/share/doc/python-genometools/
-rw-r--r-- root/root      6607 2013-03-04 14:48 ./usr/share/doc/python-genometools/copyright
-rw-r--r-- root/root      1759 2014-07-16 20:03 ./usr/share/doc/python-genometools/changelog.Debian.gz
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build                                                                   │
└──────────────────────────────────────────────────────────────────────────────┘


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

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

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

Build Architecture: armhf
Build-Space: 249996
Build-Time: 4007
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 1615
Job: genometools_1.5.3-1
Machine Architecture: armhf
Package: genometools
Package-Time: 5683
Source-Version: 1.5.3-1
Space: 249996
Status: successful
Version: 1.5.3-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20140727-0734
Build needed 01:34:43, 249996k disc space
Raspbian Package Auto-Building

Build log for genometools (1.5.3-1) on armhf
