Build log for genometools (1.5.1-1) on armhf

genometools → 1.5.1-1 → armhf → 2013-06-14 14:49:19

sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on debian-armhf

╔══════════════════════════════════════════════════════════════════════════════╗
║ genometools 1.5.1-1 (armhf)                                14 Jun 2013 14:19 ║
╚══════════════════════════════════════════════════════════════════════════════╝

Package: genometools
Version: 1.5.1-1
Source Version: 1.5.1-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'build/genometools-fZrQWs/genometools-1.5.1' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/genometools-fZrQWs' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-a2dc3636-0591-4411-a95c-468f0c744ca5' with '«CHROOT»'

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

Get:1 http://172.17.0.1 jessie-staging Release.gpg [490 B]
Get:2 http://172.17.0.1 jessie-staging Release [10.8 kB]
Get:3 http://172.17.0.1 jessie-staging/main Sources [6617 kB]
Get:4 http://172.17.0.1 jessie-staging/main armhf Packages [7643 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 14.3 MB in 42s (336 kB/s)
Reading package lists...

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


Check APT
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Checking available source versions...

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

Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'genometools' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/genometools/trunk/
Need to get 12.2 MB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main genometools 1.5.1-1 (dsc) [2653 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main genometools 1.5.1-1 (tar) [12.1 MB]
Get:3 http://172.17.0.1/private/ jessie-staging/main genometools 1.5.1-1 (diff) [42.5 kB]
Fetched 12.2 MB in 15s (803 kB/s)
Download complete and in download only mode

Check arch
──────────

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-WK316e/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 55 not upgraded.
Need to get 0 B/706 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 ... 11288 files and directories currently installed.)
Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: 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, liblua5.1-md5-dev, liblua5.1-filesystem-dev, liblua5.1-lpeg-dev, libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, libncurses5-dev, libsqlite3-dev, libbam-dev, libpango1.0-dev, texlive-latex-base, texlive-latex-extra, texlive-fonts-extra, latex-xcolor, texlive-fonts-recommended, python
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), liblua5.1-0-dev, liblua5.1-md5-dev, liblua5.1-filesystem-dev, liblua5.1-lpeg-dev, libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, libncurses5-dev, libsqlite3-dev, libbam-dev, libpango1.0-dev, texlive-latex-base, texlive-latex-extra, texlive-fonts-extra, latex-xcolor, texlive-fonts-recommended, python
dpkg-deb: building package `sbuild-build-depends-genometools-dummy' in `/«BUILDDIR»/resolver-owwG7t/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:
  bsdmainutils debhelper ed file fontconfig fontconfig-config fonts-comfortaa
  fonts-dejavu-core fonts-dejavu-extra fonts-droid 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-linuxlibertine 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 html2text intltool-debian
  latex-xcolor libasprintf-dev libasprintf0c2 libavahi-client3
  libavahi-common-data libavahi-common3 libbam-dev libbz2-dev
  libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev
  libcroco3 libcups2 libcupsimage2 libdatrie1 libelfg0 libexpat1 libexpat1-dev
  libffi6 libfontconfig1 libfontconfig1-dev libfreetype6 libfreetype6-dev
  libgcrypt11 libgettextpo-dev libgettextpo0 libgirepository-1.0-1
  libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libgnutls26
  libgpg-error0 libgraphite2-3 libgraphite3 libgs9 libgs9-common
  libgssapi-krb5-2 libharfbuzz-dev libharfbuzz-icu0 libharfbuzz0a libice-dev
  libice6 libicu48 libidn11 libijs-0.35 libjasper1 libjbig0 libjbig2dec0
  libjpeg8 libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0
  liblcms1 liblcms2-2 liblua5.1-0 liblua5.1-0-dev liblua5.1-filesystem-dev
  liblua5.1-lpeg-dev liblua5.1-md5-dev liblzo2-2 libmagic1 libncurses5
  libncurses5-dev libncursesw5 libopenjpeg2 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 libpcre3-dev libpcrecpp0 libpipeline1
  libpixman-1-0 libpixman-1-dev libpng12-0 libpng12-dev libpoppler19 libpopt0
  libptexenc1 libpthread-stubs0 libpthread-stubs0-dev libpython2.7-minimal
  libpython2.7-stdlib libreadline-dev libreadline6-dev libsm-dev libsm6
  libsqlite3-0 libsqlite3-dev libssl1.0.0 libtasn1-3 libthai-data libthai0
  libtiff4 libtinfo-dev libtinfo5 libunistring0 libx11-6 libx11-data
  libx11-dev libxau-dev libxau6 libxaw7 libxcb-render0 libxcb-render0-dev
  libxcb-shm0 libxcb-shm0-dev libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6
  libxext-dev libxext6 libxft-dev libxft2 libxml2 libxmu6 libxpm4
  libxrender-dev libxrender1 libxt6 lua-filesystem lua-filesystem-dev lua-lpeg
  lua-lpeg-dev lua-md5 lua-md5-dev luatex man-db mime-support ncurses-bin
  otf-freefont pkg-config po-debconf poppler-data preview-latex-style python
  python-minimal python2.7 python2.7-minimal tex-common texlive-base
  texlive-binaries texlive-common texlive-doc-base texlive-fonts-extra
  texlive-fonts-recommended texlive-latex-base texlive-latex-extra
  texlive-latex-recommended texlive-pictures ttf-dejavu-core ttf-dejavu-extra
  ttf-freefont ttf-marvosym ucf x11-common x11proto-core-dev
  x11proto-input-dev x11proto-kb-dev x11proto-render-dev x11proto-xext-dev
  xdg-utils xorg-sgml-doctools xtrans-dev zlib1g zlib1g-dev
Suggested packages:
  wamerican wordlist whois vacation dh-make fontforge gettext-doc groff
  libcairo2-doc cups-common rng-tools libglib2.0-doc krb5-doc krb5-user
  libice-doc libjasper-runtime liblcms-utils 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
  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-unfonts-core
  python-doc python-tk python2.7-doc binfmt-support perl-tk xpdf-reader
  pdf-viewer gv postscript-viewer cm-super libfile-which-perl dot2tex gvfs-bin
Recommended packages:
  texlive-xetex curl wget lynx-cur autopoint shared-mime-info krb5-locales
  libtool libgpm2 libx11-doc xml-core texlive-luatex libmail-sendmail-perl
  lmodern ruby wish texlive-fonts-extra-doc texlive-fonts-recommended-doc
  tex-gyre tipa texlive-latex-base-doc texlive-latex-extra-doc
  texlive-latex-recommended-doc latex-beamer prosper texlive-pictures-doc pgf
  libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils
  x11-xserver-utils
The following NEW packages will be installed:
  bsdmainutils debhelper ed file fontconfig fontconfig-config fonts-comfortaa
  fonts-dejavu-core fonts-dejavu-extra fonts-droid 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-linuxlibertine 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 html2text intltool-debian
  latex-xcolor libasprintf-dev libasprintf0c2 libavahi-client3
  libavahi-common-data libavahi-common3 libbam-dev libbz2-dev
  libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev
  libcroco3 libcups2 libcupsimage2 libdatrie1 libelfg0 libexpat1 libexpat1-dev
  libffi6 libfontconfig1 libfontconfig1-dev libfreetype6 libfreetype6-dev
  libgcrypt11 libgettextpo-dev libgettextpo0 libgirepository-1.0-1
  libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libgnutls26
  libgpg-error0 libgraphite2-3 libgraphite3 libgs9 libgs9-common
  libgssapi-krb5-2 libharfbuzz-dev libharfbuzz-icu0 libharfbuzz0a libice-dev
  libice6 libicu48 libidn11 libijs-0.35 libjasper1 libjbig0 libjbig2dec0
  libjpeg8 libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0
  liblcms1 liblcms2-2 liblua5.1-0 liblua5.1-0-dev liblua5.1-filesystem-dev
  liblua5.1-lpeg-dev liblua5.1-md5-dev liblzo2-2 libmagic1 libncurses5-dev
  libopenjpeg2 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
  libpcre3-dev libpcrecpp0 libpipeline1 libpixman-1-0 libpixman-1-dev
  libpng12-0 libpng12-dev libpoppler19 libpopt0 libptexenc1 libpthread-stubs0
  libpthread-stubs0-dev libpython2.7-minimal libpython2.7-stdlib
  libreadline-dev libreadline6-dev libsm-dev libsm6 libsqlite3-0
  libsqlite3-dev libssl1.0.0 libtasn1-3 libthai-data libthai0 libtiff4
  libtinfo-dev libunistring0 libx11-6 libx11-data libx11-dev libxau-dev
  libxau6 libxaw7 libxcb-render0 libxcb-render0-dev libxcb-shm0
  libxcb-shm0-dev libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev
  libxext6 libxft-dev libxft2 libxml2 libxmu6 libxpm4 libxrender-dev
  libxrender1 libxt6 lua-filesystem lua-filesystem-dev lua-lpeg lua-lpeg-dev
  lua-md5 lua-md5-dev luatex man-db mime-support otf-freefont pkg-config
  po-debconf poppler-data preview-latex-style python python-minimal python2.7
  python2.7-minimal sbuild-build-depends-genometools-dummy tex-common
  texlive-base texlive-binaries texlive-common texlive-doc-base
  texlive-fonts-extra texlive-fonts-recommended texlive-latex-base
  texlive-latex-extra texlive-latex-recommended texlive-pictures
  ttf-dejavu-core ttf-dejavu-extra ttf-freefont ttf-marvosym ucf x11-common
  x11proto-core-dev x11proto-input-dev x11proto-kb-dev x11proto-render-dev
  x11proto-xext-dev xdg-utils xorg-sgml-doctools xtrans-dev zlib1g-dev
The following packages will be upgraded:
  libncurses5 libncursesw5 libtinfo5 ncurses-bin zlib1g
5 upgraded, 205 newly installed, 0 to remove and 50 not upgraded.
Need to get 278 MB/278 MB of archives.
After this operation, 815 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libncursesw5 armhf 5.9+20130504-1 [122 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main libtinfo5 armhf 5.9+20130504-1 [284 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main libncurses5 armhf 5.9+20130504-1 [95.6 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main ncurses-bin armhf 5.9+20130504-1 [357 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main zlib1g armhf 1:1.2.8.dfsg-1 [88.8 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libpcre3 armhf 1:8.31-2 [248 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.2.3-1 [35.8 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libpopt0 armhf 1.16-7 [56.5 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libssl1.0.0 armhf 1.0.1e-2+rpi1 [1049 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-3 [666 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.3-6 [867 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.1.1-10 [26.8 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main libgpg-error0 armhf 1.10-3.1 [78.5 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main libgcrypt11 armhf 1.5.0-5 [299 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main libp11-kit0 armhf 0.12-3 [48.2 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main libtasn1-3 armhf 2.14-3 [64.1 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main libgnutls26 armhf 2.12.23-5 [598 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main libkeyutils1 armhf 1.5.5-7 [8024 B]
Get:20 http://172.17.0.1/private/ jessie-staging/main libkrb5support0 armhf 1.10.1+dfsg-5 [46.2 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main libk5crypto3 armhf 1.10.1+dfsg-5 [112 kB]
Get:22 http://172.17.0.1/private/ jessie-staging/main libkrb5-3 armhf 1.10.1+dfsg-5 [342 kB]
Get:23 http://172.17.0.1/private/ jessie-staging/main libgssapi-krb5-2 armhf 1.10.1+dfsg-5 [131 kB]
Get:24 http://172.17.0.1/private/ jessie-staging/main libidn11 armhf 1.25-2 [175 kB]
Get:25 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.14-2 [213 kB]
Get:26 http://172.17.0.1/private/ jessie-staging/main libsqlite3-0 armhf 3.7.17-1 [436 kB]
Get:27 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.8.0+dfsg1-7+nmu1 [822 kB]
Get:28 http://172.17.0.1/private/ jessie-staging/main libpython2.7-minimal armhf 2.7.5-4 [520 kB]
Get:29 http://172.17.0.1/private/ jessie-staging/main python2.7-minimal armhf 2.7.5-4 [1195 kB]
Get:30 http://172.17.0.1/private/ jessie-staging/main fonts-junicode all 0.7.8-1 [1239 kB]
Get:31 http://172.17.0.1/private/ jessie-staging/main libavahi-common-data armhf 0.6.31-2 [137 kB]
Get:32 http://172.17.0.1/private/ jessie-staging/main libavahi-common3 armhf 0.6.31-2 [52.6 kB]
Get:33 http://172.17.0.1/private/ jessie-staging/main libavahi-client3 armhf 0.6.31-2 [55.4 kB]
Get:34 http://172.17.0.1/private/ jessie-staging/main libexpat1 armhf 2.1.0-3 [117 kB]
Get:35 http://172.17.0.1/private/ jessie-staging/main libfreetype6 armhf 2.4.9-1.1 [401 kB]
Get:36 http://172.17.0.1/private/ jessie-staging/main ucf all 3.0027 [71.4 kB]
Get:37 http://172.17.0.1/private/ jessie-staging/main fonts-dejavu-core all 2.33+svn2514-3 [1042 kB]
Get:38 http://172.17.0.1/private/ jessie-staging/main ttf-dejavu-core all 2.33+svn2514-3 [29.8 kB]
Get:39 http://172.17.0.1/private/ jessie-staging/main fonts-freefont-ttf all 20120503-1 [6024 kB]
Get:40 http://172.17.0.1/private/ jessie-staging/main ttf-freefont all 20120503-1 [118 kB]
Get:41 http://172.17.0.1/private/ jessie-staging/main fontconfig-config all 2.9.0-7.1 [233 kB]
Get:42 http://172.17.0.1/private/ jessie-staging/main libfontconfig1 armhf 2.9.0-7.1 [285 kB]
Get:43 http://172.17.0.1/private/ jessie-staging/main libpixman-1-0 armhf 0.26.0-4 [413 kB]
Get:44 http://172.17.0.1/private/ jessie-staging/main libpng12-0 armhf 1.2.49-4 [179 kB]
Get:45 http://172.17.0.1/private/ jessie-staging/main libxau6 armhf 1:1.0.7-1 [17.6 kB]
Get:46 http://172.17.0.1/private/ jessie-staging/main libxdmcp6 armhf 1:1.1.1-1 [24.6 kB]
Get:47 http://172.17.0.1/private/ jessie-staging/main libxcb1 armhf 1.8.1-2+deb7u1 [42.9 kB]
Get:48 http://172.17.0.1/private/ jessie-staging/main libx11-data all 2:1.5.0-1+deb7u1 [189 kB]
Get:49 http://172.17.0.1/private/ jessie-staging/main libx11-6 armhf 2:1.5.0-1+deb7u1 [837 kB]
Get:50 http://172.17.0.1/private/ jessie-staging/main libxcb-render0 armhf 1.8.1-2+deb7u1 [16.5 kB]
Get:51 http://172.17.0.1/private/ jessie-staging/main libxcb-shm0 armhf 1.8.1-2+deb7u1 [10.0 kB]
Get:52 http://172.17.0.1/private/ jessie-staging/main libxext6 armhf 2:1.3.1-2+deb7u1 [49.1 kB]
Get:53 http://172.17.0.1/private/ jessie-staging/main libxrender1 armhf 1:0.9.7-1+deb7u1 [29.6 kB]
Get:54 http://172.17.0.1/private/ jessie-staging/main libcairo2 armhf 1.12.14-4 [936 kB]
Get:55 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.0.13-4 [19.8 kB]
Get:56 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.36.1-2build1 [1895 kB]
Get:57 http://172.17.0.1/private/ jessie-staging/main libcairo-gobject2 armhf 1.12.14-4 [506 kB]
Get:58 http://172.17.0.1/private/ jessie-staging/main liblzo2-2 armhf 2.06-1 [56.0 kB]
Get:59 http://172.17.0.1/private/ jessie-staging/main libcairo-script-interpreter2 armhf 1.12.14-4 [542 kB]
Get:60 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
Get:61 http://172.17.0.1/private/ jessie-staging/main libcups2 armhf 1.5.3-5 [237 kB]
Get:62 http://172.17.0.1/private/ jessie-staging/main libjpeg8 armhf 8d-1 [132 kB]
Get:63 http://172.17.0.1/private/ jessie-staging/main libjbig0 armhf 2.0-2 [31.5 kB]
Get:64 http://172.17.0.1/private/ jessie-staging/main libtiff4 armhf 3.9.6-11 [188 kB]
Get:65 http://172.17.0.1/private/ jessie-staging/main libcupsimage2 armhf 1.5.3-5 [131 kB]
Get:66 http://172.17.0.1/private/ jessie-staging/main libdatrie1 armhf 0.2.6-2 [27.0 kB]
Get:67 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:68 http://172.17.0.1/private/ jessie-staging/main libgettextpo0 armhf 0.18.1.1-10 [131 kB]
Get:69 http://172.17.0.1/private/ jessie-staging/main libelfg0 armhf 0.8.13-3 [56.5 kB]
Get:70 http://172.17.0.1/private/ jessie-staging/main libglib2.0-data all 2.36.1-2build1 [1835 kB]
Get:71 http://172.17.0.1/private/ jessie-staging/main libglib2.0-bin armhf 2.36.1-2build1 [1050 kB]
Get:72 http://172.17.0.1/private/ jessie-staging/main libgraphite2-3 armhf 1.2.2-2 [54.8 kB]
Get:73 http://172.17.0.1/private/ jessie-staging/main libharfbuzz0a armhf 0.9.18-3 [394 kB]
Get:74 http://172.17.0.1/private/ jessie-staging/main libicu48 armhf 4.8.1.1-12 [4494 kB]
Get:75 http://172.17.0.1/private/ jessie-staging/main libharfbuzz-icu0 armhf 0.9.18-3 [261 kB]
Get:76 http://172.17.0.1/private/ jessie-staging/main x11-common all 1:7.7+3 [284 kB]
Get:77 http://172.17.0.1/private/ jessie-staging/main libice6 armhf 2:1.0.8-2 [56.2 kB]
Get:78 http://172.17.0.1/private/ jessie-staging/main libjasper1 armhf 1.900.1-14 [141 kB]
Get:79 http://172.17.0.1/private/ jessie-staging/main liblcms1 armhf 1.19.dfsg-1.2 [98.5 kB]
Get:80 http://172.17.0.1/private/ jessie-staging/main liblcms2-2 armhf 2.2+git20110628-2.2 [120 kB]
Get:81 http://172.17.0.1/private/ jessie-staging/main liblua5.1-0 armhf 5.1.5-4 [145 kB]
Get:82 http://172.17.0.1/private/ jessie-staging/main libthai-data all 0.1.19-2 [156 kB]
Get:83 http://172.17.0.1/private/ jessie-staging/main libthai0 armhf 0.1.19-2 [40.5 kB]
Get:84 http://172.17.0.1/private/ jessie-staging/main fontconfig armhf 2.9.0-7.1 [348 kB]
Get:85 http://172.17.0.1/private/ jessie-staging/main libpango-1.0-0 armhf 1.32.5-5 [251 kB]
Get:86 http://172.17.0.1/private/ jessie-staging/main libpangoft2-1.0-0 armhf 1.32.5-5 [186 kB]
Get:87 http://172.17.0.1/private/ jessie-staging/main libpangocairo-1.0-0 armhf 1.32.5-5 [176 kB]
Get:88 http://172.17.0.1/private/ jessie-staging/main libxft2 armhf 2.3.1-1 [55.4 kB]
Get:89 http://172.17.0.1/private/ jessie-staging/main libpangoxft-1.0-0 armhf 1.32.5-5 [171 kB]
Get:90 http://172.17.0.1/private/ jessie-staging/main libpaper1 armhf 1.1.24+nmu2 [20.9 kB]
Get:91 http://172.17.0.1/private/ jessie-staging/main libpcrecpp0 armhf 1:8.31-2 [125 kB]
Get:92 http://172.17.0.1/private/ jessie-staging/main libopenjpeg2 armhf 1.3+dfsg-4.6 [75.9 kB]
Get:93 http://172.17.0.1/private/ jessie-staging/main libpoppler19 armhf 0.18.4-6 [996 kB]
Get:94 http://172.17.0.1/private/ jessie-staging/main libsm6 armhf 2:1.2.1-2 [32.5 kB]
Get:95 http://172.17.0.1/private/ jessie-staging/main libxt6 armhf 1:1.1.3-1+deb7u1 [181 kB]
Get:96 http://172.17.0.1/private/ jessie-staging/main libxmu6 armhf 2:1.1.1-1 [59.1 kB]
Get:97 http://172.17.0.1/private/ jessie-staging/main libxpm4 armhf 1:3.5.10-1 [44.9 kB]
Get:98 http://172.17.0.1/private/ jessie-staging/main libxaw7 armhf 2:1.0.10-2 [192 kB]
Get:99 http://172.17.0.1/private/ jessie-staging/main lua-filesystem armhf 1.5.0+16+g84f1af5-1 [11.0 kB]
Get:100 http://172.17.0.1/private/ jessie-staging/main lua-filesystem-dev armhf 1.5.0+16+g84f1af5-1 [25.8 kB]
Get:101 http://172.17.0.1/private/ jessie-staging/main lua-lpeg armhf 0.10.2-5 [42.0 kB]
Get:102 http://172.17.0.1/private/ jessie-staging/main lua-lpeg-dev armhf 0.10.2-5 [62.9 kB]
Get:103 http://172.17.0.1/private/ jessie-staging/main lua-md5 armhf 1.1.2-6 [11.9 kB]
Get:104 http://172.17.0.1/private/ jessie-staging/main lua-md5-dev armhf 1.1.2-6 [20.3 kB]
Get:105 http://172.17.0.1/private/ jessie-staging/main tex-common all 4.03 [639 kB]
Get:106 http://172.17.0.1/private/ jessie-staging/main libkpathsea6 armhf 2012.20120628-4 [158 kB]
Get:107 http://172.17.0.1/private/ jessie-staging/main luatex armhf 0.70.1.20120524-3 [2268 kB]
Get:108 http://172.17.0.1/private/ jessie-staging/main poppler-data all 0.4.6-3 [1478 kB]
Get:109 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.14-2 [53.8 kB]
Get:110 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.1.1-10 [130 kB]
Get:111 http://172.17.0.1/private/ jessie-staging/main mime-support all 3.54 [36.4 kB]
Get:112 http://172.17.0.1/private/ jessie-staging/main libpython2.7-stdlib armhf 2.7.5-4 [2411 kB]
Get:113 http://172.17.0.1/private/ jessie-staging/main python2.7 armhf 2.7.5-4 [228 kB]
Get:114 http://172.17.0.1/private/ jessie-staging/main python-minimal all 2.7.3-5 [41.8 kB]
Get:115 http://172.17.0.1/private/ jessie-staging/main python all 2.7.3-5 [184 kB]
Get:116 http://172.17.0.1/private/ jessie-staging/main html2text armhf 1.3.2a-16 [97.6 kB]
Get:117 http://172.17.0.1/private/ jessie-staging/main libasprintf-dev armhf 0.18.1.1-10 [26.7 kB]
Get:118 http://172.17.0.1/private/ jessie-staging/main libgettextpo-dev armhf 0.18.1.1-10 [160 kB]
Get:119 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.1.1-10 [1721 kB]
Get:120 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:121 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:122 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20120909 [705 kB]
Get:123 http://172.17.0.1/private/ jessie-staging/main ed armhf 1.6-2 [53.5 kB]
Get:124 http://172.17.0.1/private/ jessie-staging/main fonts-comfortaa all 2.003-1 [133 kB]
Get:125 http://172.17.0.1/private/ jessie-staging/main fonts-dejavu-extra all 2.33+svn2514-3 [1758 kB]
Get:126 http://172.17.0.1/private/ jessie-staging/main fonts-droid all 20111207+git-1 [4312 kB]
Get:127 http://172.17.0.1/private/ jessie-staging/main fonts-freefont-otf all 20120503-1 [4428 kB]
Get:128 http://172.17.0.1/private/ jessie-staging/main fonts-gfs-artemisia all 1.1-4 [339 kB]
Get:129 http://172.17.0.1/private/ jessie-staging/main fonts-gfs-complutum all 1.1-5 [47.9 kB]
Get:130 http://172.17.0.1/private/ jessie-staging/main fonts-gfs-didot all 1.1-5 [371 kB]
Get:131 http://172.17.0.1/private/ jessie-staging/main fonts-gfs-neohellenic all 1.1-4 [282 kB]
Get:132 http://172.17.0.1/private/ jessie-staging/main fonts-gfs-olga all 1.1-3 [36.0 kB]
Get:133 http://172.17.0.1/private/ jessie-staging/main fonts-gfs-solomos all 1.1-5 [40.6 kB]
Get:134 http://172.17.0.1/private/ jessie-staging/main fonts-inconsolata all 001.010-4 [65.6 kB]
Get:135 http://172.17.0.1/private/ jessie-staging/main fonts-linuxlibertine all 5.1.3-1 [12.8 MB]
Get:136 http://172.17.0.1/private/ jessie-staging/main fonts-oflb-asana-math all 000.907-4 [297 kB]
Get:137 http://172.17.0.1/private/ jessie-staging/main fonts-sil-gentium all 20081126:1.02-12 [685 kB]
Get:138 http://172.17.0.1/private/ jessie-staging/main fonts-sil-gentium-basic all 1.1-5 [871 kB]
Get:139 http://172.17.0.1/private/ jessie-staging/main libgirepository-1.0-1 armhf 1.36.0-2 [97.0 kB]
Get:140 http://172.17.0.1/private/ jessie-staging/main gir1.2-glib-2.0 armhf 1.36.0-2 [177 kB]
Get:141 http://172.17.0.1/private/ jessie-staging/main gir1.2-freedesktop armhf 1.36.0-2 [20.7 kB]
Get:142 http://172.17.0.1/private/ jessie-staging/main gir1.2-pango-1.0 armhf 1.32.5-5 [178 kB]
Get:143 http://172.17.0.1/private/ jessie-staging/main libgraphite3 armhf 1:2.3.1-0.2 [166 kB]
Get:144 http://172.17.0.1/private/ jessie-staging/main libijs-0.35 armhf 0.35-8 [19.0 kB]
Get:145 http://172.17.0.1/private/ jessie-staging/main libjbig2dec0 armhf 0.11+20120125-1 [46.4 kB]
Get:146 http://172.17.0.1/private/ jessie-staging/main libgs9-common all 9.05~dfsg-6.3 [1977 kB]
Get:147 http://172.17.0.1/private/ jessie-staging/main libgs9 armhf 9.05~dfsg-6.3 [1541 kB]
Get:148 http://172.17.0.1/private/ jessie-staging/main libptexenc1 armhf 2012.20120628-4 [53.0 kB]
Get:149 http://172.17.0.1/private/ jessie-staging/main texlive-common all 2012.20120611-5 [200 kB]
Get:150 http://172.17.0.1/private/ jessie-staging/main texlive-binaries armhf 2012.20120628-4 [16.8 MB]
Get:151 http://172.17.0.1/private/ jessie-staging/main texlive-doc-base all 2012.20120611-1 [1651 kB]
Get:152 http://172.17.0.1/private/ jessie-staging/main xdg-utils all 1.1.0~rc1+git20111210-7 [83.7 kB]
Get:153 http://172.17.0.1/private/ jessie-staging/main libpaper-utils armhf 1.1.24+nmu2 [17.9 kB]
Get:154 http://172.17.0.1/private/ jessie-staging/main texlive-base all 2012.20120611-5 [14.2 MB]
Get:155 http://172.17.0.1/private/ jessie-staging/main texlive-latex-base all 2012.20120611-5 [894 kB]
Get:156 http://172.17.0.1/private/ jessie-staging/main texlive-latex-recommended all 2012.20120611-5 [6779 kB]
Get:157 http://172.17.0.1/private/ jessie-staging/main latex-xcolor all 2.11-1.1 [610 kB]
Get:158 http://172.17.0.1/private/ jessie-staging/main libbam-dev armhf 0.1.19-1 [110 kB]
Get:159 http://172.17.0.1/private/ jessie-staging/main libbz2-dev armhf 1.0.6-4 [33.9 kB]
Get:160 http://172.17.0.1/private/ jessie-staging/main libexpat1-dev armhf 2.1.0-3 [210 kB]
Get:161 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-1 [212 kB]
Get:162 http://172.17.0.1/private/ jessie-staging/main libfreetype6-dev armhf 2.4.9-1.1 [748 kB]
Get:163 http://172.17.0.1/private/ jessie-staging/main pkg-config armhf 0.26-1 [56.9 kB]
Get:164 http://172.17.0.1/private/ jessie-staging/main libfontconfig1-dev armhf 2.9.0-7.1 [840 kB]
Get:165 http://172.17.0.1/private/ jessie-staging/main xorg-sgml-doctools all 1:1.10-1 [24.1 kB]
Get:166 http://172.17.0.1/private/ jessie-staging/main x11proto-core-dev all 7.0.23-1 [774 kB]
Get:167 http://172.17.0.1/private/ jessie-staging/main libxau-dev armhf 1:1.0.7-1 [21.0 kB]
Get:168 http://172.17.0.1/private/ jessie-staging/main libxdmcp-dev armhf 1:1.1.1-1 [40.8 kB]
Get:169 http://172.17.0.1/private/ jessie-staging/main x11proto-input-dev all 2.2-1 [172 kB]
Get:170 http://172.17.0.1/private/ jessie-staging/main x11proto-kb-dev all 1.0.6-2 [269 kB]
Get:171 http://172.17.0.1/private/ jessie-staging/main xtrans-dev all 1.2.7-1 [112 kB]
Get:172 http://172.17.0.1/private/ jessie-staging/main libpthread-stubs0 armhf 0.3-3 [3230 B]
Get:173 http://172.17.0.1/private/ jessie-staging/main libpthread-stubs0-dev armhf 0.3-3 [3996 B]
Get:174 http://172.17.0.1/private/ jessie-staging/main libxcb1-dev armhf 1.8.1-2+deb7u1 [82.1 kB]
Get:175 http://172.17.0.1/private/ jessie-staging/main libx11-dev armhf 2:1.5.0-1+deb7u1 [957 kB]
Get:176 http://172.17.0.1/private/ jessie-staging/main x11proto-render-dev all 2:0.11.1-2 [20.8 kB]
Get:177 http://172.17.0.1/private/ jessie-staging/main libxrender-dev armhf 1:0.9.7-1+deb7u1 [37.8 kB]
Get:178 http://172.17.0.1/private/ jessie-staging/main x11proto-xext-dev all 7.2.1-1 [273 kB]
Get:179 http://172.17.0.1/private/ jessie-staging/main libxext-dev armhf 2:1.3.1-2+deb7u1 [108 kB]
Get:180 http://172.17.0.1/private/ jessie-staging/main libpng12-dev armhf 1.2.49-4 [260 kB]
Get:181 http://172.17.0.1/private/ jessie-staging/main libice-dev armhf 2:1.0.8-2 [65.9 kB]
Get:182 http://172.17.0.1/private/ jessie-staging/main libsm-dev armhf 2:1.2.1-2 [35.6 kB]
Get:183 http://172.17.0.1/private/ jessie-staging/main libpixman-1-dev armhf 0.26.0-4 [439 kB]
Get:184 http://172.17.0.1/private/ jessie-staging/main libxcb-render0-dev armhf 1.8.1-2+deb7u1 [24.8 kB]
Get:185 http://172.17.0.1/private/ jessie-staging/main libxcb-shm0-dev armhf 1.8.1-2+deb7u1 [11.6 kB]
Get:186 http://172.17.0.1/private/ jessie-staging/main libpcre3-dev armhf 1:8.31-2 [350 kB]
Get:187 http://172.17.0.1/private/ jessie-staging/main libglib2.0-dev armhf 2.36.1-2build1 [2104 kB]
Get:188 http://172.17.0.1/private/ jessie-staging/main libcairo2-dev armhf 1.12.14-4 [1149 kB]
Get:189 http://172.17.0.1/private/ jessie-staging/main libharfbuzz-dev armhf 0.9.18-3 [273 kB]
Get:190 http://172.17.0.1/private/ jessie-staging/main libtinfo-dev armhf 5.9+20130504-1 [92.5 kB]
Get:191 http://172.17.0.1/private/ jessie-staging/main libreadline6-dev armhf 6.2+dfsg-0.1 [164 kB]
Get:192 http://172.17.0.1/private/ jessie-staging/main libreadline-dev armhf 6.2+dfsg-0.1 [898 B]
Get:193 http://172.17.0.1/private/ jessie-staging/main liblua5.1-0-dev armhf 5.1.5-4 [202 kB]
Get:194 http://172.17.0.1/private/ jessie-staging/main liblua5.1-filesystem-dev all 1.5.0+16+g84f1af5-1 [3208 B]
Get:195 http://172.17.0.1/private/ jessie-staging/main liblua5.1-lpeg-dev all 0.10.2-5 [4000 B]
Get:196 http://172.17.0.1/private/ jessie-staging/main liblua5.1-md5-dev all 1.1.2-6 [2460 B]
Get:197 http://172.17.0.1/private/ jessie-staging/main libncurses5-dev armhf 5.9+20130504-1 [201 kB]
Get:198 http://172.17.0.1/private/ jessie-staging/main libxft-dev armhf 2.3.1-1 [68.1 kB]
Get:199 http://172.17.0.1/private/ jessie-staging/main libpango1.0-dev armhf 1.32.5-5 [397 kB]
Get:200 http://172.17.0.1/private/ jessie-staging/main libsqlite3-dev armhf 3.7.17-1 [564 kB]
Get:201 http://172.17.0.1/private/ jessie-staging/main preview-latex-style all 11.87-1 [317 kB]
Get:202 http://172.17.0.1/private/ jessie-staging/main otf-freefont all 20120503-1 [118 kB]
Get:203 http://172.17.0.1/private/ jessie-staging/main ttf-dejavu-extra all 2.33+svn2514-3 [30.0 kB]
Get:204 http://172.17.0.1/private/ jessie-staging/main fonts-stix all 1.1.0-1 [763 kB]
Get:205 http://172.17.0.1/private/ jessie-staging/main texlive-fonts-extra all 2012.20120611-2 [130 MB]
Get:206 http://172.17.0.1/private/ jessie-staging/main ttf-marvosym all 0.1+dfsg-2 [46.8 kB]
Get:207 http://172.17.0.1/private/ jessie-staging/main texlive-fonts-recommended all 2012.20120611-5 [5486 kB]
Get:208 http://172.17.0.1/private/ jessie-staging/main texlive-pictures all 2012.20120611-5 [2276 kB]
Get:209 http://172.17.0.1/private/ jessie-staging/main texlive-latex-extra all 2012.20120611-2 [6397 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 278 MB in 4min 25s (1047 kB/s)
(Reading database ... 11288 files and directories currently installed.)
Preparing to replace libncursesw5:armhf 5.9-10 (using .../libncursesw5_5.9+20130504-1_armhf.deb) ...
Unpacking replacement libncursesw5:armhf ...
Preparing to replace libtinfo5:armhf 5.9-10 (using .../libtinfo5_5.9+20130504-1_armhf.deb) ...
Unpacking replacement libtinfo5:armhf ...
Setting up libtinfo5:armhf (5.9+20130504-1) ...
(Reading database ... 11288 files and directories currently installed.)
Preparing to replace libncurses5:armhf 5.9-10 (using .../libncurses5_5.9+20130504-1_armhf.deb) ...
Unpacking replacement libncurses5:armhf ...
Setting up libncurses5:armhf (5.9+20130504-1) ...
(Reading database ... 11288 files and directories currently installed.)
Preparing to replace ncurses-bin 5.9-10 (using .../ncurses-bin_5.9+20130504-1_armhf.deb) ...
Unpacking replacement ncurses-bin ...
Setting up ncurses-bin (5.9+20130504-1) ...
(Reading database ... 11286 files and directories currently installed.)
Preparing to replace zlib1g:armhf 1:1.2.7.dfsg-13 (using .../zlib1g_1%3a1.2.8.dfsg-1_armhf.deb) ...
Unpacking replacement zlib1g:armhf ...
Setting up zlib1g:armhf (1:1.2.8.dfsg-1) ...
Selecting previously unselected package libpcre3:armhf.
(Reading database ... 11286 files and directories currently installed.)
Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.31-2_armhf.deb) ...
Selecting previously unselected package libpipeline1:armhf.
Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.3-1_armhf.deb) ...
Selecting previously unselected package libpopt0:armhf.
Unpacking libpopt0:armhf (from .../libpopt0_1.16-7_armhf.deb) ...
Selecting previously unselected package libssl1.0.0:armhf.
Unpacking libssl1.0.0:armhf (from .../libssl1.0.0_1.0.1e-2+rpi1_armhf.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.22.2-3_armhf.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_9.0.5_armhf.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.3-6_armhf.deb) ...
Selecting previously unselected package libasprintf0c2:armhf.
Unpacking libasprintf0c2:armhf (from .../libasprintf0c2_0.18.1.1-10_armhf.deb) ...
Selecting previously unselected package libgpg-error0:armhf.
Unpacking libgpg-error0:armhf (from .../libgpg-error0_1.10-3.1_armhf.deb) ...
Selecting previously unselected package libgcrypt11:armhf.
Unpacking libgcrypt11:armhf (from .../libgcrypt11_1.5.0-5_armhf.deb) ...
Selecting previously unselected package libp11-kit0:armhf.
Unpacking libp11-kit0:armhf (from .../libp11-kit0_0.12-3_armhf.deb) ...
Selecting previously unselected package libtasn1-3:armhf.
Unpacking libtasn1-3:armhf (from .../libtasn1-3_2.14-3_armhf.deb) ...
Selecting previously unselected package libgnutls26:armhf.
Unpacking libgnutls26:armhf (from .../libgnutls26_2.12.23-5_armhf.deb) ...
Selecting previously unselected package libkeyutils1:armhf.
Unpacking libkeyutils1:armhf (from .../libkeyutils1_1.5.5-7_armhf.deb) ...
Selecting previously unselected package libkrb5support0:armhf.
Unpacking libkrb5support0:armhf (from .../libkrb5support0_1.10.1+dfsg-5_armhf.deb) ...
Selecting previously unselected package libk5crypto3:armhf.
Unpacking libk5crypto3:armhf (from .../libk5crypto3_1.10.1+dfsg-5_armhf.deb) ...
Selecting previously unselected package libkrb5-3:armhf.
Unpacking libkrb5-3:armhf (from .../libkrb5-3_1.10.1+dfsg-5_armhf.deb) ...
Selecting previously unselected package libgssapi-krb5-2:armhf.
Unpacking libgssapi-krb5-2:armhf (from .../libgssapi-krb5-2_1.10.1+dfsg-5_armhf.deb) ...
Selecting previously unselected package libidn11:armhf.
Unpacking libidn11:armhf (from .../libidn11_1.25-2_armhf.deb) ...
Selecting previously unselected package libmagic1:armhf.
Unpacking libmagic1:armhf (from .../libmagic1_1%3a5.14-2_armhf.deb) ...
Selecting previously unselected package libsqlite3-0:armhf.
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Setting up libncursesw5:armhf (5.9+20130504-1) ...
Setting up libpcre3:armhf (1:8.31-2) ...
Setting up libpipeline1:armhf (1.2.3-1) ...
Setting up libpopt0:armhf (1.16-7) ...
Setting up libssl1.0.0:armhf (1.0.1e-2+rpi1) ...
Setting up groff-base (1.22.2-3) ...
Setting up bsdmainutils (9.0.5) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.6.3-6) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.18.1.1-10) ...
Setting up libgpg-error0:armhf (1.10-3.1) ...
Setting up libgcrypt11:armhf (1.5.0-5) ...
Setting up libp11-kit0:armhf (0.12-3) ...
Setting up libtasn1-3:armhf (2.14-3) ...
Setting up libgnutls26:armhf (2.12.23-5) ...
Setting up libkeyutils1:armhf (1.5.5-7) ...
Setting up libkrb5support0:armhf (1.10.1+dfsg-5) ...
Setting up libk5crypto3:armhf (1.10.1+dfsg-5) ...
Setting up libkrb5-3:armhf (1.10.1+dfsg-5) ...
Setting up libgssapi-krb5-2:armhf (1.10.1+dfsg-5) ...
Setting up libidn11:armhf (1.25-2) ...
Setting up libmagic1:armhf (1:5.14-2) ...
Setting up libsqlite3-0:armhf (3.7.17-1) ...
Setting up libxml2:armhf (2.8.0+dfsg1-7+nmu1) ...
Setting up libpython2.7-minimal (2.7.5-4) ...
Setting up python2.7-minimal (2.7.5-4) ...
Setting up fonts-junicode (0.7.8-1) ...
Setting up libavahi-common-data:armhf (0.6.31-2) ...
Setting up libavahi-common3:armhf (0.6.31-2) ...
Setting up libavahi-client3:armhf (0.6.31-2) ...
Setting up libexpat1:armhf (2.1.0-3) ...
Setting up libfreetype6:armhf (2.4.9-1.1) ...
Setting up ucf (3.0027) ...
Setting up fonts-dejavu-core (2.33+svn2514-3) ...
Setting up ttf-dejavu-core (2.33+svn2514-3) ...
Setting up fonts-freefont-ttf (20120503-1) ...
Setting up ttf-freefont (20120503-1) ...
Setting up fontconfig-config (2.9.0-7.1) ...
Setting up libfontconfig1:armhf (2.9.0-7.1) ...
Setting up libpixman-1-0:armhf (0.26.0-4) ...
Setting up libpng12-0:armhf (1.2.49-4) ...
Setting up libxau6:armhf (1:1.0.7-1) ...
Setting up libxdmcp6:armhf (1:1.1.1-1) ...
Setting up libxcb1:armhf (1.8.1-2+deb7u1) ...
Setting up libx11-data (2:1.5.0-1+deb7u1) ...
Setting up libx11-6:armhf (2:1.5.0-1+deb7u1) ...
Setting up libxcb-render0:armhf (1.8.1-2+deb7u1) ...
Setting up libxcb-shm0:armhf (1.8.1-2+deb7u1) ...
Setting up libxext6:armhf (2:1.3.1-2+deb7u1) ...
Setting up libxrender1:armhf (1:0.9.7-1+deb7u1) ...
Setting up libcairo2:armhf (1.12.14-4) ...
Setting up libffi6:armhf (3.0.13-4) ...
Setting up libglib2.0-0:armhf (2.36.1-2build1) ...
No schema files found: doing nothing.
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Setting up liblzo2-2:armhf (2.06-1) ...
Setting up libcairo-script-interpreter2:armhf (1.12.14-4) ...
Setting up libcroco3:armhf (0.6.8-2) ...
Setting up libcups2:armhf (1.5.3-5) ...
Setting up libjpeg8:armhf (8d-1) ...
Setting up libjbig0:armhf (2.0-2) ...
Setting up libtiff4:armhf (3.9.6-11) ...
Setting up libcupsimage2:armhf (1.5.3-5) ...
Setting up libdatrie1:armhf (0.2.6-2) ...
Setting up libunistring0:armhf (0.9.3-5) ...
Setting up libgettextpo0:armhf (0.18.1.1-10) ...
Setting up libelfg0 (0.8.13-3) ...
Setting up libglib2.0-data (2.36.1-2build1) ...
Setting up libglib2.0-bin (2.36.1-2build1) ...
Setting up libgraphite2-3:armhf (1.2.2-2) ...
Setting up libharfbuzz0a:armhf (0.9.18-3) ...
Setting up libicu48:armhf (4.8.1.1-12) ...
Setting up libharfbuzz-icu0:armhf (0.9.18-3) ...
Setting up x11-common (1:7.7+3) ...
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libice6:armhf (2:1.0.8-2) ...
Setting up libjasper1:armhf (1.900.1-14) ...
Setting up liblcms1:armhf (1.19.dfsg-1.2) ...
Setting up liblcms2-2:armhf (2.2+git20110628-2.2) ...
Setting up liblua5.1-0:armhf (5.1.5-4) ...
Setting up libthai-data (0.1.19-2) ...
Setting up libthai0:armhf (0.1.19-2) ...
Setting up fontconfig (2.9.0-7.1) ...
Regenerating fonts cache... done.
Setting up libpango-1.0-0:armhf (1.32.5-5) ...
Setting up libpangoft2-1.0-0:armhf (1.32.5-5) ...
Setting up libpangocairo-1.0-0:armhf (1.32.5-5) ...
Setting up libxft2:armhf (2.3.1-1) ...
Setting up libpangoxft-1.0-0:armhf (1.32.5-5) ...
Setting up libpaper1:armhf (1.1.24+nmu2) ...

Creating config file /etc/papersize with new version
Setting up libpcrecpp0:armhf (1:8.31-2) ...
Setting up libopenjpeg2:armhf (1.3+dfsg-4.6) ...
Setting up libpoppler19:armhf (0.18.4-6) ...
Setting up libsm6:armhf (2:1.2.1-2) ...
Setting up libxt6:armhf (1:1.1.3-1+deb7u1) ...
Setting up libxmu6:armhf (2:1.1.1-1) ...
Setting up libxpm4:armhf (1:3.5.10-1) ...
Setting up libxaw7:armhf (2:1.0.10-2) ...
Setting up lua-filesystem:armhf (1.5.0+16+g84f1af5-1) ...
Setting up lua-filesystem-dev:armhf (1.5.0+16+g84f1af5-1) ...
Setting up lua-lpeg:armhf (0.10.2-5) ...
Setting up lua-lpeg-dev:armhf (0.10.2-5) ...
Setting up lua-md5:armhf (1.1.2-6) ...
Setting up lua-md5-dev:armhf (1.1.2-6) ...
Setting up tex-common (4.03) ...
Running mktexlsr. This may take some time... done.
texlive-base is not ready, delaying updmap-sys call
texlive-base is not ready, skipping fmtutil-sys --all call
Setting up libkpathsea6 (2012.20120628-4) ...
Setting up luatex (0.70.1.20120524-3) ...
texlive-base is not ready, cannot create formats
Setting up poppler-data (0.4.6-3) ...
Setting up file (1:5.14-2) ...
Setting up gettext-base (0.18.1.1-10) ...
Setting up mime-support (3.54) ...
update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode
Setting up libpython2.7-stdlib (2.7.5-4) ...
Setting up python2.7 (2.7.5-4) ...
Setting up python-minimal (2.7.3-5) ...
Setting up python (2.7.3-5) ...
Setting up html2text (1.3.2a-16) ...
Setting up libasprintf-dev:armhf (0.18.1.1-10) ...
Setting up libgettextpo-dev:armhf (0.18.1.1-10) ...
Setting up gettext (0.18.1.1-10) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20120909) ...
Setting up ed (1.6-2) ...
Setting up fonts-comfortaa (2.003-1) ...
Setting up fonts-dejavu-extra (2.33+svn2514-3) ...
Setting up fonts-droid (20111207+git-1) ...
Setting up fonts-freefont-otf (20120503-1) ...
Setting up fonts-gfs-artemisia (1.1-4) ...
Setting up fonts-gfs-complutum (1.1-5) ...
Setting up fonts-gfs-didot (1.1-5) ...
Setting up fonts-gfs-neohellenic (1.1-4) ...
Setting up fonts-gfs-olga (1.1-3) ...
Setting up fonts-gfs-solomos (1.1-5) ...
Setting up fonts-inconsolata (001.010-4) ...
Setting up fonts-linuxlibertine (5.1.3-1) ...
Setting up fonts-oflb-asana-math (000.907-4) ...
Setting up fonts-sil-gentium (20081126:1.02-12) ...
Setting up fonts-sil-gentium-basic (1.1-5) ...
Setting up libgirepository-1.0-1 (1.36.0-2) ...
Setting up gir1.2-glib-2.0 (1.36.0-2) ...
Setting up gir1.2-freedesktop (1.36.0-2) ...
Setting up gir1.2-pango-1.0 (1.32.5-5) ...
Setting up libgraphite3 (1:2.3.1-0.2) ...
Setting up libijs-0.35 (0.35-8) ...
Setting up libjbig2dec0 (0.11+20120125-1) ...
Setting up libgs9-common (9.05~dfsg-6.3) ...
Setting up libgs9 (9.05~dfsg-6.3) ...
Setting up libptexenc1 (2012.20120628-4) ...
Setting up texlive-common (2012.20120611-5) ...
Setting up texlive-binaries (2012.20120628-4) ...
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-doc-base (2012.20120611-1) ...
Setting up xdg-utils (1.1.0~rc1+git20111210-7) ...
Setting up libpaper-utils (1.1.24+nmu2) ...
Setting up libbam-dev (0.1.19-1) ...
Setting up libbz2-dev:armhf (1.0.6-4) ...
Setting up libexpat1-dev:armhf (2.1.0-3) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-1) ...
Setting up libfreetype6-dev (2.4.9-1.1) ...
Setting up pkg-config (0.26-1) ...
Setting up libfontconfig1-dev (2.9.0-7.1) ...
Setting up xorg-sgml-doctools (1:1.10-1) ...
Setting up x11proto-core-dev (7.0.23-1) ...
Setting up libxau-dev:armhf (1:1.0.7-1) ...
Setting up libxdmcp-dev:armhf (1:1.1.1-1) ...
Setting up x11proto-input-dev (2.2-1) ...
Setting up x11proto-kb-dev (1.0.6-2) ...
Setting up xtrans-dev (1.2.7-1) ...
Setting up libpthread-stubs0:armhf (0.3-3) ...
Setting up libpthread-stubs0-dev:armhf (0.3-3) ...
Setting up libxcb1-dev:armhf (1.8.1-2+deb7u1) ...
Setting up libx11-dev:armhf (2:1.5.0-1+deb7u1) ...
Setting up x11proto-render-dev (2:0.11.1-2) ...
Setting up libxrender-dev:armhf (1:0.9.7-1+deb7u1) ...
Setting up x11proto-xext-dev (7.2.1-1) ...
Setting up libxext-dev:armhf (2:1.3.1-2+deb7u1) ...
Setting up libpng12-dev (1.2.49-4) ...
Setting up libice-dev:armhf (2:1.0.8-2) ...
Setting up libsm-dev:armhf (2:1.2.1-2) ...
Setting up libpixman-1-dev (0.26.0-4) ...
Setting up libxcb-render0-dev:armhf (1.8.1-2+deb7u1) ...
Setting up libxcb-shm0-dev:armhf (1.8.1-2+deb7u1) ...
Setting up libpcre3-dev:armhf (1:8.31-2) ...
Setting up libglib2.0-dev (2.36.1-2build1) ...
Setting up libcairo2-dev (1.12.14-4) ...
Setting up libharfbuzz-dev (0.9.18-3) ...
Setting up libtinfo-dev:armhf (5.9+20130504-1) ...
Setting up libreadline6-dev:armhf (6.2+dfsg-0.1) ...
Setting up libreadline-dev:armhf (6.2+dfsg-0.1) ...
Setting up liblua5.1-0-dev:armhf (5.1.5-4) ...
Setting up liblua5.1-filesystem-dev (1.5.0+16+g84f1af5-1) ...
Setting up liblua5.1-lpeg-dev (0.10.2-5) ...
Setting up liblua5.1-md5-dev (1.1.2-6) ...
Setting up libncurses5-dev:armhf (5.9+20130504-1) ...
Setting up libxft-dev (2.3.1-1) ...
Setting up libpango1.0-dev (1.32.5-5) ...
Setting up libsqlite3-dev:armhf (3.7.17-1) ...
Setting up preview-latex-style (11.87-1) ...
Setting up otf-freefont (20120503-1) ...
Setting up ttf-dejavu-extra (2.33+svn2514-3) ...
Setting up fonts-stix (1.1.0-1) ...
Setting up ttf-marvosym (0.1+dfsg-2) ...
Processing triggers for tex-common ...
Running mktexlsr. This may take some time... done.
Setting up texlive-base (2012.20120611-5) ...
/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.
Processing triggers for tex-common ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Setting up texlive-fonts-extra (2012.20120611-2) ...
Setting up texlive-fonts-recommended (2012.20120611-5) ...
Setting up texlive-pictures (2012.20120611-5) ...
Setting up texlive-latex-base (2012.20120611-5) ...
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.
Processing triggers for tex-common ...
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 (2012.20120611-5) ...
Processing triggers for tex-common ...
Running mktexlsr. This may take some time... done.
Setting up latex-xcolor (2.11-1.1) ...
Setting up texlive-latex-extra (2012.20120611-2) ...
Processing triggers for tex-common ...
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) ...

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

Kernel: Linux 3.9.4-imx4 armhf (armv7l)
Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.6_4.6.3-14+rpi1 gcc-4.6_4.6.3-14+rpi1 libc6-dev_2.13-38+rpi2 libstdc++6_4.7.2-5+rpi1 libstdc++6-4.6-dev_4.6.3-14+rpi1 linux-libc-dev_3.2.41-2+rpi1
Package versions: apt_0.9.7.8+rpi1 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 binutils_2.22-8 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.3 build-essential_11.5+b1 bzip2_1.0.6-4 coreutils_8.13-3.5 cpio_2.11+dfsg-0.1 cpp_4:4.6.3-8 cpp-4.6_4.6.3-14+rpi1 dash_0.5.7-3 debconf_1.5.50 debconf-i18n_1.5.50 debfoster_2.7-1.2 debhelper_9.20120909 debianutils_4.3.2 diffutils_1:3.2-6 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.42.5-1.1 ed_1.6-2 fakeroot_1.18.4-2 file_1:5.14-2 findutils_4.4.2-4 fontconfig_2.9.0-7.1 fontconfig-config_2.9.0-7.1 fonts-comfortaa_2.003-1 fonts-dejavu-core_2.33+svn2514-3 fonts-dejavu-extra_2.33+svn2514-3 fonts-droid_20111207+git-1 fonts-freefont-otf_20120503-1 fonts-freefont-ttf_20120503-1 fonts-gfs-artemisia_1.1-4 fonts-gfs-complutum_1.1-5 fonts-gfs-didot_1.1-5 fonts-gfs-neohellenic_1.1-4 fonts-gfs-olga_1.1-3 fonts-gfs-solomos_1.1-5 fonts-inconsolata_001.010-4 fonts-junicode_0.7.8-1 fonts-linuxlibertine_5.1.3-1 fonts-oflb-asana-math_000.907-4 fonts-sil-gentium_20081126:1.02-12 fonts-sil-gentium-basic_1.1-5 fonts-stix_1.1.0-1 g++_4:4.6.3-8 g++-4.6_4.6.3-14+rpi1 gcc_4:4.6.3-8 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-14+rpi1 gcc-4.6-base_4.6.3-14+rpi1 gcc-4.7-base_4.7.2-5+rpi1 gettext_0.18.1.1-10 gettext-base_0.18.1.1-10 gir1.2-freedesktop_1.36.0-2 gir1.2-glib-2.0_1.36.0-2 gir1.2-pango-1.0_1.32.5-5 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.12-2 groff-base_1.22.2-3 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-16 initramfs-tools_0.112 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.1-3.1+rpi1 kmod_9-3 latex-xcolor_2.11-1.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.8+rpi1 libasprintf-dev_0.18.1.1-10 libasprintf0c2_0.18.1.1-10 libattr1_1:2.4.46-8 libavahi-client3_0.6.31-2 libavahi-common-data_0.6.31-2 libavahi-common3_0.6.31-2 libbam-dev_0.1.19-1 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libbz2-dev_1.0.6-4 libc-bin_2.13-38+rpi2 libc-dev-bin_2.13-38+rpi2 libc6_2.13-38+rpi2 libc6-dev_2.13-38+rpi2 libcairo-gobject2_1.12.14-4 libcairo-script-interpreter2_1.12.14-4 libcairo2_1.12.14-4 libcairo2-dev_1.12.14-4 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1.1 libcroco3_0.6.8-2 libcups2_1.5.3-5 libcupsimage2_1.5.3-5 libdatrie1_0.2.6-2 libdb5.1_5.1.29-5 libdbus-1-3_1.6.8-1 libdpkg-perl_1.16.10 libelfg0_0.8.13-3 libexpat1_2.1.0-3 libexpat1-dev_2.1.0-3 libffi6_3.0.13-4 libfontconfig1_2.9.0-7.1 libfontconfig1-dev_2.9.0-7.1 libfreetype6_2.4.9-1.1 libfreetype6-dev_2.4.9-1.1 libgc1c2_1:7.1-9.1 libgcc1_1:4.7.2-5+rpi1 libgcrypt11_1.5.0-5 libgdbm3_1.8.3-11 libgettextpo-dev_0.18.1.1-10 libgettextpo0_0.18.1.1-10 libgirepository-1.0-1_1.36.0-2 libglib2.0-0_2.36.1-2build1 libglib2.0-bin_2.36.1-2build1 libglib2.0-data_2.36.1-2build1 libglib2.0-dev_2.36.1-2build1 libgmp10_2:5.0.5+dfsg-2 libgnutls26_2.12.23-5 libgomp1_4.7.2-5+rpi1 libgpg-error0_1.10-3.1 libgraphite2-3_1.2.2-2 libgraphite3_1:2.3.1-0.2 libgs9_9.05~dfsg-6.3 libgs9-common_9.05~dfsg-6.3 libgssapi-krb5-2_1.10.1+dfsg-5 libharfbuzz-dev_0.9.18-3 libharfbuzz-icu0_0.9.18-3 libharfbuzz0a_0.9.18-3 libice-dev_2:1.0.8-2 libice6_2:1.0.8-2 libicu48_4.8.1.1-12 libidn11_1.25-2 libijs-0.35_0.35-8 libjasper1_1.900.1-14 libjbig0_2.0-2 libjbig2dec0_0.11+20120125-1 libjpeg8_8d-1 libk5crypto3_1.10.1+dfsg-5 libkeyutils1_1.5.5-7 libklibc_2.0.1-3.1+rpi1 libkmod2_9-3 libkpathsea6_2012.20120628-4 libkrb5-3_1.10.1+dfsg-5 libkrb5support0_1.10.1+dfsg-5 liblcms1_1.19.dfsg-1.2 liblcms2-2_2.2+git20110628-2.2 liblocale-gettext-perl_1.05-7 liblua5.1-0_5.1.5-4 liblua5.1-0-dev_5.1.5-4 liblua5.1-filesystem-dev_1.5.0+16+g84f1af5-1 liblua5.1-lpeg-dev_0.10.2-5 liblua5.1-md5-dev_1.1.2-6 liblzma5_5.1.1alpha+20120614-2 liblzo2-2_2.06-1 libmagic1_1:5.14-2 libmount1_2.20.1-5.3 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9+20130504-1 libncurses5-dev_5.9+20130504-1 libncursesw5_5.9+20130504-1 libnih-dbus1_1.0.3-4.1 libnih1_1.0.3-4.1 libopenjpeg2_1.3+dfsg-4.6 libp11-kit0_0.12-3 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-9 libpam0g_1.1.3-7.1 libpango-1.0-0_1.32.5-5 libpango1.0-dev_1.32.5-5 libpangocairo-1.0-0_1.32.5-5 libpangoft2-1.0-0_1.32.5-5 libpangoxft-1.0-0_1.32.5-5 libpaper-utils_1.1.24+nmu2 libpaper1_1.1.24+nmu2 libpcre3_1:8.31-2 libpcre3-dev_1:8.31-2 libpcrecpp0_1:8.31-2 libpipeline1_1.2.3-1 libpixman-1-0_0.26.0-4 libpixman-1-dev_0.26.0-4 libpng12-0_1.2.49-4 libpng12-dev_1.2.49-4 libpoppler19_0.18.4-6 libpopt0_1.16-7 libprocps0_1:3.3.3-3 libptexenc1_2012.20120628-4 libpthread-stubs0_0.3-3 libpthread-stubs0-dev_0.3-3 libpython2.7-minimal_2.7.5-4 libpython2.7-stdlib_2.7.5-4 libreadline-dev_6.2+dfsg-0.1 libreadline6_6.2+dfsg-0.1 libreadline6-dev_6.2+dfsg-0.1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libsm-dev_2:1.2.1-2 libsm6_2:1.2.1-2 libsqlite3-0_3.7.17-1 libsqlite3-dev_3.7.17-1 libss2_1.42.5-1.1 libssl1.0.0_1.0.1e-2+rpi1 libstdc++6_4.7.2-5+rpi1 libstdc++6-4.6-dev_4.6.3-14+rpi1 libswitch-perl_2.16-2 libtasn1-3_2.14-3 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libthai-data_0.1.19-2 libthai0_0.1.19-2 libtiff4_3.9.6-11 libtimedate-perl_1.2000-1 libtinfo-dev_5.9+20130504-1 libtinfo5_5.9+20130504-1 libudev0_175-7.2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libx11-6_2:1.5.0-1+deb7u1 libx11-data_2:1.5.0-1+deb7u1 libx11-dev_2:1.5.0-1+deb7u1 libxau-dev_1:1.0.7-1 libxau6_1:1.0.7-1 libxaw7_2:1.0.10-2 libxcb-render0_1.8.1-2+deb7u1 libxcb-render0-dev_1.8.1-2+deb7u1 libxcb-shm0_1.8.1-2+deb7u1 libxcb-shm0-dev_1.8.1-2+deb7u1 libxcb1_1.8.1-2+deb7u1 libxcb1-dev_1.8.1-2+deb7u1 libxdmcp-dev_1:1.1.1-1 libxdmcp6_1:1.1.1-1 libxext-dev_2:1.3.1-2+deb7u1 libxext6_2:1.3.1-2+deb7u1 libxft-dev_2.3.1-1 libxft2_2.3.1-1 libxml2_2.8.0+dfsg1-7+nmu1 libxmu6_2:1.1.1-1 libxpm4_1:3.5.10-1 libxrender-dev_1:0.9.7-1+deb7u1 libxrender1_1:0.9.7-1+deb7u1 libxt6_1:1.1.3-1+deb7u1 linux-libc-dev_3.2.41-2+rpi1 login_1:4.1.5.1-1 lsb-base_4.1+Debian8+rpi1 lua-filesystem_1.5.0+16+g84f1af5-1 lua-filesystem-dev_1.5.0+16+g84f1af5-1 lua-lpeg_0.10.2-5 lua-lpeg-dev_0.10.2-5 lua-md5_1.1.2-6 lua-md5-dev_1.1.2-6 luatex_0.70.1.20120524-3 make_3.81-8.2 makedev_2.3.1-92 man-db_2.6.3-6 mawk_1.3.3-17 mime-support_3.54 mount_2.20.1-5.3 mountall_2.46 multiarch-support_2.13-38+rpi2 ncurses-base_5.9-10 ncurses-bin_5.9+20130504-1 otf-freefont_20120503-1 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-21+rpi1 perl-base_5.14.2-21+rpi1 perl-modules_5.14.2-21+rpi1 pkg-config_0.26-1 plymouth_0.8.5.1-5 po-debconf_1.0.16+nmu2 poppler-data_0.4.6-3 preview-latex-style_11.87-1 procps_1:3.3.3-3 python_2.7.3-5 python-minimal_2.7.3-5 python2.7_2.7.5-4 python2.7-minimal_2.7.5-4 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-genometools-dummy_0.invalid.0 sed_4.2.1-10 sensible-utils_0.0.7 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-0.1 tex-common_4.03 texlive-base_2012.20120611-5 texlive-binaries_2012.20120628-4 texlive-common_2012.20120611-5 texlive-doc-base_2012.20120611-1 texlive-fonts-extra_2012.20120611-2 texlive-fonts-recommended_2012.20120611-5 texlive-latex-base_2012.20120611-5 texlive-latex-extra_2012.20120611-2 texlive-latex-recommended_2012.20120611-5 texlive-pictures_2012.20120611-5 ttf-dejavu-core_2.33+svn2514-3 ttf-dejavu-extra_2.33+svn2514-3 ttf-freefont_20120503-1 ttf-marvosym_0.1+dfsg-2 tzdata_2013b-2 ucf_3.0027 udev_175-7.2 util-linux_2.20.1-5.3 x11-common_1:7.7+3 x11proto-core-dev_7.0.23-1 x11proto-input-dev_2.2-1 x11proto-kb-dev_1.0.6-2 x11proto-render-dev_2:0.11.1-2 x11proto-xext-dev_7.2.1-1 xdg-utils_1.1.0~rc1+git20111210-7 xorg-sgml-doctools_1:1.10-1 xtrans-dev_1.2.7-1 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1 zlib1g-dev_1:1.2.8.dfsg-1

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


Unpack source
─────────────

gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Thu Mar  7 13:27:04 2013 UTC using RSA key ID 04A3610B
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./genometools_1.5.1-1.dsc
dpkg-source: info: extracting genometools in genometools-1.5.1
dpkg-source: info: unpacking genometools_1.5.1.orig.tar.gz
dpkg-source: info: unpacking genometools_1.5.1-1.debian.tar.gz
dpkg-source: info: applying split_manuals
dpkg-source: info: applying adding_soname
dpkg-source: info: applying libbam-fix
dpkg-source: info: applying remove-gitignores

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=111
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-a2dc3636-0591-4411-a95c-468f0c744ca5
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
previous=N
runlevel=2

dpkg-buildpackage
─────────────────

dpkg-buildpackage: source package genometools
dpkg-buildpackage: source version 1.5.1-1
dpkg-buildpackage: source changed by Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
 dpkg-source --before-build genometools-1.5.1
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
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 cleanup
make[3]: Entering directory `/«PKGBUILDDIR»/doc/manuals'
make[3]: Leaving directory `/«PKGBUILDDIR»/doc/manuals'
test -d "src/external/hmmer-3.0" && /usr/bin/make -s -C src/external/hmmer-3.0 clean || true
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/docs.html \
          www/genometools.org/htdocs/examples.html \
          www/genometools.org/htdocs/libgenometools.html
rm -rf lib bin
rm -rf gtpython/build
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
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
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 opt=no errorcheck=no docs manuals
make[2]: Entering directory `/«PKGBUILDDIR»'
[compile gt.o]
[compile gtr.o]
[compile gtt.o]
[compile interactive.o]
[compile gt_bed_to_gff3.o]
[compile gt_cds.o]
[compile gt_chain2dim.o]
[compile gt_chseqids.o]
[compile gt_clean.o]
[compile gt_compreads.o]
[compile gt_compreads_compress.o]
[compile gt_compreads_decompress.o]
[compile gt_compreads_refcompress.o]
[compile gt_compreads_refdecompress.o]
[compile gt_congruence.o]
[compile gt_consensus_sa.o]
[compile gt_convertseq.o]
[compile gt_csa.o]
[compile gt_dev.o]
[compile gt_dot.o]
[compile gt_dupfeat.o]
[compile gt_encseq.o]
[compile gt_encseq2spm.o]
[compile gt_encseq_bench.o]
[compile gt_encseq_bitextract.o]
[compile gt_encseq_check.o]
[compile gt_encseq_decode.o]
[compile gt_encseq_encode.o]
[compile gt_encseq_info.o]
[compile gt_encseq_md5.o]
[compile gt_eval.o]
[compile gt_extractfeat.o]
[compile gt_extractseq.o]
[compile gt_extracttarget.o]
[compile gt_featureindex.o]
[compile gt_fingerprint.o]
[compile gt_gdiffcalc.o]
[compile gt_genomediff.o]
[compile gt_gff3.o]
[compile gt_gff3_to_gtf.o]
[compile gt_gff3validator.o]
[compile gt_gtf_to_gff3.o]
[compile gt_guessprot.o]
[compile gt_hop.o]
[compile gt_id_to_md5.o]
[compile gt_idxlocali.o]
[compile gt_interfeat.o]
[compile gt_magicmatch.o]
[compile gt_matchtool.o]
[compile gt_matstat.o]
[compile gt_maxpairs.o]
[compile gt_md5_to_id.o]
[compile gt_merge.o]
[compile gt_mergeesa.o]
[compile gt_mergefeat.o]
[compile gt_mgth.o]
[compile gt_mkfeatureindex.o]
[compile gt_mkfmindex.o]
[compile gt_mmapandread.o]
[compile gt_orffinder.o]
[compile gt_packedindex.o]
[compile gt_packedindex_chk_integrity.o]
[compile gt_packedindex_chk_search.o]
[compile gt_packedindex_mkctxmap.o]
[compile gt_packedindex_trsuftab.o]
[compile gt_paircmp.o]
[compile gt_patternmatch.o]
[compile gt_prebwt.o]
[compile gt_readjoiner.o]
[compile gt_readjoiner_asqg.o]
[compile gt_readjoiner_assembly.o]
[compile gt_readjoiner_cnttest.o]
[compile gt_readjoiner_correct.o]
[compile gt_readjoiner_overlap.o]
[compile gt_readjoiner_prefilter.o]
[compile gt_readjoiner_spmtest.o]
[compile gt_readreads.o]
[compile gt_regioncov.o]
[compile gt_sain.o]
[compile gt_sam_interface.o]
[compile gt_script_filter.o]
[compile gt_select.o]
[compile gt_seq.o]
[compile gt_seqcorrect.o]
[compile gt_seqfilter.o]
[compile gt_seqids.o]
[compile gt_seqlensort.o]
[compile gt_seqmutate.o]
[compile gt_seqorder.o]
[compile gt_seqstat.o]
[compile gt_seqtransform.o]
[compile gt_seqtranslate.o]
[compile gt_sequniq.o]
[compile gt_sfxmap.o]
[compile gt_shredder.o]
[compile gt_shulen.o]
[compile gt_simreads.o]
[compile gt_skproto.o]
[compile gt_snpper.o]
[compile gt_sortbench.o]
[compile gt_splicesiteinfo.o]
[compile gt_splitfasta.o]
[compile gt_stat.o]
[compile gt_suffixerator.o]
[compile gt_tagerator.o]
[compile gt_tallymer.o]
[compile gt_template.o]
[compile gt_trieins.o]
[compile gt_uniq.o]
[create obj/gt_config.h]
[compile alphabet.o]
[compile array.o]
[compile array2dim.o]
[compile array2dim_sparse.o]
[compile array3dim.o]
[compile basename.o]
[compile bioseq.o]
[compile bioseq_col.o]
[compile bioseq_iterator.o]
[compile bitpackstringop.o]
[compile bitpackstringop16.o]
[compile bitpackstringop32.o]
[compile bitpackstringop64.o]
[compile bitpackstringop8.o]
[compile bittab.o]
[compile bool_matrix.o]
[compile bsearch.o]
[compile checkbitpackarray.o]
[compile checkbitpackstring-int.o]
[compile checkbitpackstring.o]
[compile checkbitpackstring16.o]
[compile checkbitpackstring32.o]
[compile checkbitpackstring64.o]
[compile checkbitpackstring8.o]
[compile class_alloc.o]
[compile class_alloc_lock.o]
[compile codon_iterator.o]
[compile codon_iterator_encseq.o]
[compile codon_iterator_simple.o]
[compile colorspace.o]
[compile combinatorics.o]
[compile compact_ulong_store.o]
[compile complement.o]
[compile countingsort.o]
[compile cstr.o]
[compile cstr_array.o]
[compile cstr_table.o]
[compile desc_buffer.o]
[compile disc_distri.o]
[compile dlist.o]
[compile dyn_bittab.o]
[compile dynalloc.o]
[compile eansi.o]
[compile ebzlib.o]
[compile encseq.o]
[compile encseq_access_type.o]
[compile encseq_col.o]
[compile encseq_metadata.o]
[compile encseq_options.o]
[compile encseq_ptr.o]
[compile endianess.o]
[compile error.o]
[compile example.o]
[compile example_a.o]
[compile example_b.o]
[compile ezlib.o]
[compile fa.o]
[compile fasta.o]
[compile fasta_reader.o]
[compile fasta_reader_fsm.o]
[compile fasta_reader_rec.o]
[compile fasta_reader_seqit.o]
[compile fastq.o]
[compile file.o]
[compile fileutils.o]
[compile gc_content.o]
[compile grep.o]
[compile gtdatapath.o]
[compile hashmap.o]
[compile hashtable.o]
[compile init.o]
[compile interval_tree.o]
[compile io.o]
[compile log.o]
[compile logger.o]
[compile ma.o]
[compile mapspec.o]
[compile mathsupport.o]
[compile md5_encoder.o]
[compile md5_fingerprint.o]
[compile md5_seqid.o]
[compile md5_tab.o]
[compile msort.o]
[compile option.o]
[compile orf.o]
[compile output_file.o]
[compile parseutils.o]
[compile password_entry.o]
[compile phase.o]
[compile process.o]
[compile progressbar.o]
[compile qsort-ulong.o]
[compile qsort_r.o]
[compile quality.o]
[compile queue.o]
[compile radix_sort.o]
[compile range.o]
[compile readmode.o]
[compile safearith.o]
[compile score_function.o]
[compile score_matrix.o]
[compile seq.o]
[compile seq_col.o]
[compile seq_info_cache.o]
[compile seq_iterator.o]
[compile seq_iterator_fastq.o]
[compile seq_iterator_sequence_buffer.o]
[compile sequence_buffer.o]
[compile sequence_buffer_embl.o]
[compile sequence_buffer_fasta.o]
[compile sequence_buffer_fastq.o]
[compile sequence_buffer_gb.o]
[compile sequence_buffer_plain.o]
[compile showtime.o]
[compile sig.o]
[compile spacepeak.o]
[compile splitter.o]
[compile str.o]
[compile str_array.o]
[compile str_cache.o]
[compile strand.o]
[compile strcmp.o]
[compile string_distri.o]
[compile symbol.o]
[compile thread.o]
[compile timer.o]
[compile tokenizer.o]
[compile tool.o]
[compile tooldriver.o]
[compile trans_table.o]
[compile translator.o]
[compile unit_testing.o]
[compile version.o]
[compile versionfunc.o]
[compile warning.o]
[compile xansi.o]
[compile xbsd.o]
[compile xbzlib.o]
[compile xposix.o]
[compile xzlib.o]
[compile yarandom.o]
[compile add_ids_stream.o]
[compile add_ids_visitor.o]
[compile add_introns_stream.o]
[compile affinealign.o]
[compile aligned_segment.o]
[compile aligned_segments_pile.o]
[compile alignment.o]
[compile anno_db_gfflike.o]
[compile anno_db_schema.o]
[compile array_in_stream.o]
[compile array_out_stream.o]
[compile assembly_stats_calculator.o]
[compile bed_in_stream.o]
[compile bed_parser.o]
[compile bitinstream.o]
src/extended/bed_parser.c: In function 'rest_line':
src/extended/bed_parser.c:116:7: warning: case label value is less than minimum value for type [enabled by default]
src/extended/bed_parser.c: In function 'word':
src/extended/bed_parser.c:144:7: warning: case label value is less than minimum value for type [enabled by default]
src/extended/bed_parser.c: In function 'quoted_word':
src/extended/bed_parser.c:164:7: warning: case label value is less than minimum value for type [enabled by default]
[compile bitoutstream.o]
[compile buffer_stream.o]
[compile cds_check_stream.o]
[compile cds_check_visitor.o]
[compile cds_stream.o]
[compile cds_visitor.o]
[compile chain.o]
[compile chseqids_stream.o]
[compile clustered_set.o]
[compile clustered_set_uf.o]
[compile coin_hmm.o]
[compile collect_ids_visitor.o]
[compile comment_node.o]
[compile consensus_sa.o]
[compile csa_gene.o]
[compile csa_splice_form.o]
[compile csa_stream.o]
[compile csa_variable_strands.o]
[compile csa_visitor.o]
[compile cstr_iterator.o]
[compile dice_hmm.o]
[compile dot_out_stream.o]
[compile dot_visitor.o]
[compile dup_feature_stream.o]
[compile dup_feature_visitor.o]
[compile elias_gamma.o]
[compile encdesc.o]
[compile encdesc_header_io.o]
[compile eof_node.o]
[compile evaluator.o]
[compile extract_feature_sequence.o]
[compile extract_feature_stream.o]
[compile extract_feature_visitor.o]
[compile fasta_header_iterator.o]
[compile feature_index.o]
[compile feature_index_memory.o]
[compile feature_info.o]
[compile feature_node.o]
[compile feature_node_iterator.o]
[compile feature_node_observer.o]
[compile feature_stream.o]
[compile feature_visitor.o]
[compile genome_node.o]
[compile gff3_escaping.o]
[compile gff3_in_stream.o]
[compile gff3_in_stream_plain.o]
[compile gff3_out_stream.o]
[compile gff3_output.o]
[compile gff3_parser.o]
[compile gff3_visitor.o]
[compile globalchaining.o]
[compile golomb.o]
[compile gtdatahelp.o]
[compile gtf_in_stream.o]
[compile gtf_out_stream.o]
[compile gtf_parser.o]
[compile gtf_visitor.o]
[compile hcr.o]
[compile hmm.o]
[compile hpol_processor.o]
[compile huffcode.o]
[compile id_to_md5_stream.o]
[compile id_to_md5_visitor.o]
[compile inter_feature_stream.o]
[compile inter_feature_visitor.o]
[compile linearedist.o]
[compile load_stream.o]
[compile luahelper.o]
[compile luaserialize.o]
[compile mapping.o]
[compile match.o]
[compile match_blast.o]
[compile match_iterator.o]
[compile match_iterator_blast.o]
[compile match_iterator_last.o]
[compile match_iterator_open.o]
[compile match_iterator_sw.o]
[compile match_last.o]
[compile match_open.o]
[compile match_sw.o]
[compile match_visitor.o]
[compile md5_to_id_stream.o]
[compile md5_to_id_visitor.o]
[compile md5set.o]
[compile merge_feature_stream.o]
[compile merge_feature_visitor.o]
[compile merge_stream.o]
[compile meta_node.o]
[compile multi_sanitizer_visitor.o]
[compile mutate.o]
[compile node_stream.o]
[compile node_visitor.o]
[compile obo_parse_tree.o]
src/extended/obo_parse_tree.c: In function 'any_char':
src/extended/obo_parse_tree.c:176:5: warning: case label value is less than minimum value for type [enabled by default]
src/extended/obo_parse_tree.c: In function 'comment_line':
src/extended/obo_parse_tree.c:206:7: warning: case label value is less than minimum value for type [enabled by default]
[compile obo_stanza.o]
[compile orf_finder_stream.o]
[compile orf_finder_visitor.o]
[compile orf_iterator.o]
[compile orphanage.o]
[compile permute_words.o]
[compile popcount_tab.o]
[compile priorityqueue.o]
[compile ranked_list.o]
[compile rbtree.o]
[compile rcr.o]
[compile rdb.o]
[compile rdb_sqlite.o]
[compile rdb_visitor.o]
[compile region_mapping.o]
[compile region_node.o]
[compile region_node_builder.o]
[compile regioncov_visitor.o]
[compile regular_seqid.o]
[compile reverse.o]
[compile rmq.o]
[compile sam_alignment.o]
[compile sam_query_name_iterator.o]
[compile samfile_encseq_mapping.o]
[compile samfile_iterator.o]
[compile sampling.o]
[compile script_filter.o]
[compile script_wrapper_stream.o]
[compile script_wrapper_visitor.o]
[compile select_stream.o]
[compile select_visitor.o]
[compile seqid2file.o]
[compile seqid2seqnum_mapping.o]
[compile seqpos_classifier.o]
[compile sequence_node.o]
[compile shredder.o]
[compile snp_annotator_stream.o]
[compile snp_annotator_visitor.o]
[compile sort_stream.o]
[compile splice_site_info_stream.o]
[compile splice_site_info_visitor.o]
[compile splicedseq.o]
[compile sspliced_alignment.o]
[compile sspliced_alignment_parsing.o]
[compile stat_stream.o]
[compile stat_visitor.o]
[compile stream_evaluator.o]
[compile string_matching.o]
[compile swalign.o]
[compile tag_value_map.o]
[compile targetbest_select_stream.o]
[compile tidy_region_node_stream.o]
[compile tidy_region_node_visitor.o]
[compile toolbox.o]
[compile transcript_bittabs.o]
[compile transcript_counts.o]
[compile transcript_evaluators.o]
[compile transcript_exons.o]
[compile transcript_used_exons.o]
[compile type_checker.o]
[compile type_checker_builtin.o]
[compile type_checker_obo.o]
[compile type_graph.o]
[compile type_node.o]
[compile typecheck_info.o]
[compile uint64hashtable.o]
[compile union_find.o]
[compile uniq_stream.o]
[compile visitor_stream.o]
[compile alphabet_lua.o]
[compile annotationsketch_lua.o]
[compile bittab_lua.o]
[compile canvas_lua.o]
[compile cds_stream_lua.o]
[compile csa_stream_lua.o]
[compile diagram_lua.o]
[compile encseq_lua.o]
[compile feature_index_lua.o]
[compile feature_node_iterator_lua.o]
[compile feature_stream_lua.o]
[compile feature_visitor_lua.o]
[compile genome_node_lua.o]
[compile genome_stream_lua.o]
[compile genome_visitor_lua.o]
[compile gt_lua.o]
[compile gtcore_lua.o]
[compile gtext_lua.o]
[compile image_info_lua.o]
[compile layout_lua.o]
[compile mathsupport_lua.o]
[compile range_lua.o]
[compile region_mapping_lua.o]
[compile score_matrix_lua.o]
[compile stream_evaluator_lua.o]
[compile translate_lua.o]
[compile apmeoveridx.o]
[compile asqg_writer.o]
[compile bcktab.o]
[compile cgr_spacedseed.o]
[compile chain2dim.o]
[compile chainofin.o]
[compile cutendpfx.o]
[compile dist-short.o]
[compile echoseq.o]
[compile eis-blockcomp-param.o]
[compile eis-blockcomp.o]
[compile eis-bwtseq-construct.o]
[compile eis-bwtseq-context-param.o]
[compile eis-bwtseq-context.o]
[compile eis-bwtseq-extinfo.o]
[compile eis-bwtseq-param.o]
[compile eis-bwtseq-sass.o]
[compile eis-bwtseq.o]
[compile eis-encidxseq-construct.o]
[compile eis-encidxseq-param.o]
[compile eis-encidxseq.o]
[compile eis-mrangealphabet.o]
[compile eis-sa-common.o]
[compile eis-seqblocktranslate.o]
[compile eis-seqranges.o]
[compile eis-sequencemultiread.o]
[compile eis-specialsrank.o]
[compile eis-suffixarray-interface.o]
[compile eis-suffixerator-interface.o]
[compile eis-voiditf.o]
[compile encseq2offset.o]
[compile enum-patt.o]
[compile esa-bottomup.o]
[compile esa-dfs.o]
[compile esa-lcpintervals.o]
[compile esa-lcpval.o]
[compile esa-map.o]
[compile esa-maxpairs.o]
[compile esa-merge.o]
[compile esa-minunique.o]
[compile esa-mmsearch.o]
[compile esa-scanprj.o]
[compile esa-seqread.o]
[compile esa-shulen.o]
[compile esa-splititv.o]
[compile esa-spmitvs.o]
[compile esa-spmsk.o]
[compile esa_lcpintervals_visitor.o]
[compile esa_spmitvs_visitor.o]
[compile esa_visitor.o]
[compile firstcodes-accum.o]
[compile firstcodes-cache.o]
[compile firstcodes-insert.o]
[compile firstcodes-psbuf.o]
[compile firstcodes-scan.o]
[compile firstcodes-spacelog.o]
[compile firstcodes-tab.o]
[compile firstcodes.o]
[compile fmi-fwduni.o]
[compile fmi-keyval.o]
[compile fmi-locate.o]
[compile fmi-map.o]
[compile fmi-mapspec.o]
[compile fmi-mkindex.o]
[compile fmi-save.o]
[compile fmi-sufbwtstream.o]
[compile giextract.o]
[compile greedyedist.o]
[compile greedyfwdmat.o]
[compile hashfirstcodes.o]
[compile idx-limdfs.o]
[compile idxlocali.o]
[compile idxlocalidp.o]
[compile idxlocalisw.o]
[compile index_options.o]
[compile initbasepower.o]
[compile initeqsvec.o]
[compile iter-window.o]
[compile kmer2string.o]
[compile lua_tools.o]
[compile marksubstring.o]
[compile merger-trie.o]
[compile mssufpat.o]
[compile myersapm.o]
[compile nullcols.o]
[compile optionargmode.o]
[compile pck-count-nodes.o]
[compile pckbucket.o]
[compile pckdfs.o]
[compile prsqualint.o]
[compile pssm.o]
[compile querymatch.o]
[compile radixsort_str.o]
[compile randomcodes-correct.o]
[compile randomcodes-insert.o]
[compile randomcodes-sfx-partssuf.o]
[compile randomcodes-tab.o]
[compile randomcodes.o]
[compile rdj-cntlist.o]
[compile rdj-contfind-bottomup.o]
[compile rdj-contfinder.o]
[compile rdj-contigpaths.o]
[compile rdj-contigs-writer.o]
[compile rdj-errfind.o]
[compile rdj-ovlfind-bf.o]
[compile rdj-ovlfind-dp.o]
[compile rdj-ovlfind-gusfield.o]
[compile rdj-ovlfind-kmp.o]
[compile rdj-pairwise.o]
[compile rdj-spmfind.o]
[compile rdj-spmlist.o]
[compile rdj-spmproc.o]
[compile rdj-ssar.o]
[compile rdj-strgraph.o]
[compile rdj-twobitenc-editor.o]
[compile rdj-version.o]
[compile reads2twobit.o]
[compile reads_library.o]
[compile revcompl.o]
[compile seqabstract.o]
[compile seqnumrelpos.o]
[compile sfx-apfxlen.o]
[compile sfx-bentsedg.o]
[compile sfx-bltrie.o]
src/match/sfx-bentsedg.c: In function 'sarrcountingsort':
src/match/sfx-bentsedg.c:1028:7: warning: case label value is less than minimum value for type [enabled by default]
[compile sfx-copysort.o]
[compile sfx-diffcov.o]
[compile sfx-enumcodes.o]
[compile sfx-lcpvalues.o]
[compile sfx-linlcp.o]
[compile sfx-mappedstr.o]
[compile sfx-maprange.o]
[compile sfx-opt.o]
[compile sfx-outprj.o]
[compile sfx-partssuf.o]
[compile sfx-radixsort.o]
[compile sfx-run.o]
[compile sfx-sain.o]
[compile sfx-shortreadsort.o]
[compile sfx-suffixer.o]
[compile sfx-suffixgetset.o]
[compile sfx-suftaborder.o]
[compile shu-dfs.o]
[compile shu-divergence.o]
[compile shu-encseq-gc.o]
[compile shu-genomediff.o]
[compile shu_unitfile.o]
[compile spaced-seeds.o]
[compile specialrank.o]
[compile spmsuftab.o]
[compile squarededist.o]
[compile substriter.o]
[compile tagerator.o]
[compile test-mappedstr.o]
[compile test-maxpairs.o]
[compile test-mergeesa.o]
[compile test-mtrieins.o]
[compile test-pairwise.o]
[compile turnwheels.o]
[compile twobits2kmers.o]
[compile tyr-map.o]
[compile tyr-mersplit.o]
[compile tyr-mkindex.o]
[compile tyr-occratio.o]
[compile tyr-search.o]
[compile xdrop.o]
[compile ags.o]
[compile ags_build.o]
[compile align_dna.o]
[compile align_protein.o]
[compile backtrace_path.o]
[compile bssm_param.o]
[compile call_info.o]
[compile chain_collection.o]
[compile chaining.o]
[compile compute_scores.o]
[compile desc_cache.o]
[compile dp_options_core.o]
[compile dp_options_est.o]
[compile dp_options_postpro.o]
[compile dp_param.o]
[compile dp_scores_protein.o]
[compile editoperation.o]
[compile gff3_pgl_visitor.o]
[compile gff3_sa_visitor.o]
[compile gt_gth.o]
[compile gt_gthbssmbuild.o]
[compile gt_gthbssmfileinfo.o]
[compile gt_gthbssmprint.o]
[compile gt_gthconsensus.o]
[compile gt_gthfilestat.o]
[compile gt_gthmkbssmfiles.o]
[compile gt_gthsplit.o]
[compile gthalignment.o]
[compile gthchain.o]
[compile gthcluster.o]
[compile gthcutoffsminimal.o]
[compile gthcutoffsrelaxed.o]
[compile gthcutoffsstrict.o]
[compile gthmatch.o]
[compile gthorf.o]
[compile gthoutput.o]
[compile gthsadistri.o]
[compile gthsortags.o]
[compile gthsplicesitescr.o]
[compile gthtrans.o]
[compile gthtravalign.o]
[compile gthverbosefunc.o]
[compile gthverbosefuncvm.o]
[compile gthxml.o]
[compile indent.o]
[compile input.o]
[compile intermediate.o]
[compile md5_cache.o]
[compile parse_options.o]
[compile path_matrix.o]
[compile path_walker.o]
[compile pgl.o]
[compile pgl_collection.o]
[compile pgl_visitor.o]
[compile proc_sa_collection.o]
[compile region_factory.o]
[compile run_header.o]
[compile sa.o]
[compile sa_cmp.o]
[compile sa_collection.o]
[compile sa_filter.o]
[compile sa_visitor.o]
[compile seq_con.o]
[compile similarity_filter.o]
[compile splice_site_model.o]
[compile spliced_seq.o]
[compile stat.o]
[compile time.o]
[compile txt_pgl_visitor.o]
[compile txt_sa_visitor.o]
[compile xml_final_sa_visitor.o]
[compile xml_inter_sa_visitor.o]
[compile xml_pgl_visitor.o]
[compile metagenomethreader.o]
[compile mg_codon.o]
[compile mg_combinedscore.o]
[compile mg_compute_gene_prediction.o]
[compile mg_computepath.o]
[compile mg_outputwriter.o]
[compile mg_reverse.o]
[compile mg_xmlparser.o]
[compile gt_ltrclustering.o]
[compile gt_ltrdigest.o]
[compile gt_ltrharvest.o]
[compile ltr_classify_stream.o]
[compile ltr_cluster_prepare_seq_visitor.o]
[compile ltr_cluster_stream.o]
[compile ltr_four_char_motif.o]
[compile ltr_orf_annotator_stream.o]
[compile ltr_refseq_match_stream.o]
[compile ltr_visitor.o]
[compile ltrdigest_stream.o]
[compile ltrelement.o]
[compile ltrfileout_stream.o]
[compile ltrharvest_fasta_out_stream.o]
[compile ltrharvest_fasta_out_visitor.o]
[compile ltrharvest_stream.o]
[compile ltrharvest_tabout_stream.o]
[compile ltrharvest_tabout_visitor.o]
[compile pbs.o]
[compile ppt.o]
[compile block.o]
[compile canvas.o]
[compile canvas_cairo.o]
[compile canvas_cairo_context.o]
[compile canvas_cairo_file.o]
[compile color.o]
[compile coords.o]
[compile custom_track.o]
[compile custom_track_example.o]
[compile custom_track_gc_content.o]
[compile custom_track_script_wrapper.o]
[compile diagram.o]
[compile drawing_range.o]
[compile element.o]
[compile graphics.o]
[compile graphics_cairo.o]
[compile gt_sketch.o]
[compile gt_sketch_page.o]
[compile image_info.o]
[compile layout.o]
[compile line.o]
[compile line_breaker.o]
[compile line_breaker_bases.o]
[compile line_breaker_captions.o]
[compile luastyle.o]
[compile rec_map.o]
[compile style.o]
[compile text_width_calculator.o]
[compile text_width_calculator_cairo.o]
[compile track.o]
[compile chrqueue.o]
[compile cplfile.o]
[compile cplmatch.o]
[compile direader.o]
[compile errmsg.o]
[compile expand.o]
[compile freelist.o]
[compile getline.o]
[compile hash.o]
[compile history.o]
[compile homedir.o]
[compile ioutil.o]
[compile keytab.o]
[compile pathutil.o]
[compile pcache.o]
[compile stringrp.o]
[compile strngmem.o]
[compile version.o]
[compile sketch_parsed.o]
[compile sketch_constructed.o]
[link libgenometools.a]
ar: creating lib/libgenometools.a
[link sketch_parsed]
[link sketch_constructed]
[link libtecla.a]
ar: creating lib/libtecla.a
[link gt]
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 > \
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make[3]: Leaving directory `/«PKGBUILDDIR»/doc/devguide'
make -C /«PKGBUILDDIR»/doc/manuals annotationsketch
make[3]: Entering directory `/«PKGBUILDDIR»/doc/manuals'
test -e annotationsketch-pdf.aux && mv annotationsketch-pdf.aux annotationsketch.aux
make[3]: [annotationsketch-pdf.aux] Error 1 (ignored)
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Chapter 1.

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Chapter 2.

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nput line 211.


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LaTeX Warning: Reference `GtTypeChecker' on page 30 undefined on input line 225
.


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


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LaTeX Warning: Reference `GtVisitorStream' on page 30 undefined on input line 2
31.


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51.


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9.


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261.


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[]\OT1/cmtt/m/n/10.95 unsigned long long gt[]disc[]distri[]get([]const GtDiscDi
stri *d, unsigned

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

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[]\OT1/cmtt/m/n/10.95 void gt[]output[]file[]register[]options([]GtOptionParser
 *op, GtFile **outfp,

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[]\OT1/cmtt/m/n/10.95 const unsigned long long* gt[]seq[]iterator[]getcurrentco
unter([]GtSeqIterator*,

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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 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, unsigned

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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/cmtt/m/n/10.95 void gt[]array[]rem[]span([]GtArray *array, unsigned long
 frompos, unsigned

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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
[37]
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]in[]stream[]new([]GtArray *nodes
, unsigned long

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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 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 unsigned long gt[]bittab[]get[]next[]bitnum([]const GtBit
tab *bittab, unsigned

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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, unsigned long

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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, unsigned long width, unsigned long height
, GtImageInfo

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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, unsigned long width, unsigned long height, Gt
ImageInfo

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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 GtCodonIteratorStatus gt[]codon[]iterator[]next([]GtCodon
Iterator *ci, char

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

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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, unsigned long startpos, unsigned long length, GtRe
admode

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

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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, unsigned

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\OT1/cmtt/m/n/10.95 long seqlen, unsigned long windowsize, unsigned long height
, double avg,

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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, unsi
gned long key,

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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, unsigned long

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

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

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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 unsigned long gt[]encseq[]seqlength([]const GtEncseq *enc
seq, unsigned long

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[]\OT1/cmtt/m/n/10.95 unsigned long gt[]encseq[]seqstartpos([]const GtEncseq *e
ncseq, unsigned long

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[]\OT1/cmtt/m/n/10.95 unsigned long gt[]encseq[]seqnum([]const GtEncseq *encseq
, unsigned long

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

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[]\OT1/cmtt/m/n/10.95 uint64[]t gt[]encseq[]effective[]filelength([]const GtEnc
seq *encseq, unsigned

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[]\OT1/cmtt/m/n/10.95 unsigned long gt[]encseq[]filestartpos([]const GtEncseq *
encseq, unsigned

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[]\OT1/cmtt/m/n/10.95 unsigned long gt[]encseq[]filenum([]const GtEncseq *encse
q, unsigned long

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[]\OT1/cmtt/m/n/10.95 unsigned long gt[]encseq[]filenum[]first[]seqnum([]const 
GtEncseq *encseq,

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[51] [52] [53]
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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 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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[56] [57] [58]
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[]\OT1/cmtt/m/n/10.95 GtEncseq* gt[]encseq[]loader[]load([]GtEncseqLoader *el, 
const char

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[59] [60] [61]
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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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[62]
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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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[63]
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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[]has[]seqid([]const GtFeatureIndex
 *feature[]index, bool

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[64]
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[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]index[]memory[]get[]node[]by[
]ptr([]GtFeatureIndexMemory*,

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[65]
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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,

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

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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 unsigned long gt[]feature[]node[]number[]of[]children([]c
onst GtFeatureNode

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

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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 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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[66] [67] [68] [69]
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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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[70]
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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 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 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 *filenamestr, unsigned long long *line[]number, GtFile *fpi
n, GtError

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

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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[], unsigned long ndata, GtRange 
valrange,

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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 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,

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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*, unsigned long

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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 GtIntervalTreeIteratorFunc func, unsigned long start, unsig
ned long end,

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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, unsigned long

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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 int gt[]layout[]get[]height([]GtLayout *layout, unsigned 
long *result, GtError

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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, unsigned

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

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[]\OT1/cmtt/m/n/10.95 void gt[]match[]set[]range[]seq1([]GtMatch *match, unsign
ed long start,

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[]\OT1/cmtt/m/n/10.95 void gt[]match[]set[]range[]seq2([]GtMatch *match, unsign
ed long start,

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

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\OT1/cmtt/m/n/10.95 start[]seq1, unsigned long start[]seq2, unsigned long end[]
seq1, unsigned

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\OT1/cmtt/m/n/10.95 long end[]seq2, double evalue, float bitscore, unsigned lon
g ali[]l, double

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[]\OT1/cmtt/m/n/10.95 void gt[]match[]blast[]set[]align[]length([]GtMatchBlast 
*mb, unsigned long

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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 unsigned long score, unsigned long seqno1, unsigned long se
qno2,

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\OT1/cmtt/m/n/10.95 unsigned long start[]seq1, unsigned long start[]seq2, unsig
ned long

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

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\OT1/cmtt/m/n/10.95 start[]seq1, unsigned long start[]seq2, unsigned long end[]
seq1, unsigned

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

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\OT1/cmtt/m/n/10.95 long seqno1, unsigned long seqno2, unsigned long length, un
signed long

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\OT1/cmtt/m/n/10.95 edist, unsigned long start[]seq1, unsigned long start[]seq2
, unsigned long

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[89]
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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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[90]
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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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[91]
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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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[92]
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[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]comment[]node([]GtNodeVisit
or *node[]visitor,

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

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

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

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

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

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

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[93]
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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[]long([]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[]ulong([]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[]ulong[]min([]const char *optio
n[]string, const char

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\OT1/cmtt/m/n/10.95 *description, unsigned long *value, unsigned long default[]
value, 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[]ulong[]min[]max([]const char *
option[]string, const

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\OT1/cmtt/m/n/10.95 char *description, unsigned long *value, unsigned long defa
ult[]value,

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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([]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,
 unsigned long

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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/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 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[]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([]unsigned long *maximum
space, const char

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[94] [95] [96] [97] [98]
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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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[99] [100]
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[101]
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[]\OT1/cmtt/m/n/10.95 GtRDB* gt[]rdb[]mysql[]new([]const char *server, unsigned
 int port, const char

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

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

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[102]
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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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[103]
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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
[104]
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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,

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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 **seq, GtStr *seqid, unsigned long start, unsigned long end
, GtError

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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, unsig
ned long

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[105] [106]
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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, unsig
ned long start,

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

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

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\OT1/cmtt/m/n/10.95 GtRange *overlap[]range, GtStrand strand, GtStrand targetst
rand,

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\OT1/cmtt/m/n/10.95 bool has[]CDS, unsigned long max[]gene[]length, unsigned lo
ng

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\OT1/cmtt/m/n/10.95 max[]gene[]num, double min[]gene[]score, double max[]gene[]
score, double

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\OT1/cmtt/m/n/10.95 min[]average[]splice[]site[]prob, unsigned long feature[]nu
m, GtStrArray

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

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[107]
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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 void gt[]seq[]iterator[]set[]quality[]buffer([]GtSeqItera
tor *seqit, const

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

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[108]
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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 unsigned long gt[]seq[]iterator[]fastq[]get[]file[]index(
[]GtSeqIteratorFastQ

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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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[109]
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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 unsigned long gt[]sequence[]node[]get[]sequence[]length([
]const GtSequenceNode

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[110]
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[]\OT1/cmtt/m/n/10.95 void gt[]splitter[]split([]GtSplitter *splitter, char *st
ring, unsigned long

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[]\OT1/cmtt/m/n/10.95 char* gt[]splitter[]get[]token([]GtSplitter *splitter, un
signed long

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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/cmtt/m/n/10.95 void gt[]str[]append[]cstr[]nt([]GtStr *str, const char *
cstr, unsigned long

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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 const char* gt[]str[]array[]get([]const GtStrArray *str[]
array, unsigned long

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

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

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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 ,
[114]
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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 void gt[]style[]set[]str([]GtStyle*, const char *section,
 const char *key,

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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 void gt[]style[]set[]bool([]GtStyle*, const char *section
, const char *key,

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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/cmtt/m/n/10.95 void gt[]timer[]show[]progress[]formatted([]GtTimer *t, F
ILE *fp, const char

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

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[]\OT1/ptm/m/n/10.95 Like \OT1/cmtt/m/n/10.95 gt[]timer[]show[]progress()\OT1/p
tm/m/n/10.95 , but al-lows to for-mat the de-scrip-tion in a

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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 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 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,

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\OT1/cmtt/m/n/10.95 unsigned long size, unsigned long max[]elemvalue, void *dat
a,

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

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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 spec-i-fied in en-vi-ron-ment vari-able

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

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

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

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

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[]\OT1/ptm/m/n/10.95 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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[5]
Chapter 1.

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[29] [30] [31] [32] [33]
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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, unsigned

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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/cmtt/m/n/10.95 void gt[]array[]rem[]span([]GtArray *array, unsigned long
 frompos, unsigned

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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
[40]
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]array[]in[]stream[]new([]GtArray *nodes
, unsigned long

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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 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 unsigned long gt[]bittab[]get[]next[]bitnum([]const GtBit
tab *bittab, unsigned

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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, unsigned long

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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, unsigned long width, unsigned long height
, GtImageInfo

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

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ImageInfo

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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 GtCodonIteratorStatus gt[]codon[]iterator[]next([]GtCodon
Iterator *ci, char

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

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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, unsigned long startpos, unsigned long length, GtRe
admode

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

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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, unsigned

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\OT1/cmtt/m/n/10.95 long seqlen, unsigned long windowsize, unsigned long height
, double avg,

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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, unsi
gned long key,

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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, unsigned long

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

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

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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 unsigned long gt[]encseq[]seqlength([]const GtEncseq *enc
seq, unsigned long

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[]\OT1/cmtt/m/n/10.95 unsigned long gt[]encseq[]seqstartpos([]const GtEncseq *e
ncseq, unsigned long

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[]\OT1/cmtt/m/n/10.95 unsigned long gt[]encseq[]seqnum([]const GtEncseq *encseq
, unsigned long

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

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[]\OT1/cmtt/m/n/10.95 uint64[]t gt[]encseq[]effective[]filelength([]const GtEnc
seq *encseq, unsigned

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[]\OT1/cmtt/m/n/10.95 unsigned long gt[]encseq[]filestartpos([]const GtEncseq *
encseq, unsigned

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[]\OT1/cmtt/m/n/10.95 unsigned long gt[]encseq[]filenum([]const GtEncseq *encse
q, unsigned long

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[]\OT1/cmtt/m/n/10.95 unsigned long gt[]encseq[]filenum[]first[]seqnum([]const 
GtEncseq *encseq,

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[54] [55] [56]
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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 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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[59] [60] [61]
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[]\OT1/cmtt/m/n/10.95 GtEncseq* gt[]encseq[]loader[]load([]GtEncseqLoader *el, 
const char

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[62] [63] [64]
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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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[65]
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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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[66]
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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[]has[]seqid([]const GtFeatureIndex
 *feature[]index, bool

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[67]
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[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]index[]memory[]get[]node[]by[
]ptr([]GtFeatureIndexMemory*,

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[68]
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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,

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

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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 unsigned long gt[]feature[]node[]number[]of[]children([]c
onst GtFeatureNode

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

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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 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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[69] [70] [71] [72]
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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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[73]
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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 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 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 *filenamestr, unsigned long long *line[]number, GtFile *fpi
n, GtError

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

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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[], unsigned long ndata, GtRange 
valrange,

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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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[80] [81] [82]
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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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[83]
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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,

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[84]
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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*, unsigned long

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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 GtIntervalTreeIteratorFunc func, unsigned long start, unsig
ned long end,

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

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[85]
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[]\OT1/cmtt/m/n/10.95 GtIntervalTreeNode* gt[]interval[]tree[]node[]new([]void 
*data, unsigned long

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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 int gt[]layout[]get[]height([]GtLayout *layout, unsigned 
long *result, GtError

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[87]
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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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[88]
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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, unsigned

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

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[]\OT1/cmtt/m/n/10.95 void gt[]match[]set[]range[]seq1([]GtMatch *match, unsign
ed long start,

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[]\OT1/cmtt/m/n/10.95 void gt[]match[]set[]range[]seq2([]GtMatch *match, unsign
ed long start,

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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, unsigned long

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\OT1/cmtt/m/n/10.95 start[]seq1, unsigned long start[]seq2, unsigned long end[]
seq1, unsigned

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\OT1/cmtt/m/n/10.95 long end[]seq2, double evalue, float bitscore, unsigned lon
g ali[]l, double

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[]\OT1/cmtt/m/n/10.95 void gt[]match[]blast[]set[]align[]length([]GtMatchBlast 
*mb, unsigned long

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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 unsigned long score, unsigned long seqno1, unsigned long se
qno2,

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\OT1/cmtt/m/n/10.95 unsigned long start[]seq1, unsigned long start[]seq2, unsig
ned long

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

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\OT1/cmtt/m/n/10.95 start[]seq1, unsigned long start[]seq2, unsigned long end[]
seq1, unsigned

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

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\OT1/cmtt/m/n/10.95 long seqno1, unsigned long seqno2, unsigned long length, un
signed long

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\OT1/cmtt/m/n/10.95 edist, unsigned long start[]seq1, unsigned long start[]seq2
, unsigned long

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[92]
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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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[93]
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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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[94]
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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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[95]
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[]\OT1/cmtt/m/n/10.95 int gt[]node[]visitor[]visit[]comment[]node([]GtNodeVisit
or *node[]visitor,

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

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

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

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

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

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

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[96]
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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[]long([]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[]ulong([]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[]ulong[]min([]const char *optio
n[]string, const char

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\OT1/cmtt/m/n/10.95 *description, unsigned long *value, unsigned long default[]
value, 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[]ulong[]min[]max([]const char *
option[]string, const

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\OT1/cmtt/m/n/10.95 char *description, unsigned long *value, unsigned long defa
ult[]value,

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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([]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,
 unsigned long

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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/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 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[]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([]unsigned long *maximum
space, const char

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[97] [98] [99] [100] [101]
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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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[102] [103]
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[104]
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[]\OT1/cmtt/m/n/10.95 GtRDB* gt[]rdb[]mysql[]new([]const char *server, unsigned
 int port, const char

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

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

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

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

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[106]
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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
[107]
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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,

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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 **seq, GtStr *seqid, unsigned long start, unsigned long end
, GtError

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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, unsig
ned long

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[108] [109]
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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, unsig
ned long start,

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

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

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\OT1/cmtt/m/n/10.95 GtRange *overlap[]range, GtStrand strand, GtStrand targetst
rand,

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\OT1/cmtt/m/n/10.95 bool has[]CDS, unsigned long max[]gene[]length, unsigned lo
ng

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\OT1/cmtt/m/n/10.95 max[]gene[]num, double min[]gene[]score, double max[]gene[]
score, double

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\OT1/cmtt/m/n/10.95 min[]average[]splice[]site[]prob, unsigned long feature[]nu
m, GtStrArray

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

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[110]
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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 void gt[]seq[]iterator[]set[]quality[]buffer([]GtSeqItera
tor *seqit, const

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

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[111]
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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 unsigned long gt[]seq[]iterator[]fastq[]get[]file[]index(
[]GtSeqIteratorFastQ

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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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[112]
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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 unsigned long gt[]sequence[]node[]get[]sequence[]length([
]const GtSequenceNode

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[113]
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[]\OT1/cmtt/m/n/10.95 void gt[]splitter[]split([]GtSplitter *splitter, char *st
ring, unsigned long

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[]\OT1/cmtt/m/n/10.95 char* gt[]splitter[]get[]token([]GtSplitter *splitter, un
signed long

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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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[114]
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[]\OT1/cmtt/m/n/10.95 void gt[]str[]append[]cstr[]nt([]GtStr *str, const char *
cstr, unsigned long

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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 const char* gt[]str[]array[]get([]const GtStrArray *str[]
array, unsigned long

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

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

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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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[116]
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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 ,
[117]
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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 void gt[]style[]set[]str([]GtStyle*, const char *section,
 const char *key,

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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 void gt[]style[]set[]bool([]GtStyle*, const char *section
, const char *key,

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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/cmtt/m/n/10.95 void gt[]timer[]show[]progress[]formatted([]GtTimer *t, F
ILE *fp, const char

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

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[]\OT1/ptm/m/n/10.95 Like \OT1/cmtt/m/n/10.95 gt[]timer[]show[]progress()\OT1/p
tm/m/n/10.95 , but al-lows to for-mat the de-scrip-tion in a

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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 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 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,

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\OT1/cmtt/m/n/10.95 unsigned long size, unsigned long max[]elemvalue, void *dat
a,

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

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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 spec-i-fied in en-vi-ron-ment vari-able

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

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

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

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

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[]\OT1/ptm/m/n/10.95 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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[138]) [139] (./annotationsketch.aux)

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Chapter 1.

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Chapter 2.
[29] [30] [31] [32] [33]
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[43] [44]
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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, unsigned long

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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, unsigned long width, unsigned long height
, GtImageInfo

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

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ImageInfo

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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 GtCodonIteratorStatus gt[]codon[]iterator[]next([]GtCodon
Iterator *ci, char

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

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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, unsigned long startpos, unsigned long length, GtRe
admode

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

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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, unsigned

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\OT1/cmtt/m/n/10.95 long seqlen, unsigned long windowsize, unsigned long height
, double avg,

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

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[50]
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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, unsi
gned long key,

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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, unsigned long

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

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

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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 unsigned long gt[]encseq[]seqlength([]const GtEncseq *enc
seq, unsigned long

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[]\OT1/cmtt/m/n/10.95 unsigned long gt[]encseq[]seqstartpos([]const GtEncseq *e
ncseq, unsigned long

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[]\OT1/cmtt/m/n/10.95 unsigned long gt[]encseq[]seqnum([]const GtEncseq *encseq
, unsigned long

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

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[]\OT1/cmtt/m/n/10.95 uint64[]t gt[]encseq[]effective[]filelength([]const GtEnc
seq *encseq, unsigned

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[]\OT1/cmtt/m/n/10.95 unsigned long gt[]encseq[]filestartpos([]const GtEncseq *
encseq, unsigned

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[]\OT1/cmtt/m/n/10.95 unsigned long gt[]encseq[]filenum([]const GtEncseq *encse
q, unsigned long

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[]\OT1/cmtt/m/n/10.95 unsigned long gt[]encseq[]filenum[]first[]seqnum([]const 
GtEncseq *encseq,

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[54] [55] [56]
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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 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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[62] [63] [64]
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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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[66]
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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[]has[]seqid([]const GtFeatureIndex
 *feature[]index, bool

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[67]
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[]\OT1/cmtt/m/n/10.95 GtFeatureNode* gt[]feature[]index[]memory[]get[]node[]by[
]ptr([]GtFeatureIndexMemory*,

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[68]
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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,

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

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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 unsigned long gt[]feature[]node[]number[]of[]children([]c
onst GtFeatureNode

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

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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 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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[69] [70] [71] [72]
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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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[73]
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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 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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[75]
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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 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 *filenamestr, unsigned long long *line[]number, GtFile *fpi
n, GtError

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

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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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[78] [79]
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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[], unsigned long ndata, GtRange 
valrange,

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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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[80] [81] [82]
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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,

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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*, unsigned long

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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 GtIntervalTreeIteratorFunc func, unsigned long start, unsig
ned long end,

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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, unsigned long

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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 int gt[]layout[]get[]height([]GtLayout *layout, unsigned 
long *result, GtError

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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, unsigned

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

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[]\OT1/cmtt/m/n/10.95 void gt[]match[]set[]range[]seq1([]GtMatch *match, unsign
ed long start,

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[]\OT1/cmtt/m/n/10.95 void gt[]match[]set[]range[]seq2([]GtMatch *match, unsign
ed long start,

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

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\OT1/cmtt/m/n/10.95 start[]seq1, unsigned long start[]seq2, unsigned long end[]
seq1, unsigned

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\OT1/cmtt/m/n/10.95 long end[]seq2, double evalue, float bitscore, unsigned lon
g ali[]l, double

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[]\OT1/cmtt/m/n/10.95 void gt[]match[]blast[]set[]align[]length([]GtMatchBlast 
*mb, unsigned long

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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 unsigned long score, unsigned long seqno1, unsigned long se
qno2,

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\OT1/cmtt/m/n/10.95 unsigned long start[]seq1, unsigned long start[]seq2, unsig
ned long

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

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\OT1/cmtt/m/n/10.95 start[]seq1, unsigned long start[]seq2, unsigned long end[]
seq1, unsigned

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

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\OT1/cmtt/m/n/10.95 long seqno1, unsigned long seqno2, unsigned long length, un
signed long

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\OT1/cmtt/m/n/10.95 edist, unsigned long start[]seq1, unsigned long start[]seq2
, unsigned long

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

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

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

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

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\OT1/ptm/m/n/10.95 (trans-fers own-er-ship to \OT1/cmtt/m/n/10.95 genome[]node\
OT1/ptm/m/n/10.95 ). If no er-ror oc-curs, 0 is re-turned and

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\OT1/ptm/m/n/10.95 is ex-hausted (0 is re-turned) or an er-ror oc-curs (-1 is r
e-turned and \OT1/cmtt/m/n/10.95 err \OT1/ptm/m/n/10.95 is

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\OT1/ptm/m/n/10.95 set). All re-trieved \OT1/cmtt/m/n/10.95 GtGenomeNode\OT1/pt
m/m/n/10.95 s are deleted au-to-mat-i-cally with calls to

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\OT1/cmtt/m/n/10.95 gt[]genome[]node[]delete()\OT1/ptm/m/n/10.95 . This method 
is ba-si-cally a con-ve-nience method

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

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

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

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

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

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

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

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

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

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

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[]\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[]long([]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[]ulong([]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[]ulong[]min([]const char *optio
n[]string, const char

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\OT1/cmtt/m/n/10.95 *description, unsigned long *value, unsigned long default[]
value, 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[]ulong[]min[]max([]const char *
option[]string, const

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\OT1/cmtt/m/n/10.95 char *description, unsigned long *value, unsigned long defa
ult[]value,

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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([]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,
 unsigned long

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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/ptm/m/n/10.95 Return a new \OT1/cmtt/m/n/10.95 GtOption \OT1/ptm/m/n/10.
95 with the given \OT1/cmtt/m/n/10.95 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[]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([]unsigned long *maximum
space, const char

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[97] [98] [99] [100] [101]
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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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[102] [103]
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[104]
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[]\OT1/cmtt/m/n/10.95 GtRDB* gt[]rdb[]mysql[]new([]const char *server, unsigned
 int port, const char

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

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

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[105]
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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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[106]
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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
[107]
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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,

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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 **seq, GtStr *seqid, unsigned long start, unsigned long end
, GtError

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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, unsig
ned long

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[108] [109]
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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, unsig
ned long start,

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

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

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\OT1/cmtt/m/n/10.95 GtRange *overlap[]range, GtStrand strand, GtStrand targetst
rand,

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\OT1/cmtt/m/n/10.95 bool has[]CDS, unsigned long max[]gene[]length, unsigned lo
ng

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\OT1/cmtt/m/n/10.95 max[]gene[]num, double min[]gene[]score, double max[]gene[]
score, double

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\OT1/cmtt/m/n/10.95 min[]average[]splice[]site[]prob, unsigned long feature[]nu
m, GtStrArray

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

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[110]
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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 void gt[]seq[]iterator[]set[]quality[]buffer([]GtSeqItera
tor *seqit, const

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

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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 unsigned long gt[]seq[]iterator[]fastq[]get[]file[]index(
[]GtSeqIteratorFastQ

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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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[]\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 unsigned long gt[]sequence[]node[]get[]sequence[]length([
]const GtSequenceNode

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

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[]\OT1/cmtt/m/n/10.95 char* gt[]splitter[]get[]token([]GtSplitter *splitter, un
signed long

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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/cmtt/m/n/10.95 void gt[]str[]append[]cstr[]nt([]GtStr *str, const char *
cstr, unsigned long

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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 const char* gt[]str[]array[]get([]const GtStrArray *str[]
array, unsigned long

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

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

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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 ,
[117]
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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 void gt[]style[]set[]str([]GtStyle*, const char *section,
 const char *key,

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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 void gt[]style[]set[]bool([]GtStyle*, const char *section
, const char *key,

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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/cmtt/m/n/10.95 void gt[]timer[]show[]progress[]formatted([]GtTimer *t, F
ILE *fp, const char

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

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[]\OT1/ptm/m/n/10.95 Like \OT1/cmtt/m/n/10.95 gt[]timer[]show[]progress()\OT1/p
tm/m/n/10.95 , but al-lows to for-mat the de-scrip-tion in a

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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 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 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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 void *data,

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

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\OT1/cmtt/m/n/10.95 unsigned long size, unsigned long max[]elemvalue, void *dat
a,

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[]\OT1/ptm/m/n/10.95 Find \OT1/cmtt/m/n/10.95 file \OT1/ptm/m/n/10.95 in $\OML/
ztmcm/m/it/10.95 PATH; ifithasnodirname\OT1/ztmcm/m/n/10.95 ; \OML/ztmcm/m/it/1
0.95 set[]todirnameotherwise:Sets[]totheemptystringif[]couldnotbefoundin$\OT1/p
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[]\OT1/cmtt/m/n/10.95 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 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
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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
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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
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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
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[]\OT1/cmtt/m/n/10.95 void gt[]msort[]r([]void *base, size[]t nmemb, size[]t si
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[]\OT1/ptm/m/n/10.95 This mod-ule im-ple-ments the func-tion\OT1/cmtt/m/n/10.95
 gt[]basename() \OT1/ptm/m/n/10.95 ac-cord-ing to the spec-i-fi-

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\OT1/ptm/m/n/10.95 ca-tions in http://www.unix-systems.org/onlinepubs/7908799/x
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[]\OT1/cmtt/m/n/10.95 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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ajor, unsigned int

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[138]) [139] (./annotationsketch.aux)

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[1 [1]]
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\OT1/ptm/m/n/12 also the sam-tools man-ual page ($\OT1/pcr/m/n/12 http : / / sa
mtools . sourceforge . net / samtools . shtml$\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 refseq.fas -f map.sam f_reads.sai r_reads.sai f_r
eads.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]

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[4]] [2 [4]}] (./hop.aux)

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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 2.3.2 man-u-ally from \OT1/pcr/m/n/12 ftp://selab.janelia.org/p
ub/software/hmmer/CURRENT/ \OT1/ptm/m/n/12 and

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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 # args=-index chr02.19970727.fsa -seed 30 -xdrop 5 -mat 2 -mi
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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/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)[] 

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[]\OT1/pcr/m/n/10 # where:                                                     
                                                                               
                # s = starting position                                        
                                                                               
              # e = ending position                                            
                                                                               
            # l = length                                                       
                                                                               
          # m = motif                                                          
                                                                               
        # ret = LTR-retrotransposon                                            
                                                                               
      # lLTR = left LTR                                                        
                                                                               
    # rLTR = right LTR                                                         
                                                                               
  # TSD = target site duplication                                              
                                                                               
# sim = similarity                                                             
                                                                             # 
seq-nr = sequence number[] 
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\OT1/ptm/m/n/12 trans-po-son it-self (\OT1/pcr/m/n/12 LTR[]retrotransposon \OT1
/ptm/m/n/12 type) and the pre-dicted LTRs (\OT1/pcr/m/n/12 long[]terminal[]repe
at

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[]\OT1/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/pcr/m/n/12 gt suffixerator -tis -des -dna -ssp -db genome.fas -indexname
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[]\OT1/ptm/m/n/12 We will also as-sume that the HMM files to be used are called
 \OT1/pcr/m/n/12 HMM1.hmm\OT1/ptm/m/n/12 , \OT1/pcr/m/n/12 HMM2.hmm \OT1/ptm/m/
n/12 and \OT1/pcr/m/n/12 HMM3.hmm\OT1/ptm/m/n/12 ,

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\OT1/pcr/m/n/12 -hmms HMM*.hmm -outfileprefix mygenome-ltrs ltrs[]sorted.gff3 g
enome.fas
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(/usr/share/texlive/texmf-dist/tex/latex/comment/comment.sty</usr/share/texlive/texmf-dist/fonts/type1/urw/ti
mes/utmri8a.pfb
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mes/utmri8a.pfb
Output written on uniquesub.pdf (3 pages, 98728 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)
pdflatex repfind.tex && rm repfind.pdf

Output written on matstat.pdf (2 pages, 92588 bytes).
Transcript written on matstat.log.
mv matstat.aux matstat-pdf.aux
head -n 6999 ../../testdata/at1MB > read1.fna

*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkiiecho ">" > read2.fna
tail -n 6945 ../../testdata/at1MB >> read2.fna

[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.stycp ../../testdata/U89959_genomic.fas U89959.fna

(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty../../bin/gt packedindex mkindex -dna -dir rev -parts 12 -bsize 10 \
                      -sprank -locfreq 32 -tis -ssp -indexname pck-human\
                      -db ../../testdata/at1MB
)
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[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.mapThis is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian)
 restricted \write18 enabled.
}]entering extended mode
(./repfind.tex

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


LaTeX Warning: Citation `journals/talg/FerraginaMMN07' on page 1 undefined on i
nput line 51.


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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

LaTeX Warning: Reference `sec:packedindex:mkindex' on page 3 undefined on input
 line 276.

[3) (./optionman.sty)]
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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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t line 308.

[4]]

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[]\OT1/ptm/m/n/12 First com-pute the \OT1/ptm/m/it/12 packedin-dex \OT1/ptm/m/n
/12 in-dex file (this as-sumes \OT1/pcr/m/sl/12 chr01.19960731.fsa.gz \OT1/ptm/
m/n/12 has been copied/linked
[5 [1{/var/lib/texmf/fo
nts/map/pdftex/updmap/pdftex.map]
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[6] (./packedindex.aux)

LaTeX Warning: There were undefined references.


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 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb

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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></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb]></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi
8.pfb>
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[]\OT1/ptm/m/n/12 . If this op-

LaTeX Warning: Reference `Examples' on page 3 undefined on input line 261.

[3</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb]><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.pfb></usr/sha
re/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/share/texlive/texmf-di
st/fonts/type1/urw/courier/ucrbo8a.pfb (/usr/share/texlive/texmf-dist/tex/latex/psnfss/omlptm.fd)} [4></usr/share/texlive/texmf-dist/fonts/typ
e1/urw/courier/ucrr8a.pfb]]
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[]\OT1/ptm/m/n/10.95 tataaaatagccaaatctgagcctaaaagcccttggatatccatgatttagaacgaac
catcccctcttattcaggagaagttttctgaactcttcaacatcctcga...| 

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[] 
[5></usr/share/texlive/texmf-dist/fonts/type1/urw/courie
r/ucrro8a.pfb] [2></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmb8a.pfb]
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[]\OT1/ptm/m/n/10.95 tataaaatagccaaatctgagcctaaaagcccttggatatccatgatttagaacgaac
catcccctcttattcaggagaagttttctgaactcttcaacatcctcga...| 

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[]\OT1/ptm/m/n/10.95 MLLREVTREERKNFYTNEWKVKDIPDFIVKTLELREFGFDHSGEGPSDRKNQYTDIRD
LEDYIRATA...| 

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[][] 

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[]\OT1/ptm/m/n/12 Content:| 

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[][]| 

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[][]| 

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[][]| 

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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 [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/tex
live/texmf-dist/fonts/type1/urw/times/utmr8a.pfb}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfb
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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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LaTeX Warning: Reference `reversedEQ' on page 4 undefined on input line 198.

[4></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi12.pfb>] (./repfind.aux</usr/share/texlive/texmf-dist
/fonts/type1/urw/times/utmri8a.pfb)

LaTeX Warning: There were undefined references.


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

 )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmmi7.pfb>></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr1
2.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
Output written on packedindex.pdf (7 pages, 157481 bytes).
Transcript written on packedindex.log.
>mv packedindex.aux packedindex-pdf.aux
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10
.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy7.pfbcp ../../testdata/Q1.gz Q1.gz
test -e genomediff-pdf.aux && mv genomediff-pdf.aux genomediff.aux
make[3]: [genomediff-pdf.aux] Error 1 (ignored)
pdflatex genomediff.tex && rm genomediff.pdf
>></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy8.pfb</usr/s
hare/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></
usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/
texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/tex
live/texmf-dist/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/font
s/type1/urw/times/utmbi8a.pfb></usr/share/texlive/texmf-dist
/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/ti
mes/utmr8a.pfb>></usr/share/texlive/texmf-dist/fonts/type1/ur
w/times/utmri8a.pfb</usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb
>>
Output written on repfind.pdf (4 pages, 103797 bytes).
Transcript written on repfind.log.

Output written on mgth.pdf (8 pages, 132038 bytes).
Transcript written on mgth.log.
mv repfind.aux repfind-pdf.aux
mv mgth.aux mgth-pdf.aux
test -e readjoiner-pdf.aux && mv readjoiner-pdf.aux readjoiner.aux
test -e hop-pdf.aux && mv hop-pdf.aux hop.aux
bibtex readjoiner
bibtex hop
This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian)
 restricted \write18 enabled.
entering extended mode
(./genomediff.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, lo
aded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size12.clo))
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)This is BibTeX, Version 0.99d (TeX Live 2012/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)
test -e readjoiner-pdf.bbl || touch readjoiner-pdf.bbl
This is BibTeX, Version 0.99d (TeX Live 2012/Debian)
The top-level auxiliary file: hop.aux
I found no \bibdata command---while reading file hop.aux
I found no \bibstyle command---while reading file hop.aux
(There were 2 error messages)
make[3]: [hop-pdf.bbl] Error 2 (ignored)
test -e hop-pdf.bbl || touch hop-pdf.bbl
diff readjoiner-pdf.bbl readjoiner.bbl || mv readjoiner.bbl readjoiner-pdf.bbl && rm -f readjoiner.bbl
diff hop-pdf.bbl hop.bbl || mv hop.bbl hop-pdf.bbl && rm -f hop.bbl
mv readjoiner.aux readjoiner-pdf.aux
mv hop.aux hop-pdf.aux
test -e ltrharvest-pdf.aux && mv ltrharvest-pdf.aux ltrharvest.aux
test -e ltrdigest-pdf.aux && mv ltrdigest-pdf.aux ltrdigest.aux
)
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.stybibtex ltrharvest
bibtex ltrdigest

(/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def
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(/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu)
(/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu)))
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(/usr/share/texlive/texmf-dist/tex/latex/listings/lstmisc.sty)
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(./optionman.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.styThis is BibTeX, Version 0.99d (TeX Live 2012/Debian)
The top-level auxiliary file: ltrharvest.aux
I found no \bibdata command---while reading file ltrharvest.aux
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(There were 2 error messages)
make[3]: [ltrharvest-pdf.bbl] Error 2 (ignored)
test -e ltrharvest-pdf.bbl || touch ltrharvest-pdf.bbl
)
(/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.stydiff ltrharvest-pdf.bbl ltrharvest.bbl || mv ltrharvest.bbl ltrharvest-pdf.bbl && rm -f ltrharvest.bbl
)This is BibTeX, Version 0.99d (TeX Live 2012/Debian)
The top-level auxiliary file: ltrdigest.aux
The style file: unsrt.bst
I found no \bibdata command---while reading file ltrdigest.aux
Warning--I didn't find a database entry for "EKW07"
Warning--I didn't find a database entry for "gff3"
Warning--I didn't find a database entry for "genometools"
Warning--I didn't find a database entry for "hmmer"
Warning--I didn't find a database entry for "pfam"
(There was 1 error message)
make[3]: [ltrdigest-pdf.bbl] Error 2 (ignored)
test -e ltrdigest-pdf.bbl || touch ltrdigest-pdf.bbl

(/usr/share/texmf/tex/latex/xcolor/xcolor.stymv ltrharvest.aux ltrharvest-pdf.aux
diff ltrdigest-pdf.bbl ltrdigest.bbl || mv ltrdigest.bbl ltrdigest-pdf.bbl && rm -f ltrdigest.bbl
test -e uniquesub-pdf.aux && mv uniquesub-pdf.aux uniquesub.aux
0a1,3
> \begin{thebibliography}{}
> 
> \end{thebibliography}

(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfgbibtex uniquesub
)mv ltrdigest.aux ltrdigest-pdf.aux
test -e matstat-pdf.aux && mv matstat-pdf.aux matstat.aux
bibtex matstat

(/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.styThis is BibTeX, Version 0.99d (TeX Live 2012/Debian)
The top-level auxiliary file: uniquesub.aux
I found no \bibdata command---while reading file uniquesub.aux
I found no \bibstyle command---while reading file uniquesub.aux
(There were 2 error messages)
make[3]: [uniquesub-pdf.bbl] Error 2 (ignored)
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
)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.styThis is BibTeX, Version 0.99d (TeX Live 2012/Debian)
The top-level auxiliary file: matstat.aux
I found no \citation commands---while reading file matstat.aux
I found no \bibdata command---while reading file matstat.aux
I found no \bibstyle command---while reading file matstat.aux
(There were 3 error messages)
make[3]: [matstat-pdf.bbl] Error 2 (ignored)
test -e matstat-pdf.bbl || touch matstat-pdf.bbl
mv uniquesub.aux uniquesub-pdf.aux
test -e mgth-pdf.aux && mv mgth-pdf.aux mgth.aux
diff matstat-pdf.bbl matstat.bbl || mv matstat.bbl matstat-pdf.bbl && rm -f matstat.bbl
bibtex mgth
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 2012/Debian)
The top-level auxiliary file: mgth.aux
I found no \bibdata command---while reading file mgth.aux
I found no \bibstyle command---while reading file mgth.aux
(There were 2 error messages)
make[3]: [mgth-pdf.bbl] Error 2 (ignored)
test -e mgth-pdf.bbl || touch mgth-pdf.bbl
diff mgth-pdf.bbl mgth.bbl || mv mgth.bbl mgth-pdf.bbl && rm -f mgth.bbl
mv mgth.aux mgth-pdf.aux
test -e repfind-pdf.aux && mv repfind-pdf.aux repfind.aux
bibtex repfind
This is BibTeX, Version 0.99d (TeX Live 2012/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

No file genomediff.aux.
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
(/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkiidiff 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}
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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
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[]\OT1/pcr/m/n/10 # where:                                                     
                                                                               
                # s = starting position                                        
                                                                               
              # e = ending position                                            
                                                                               
            # l = length                                                       
                                                                               
          # m = motif                                                          
                                                                               
        # ret = LTR-retrotransposon                                            
                                                                               
      # lLTR = left LTR                                                        
                                                                               
    # rLTR = right LTR                                                         
                                                                               
  # TSD = target site duplication                                              
                                                                               
# sim = similarity                                                             
                                                                             # 
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test -e hop.bbl && mv hop.bbl hop-pdf.bbl
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xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt12.pfbtest -e ltrdigest-pdf.aux && mv ltrdigest-pdf.aux ltrdigest.aux
></usr/share/texlive/
texmf-dist/fonts/type1/urw/courier/ucrr8a.pfbtest -e ltrdigest-pdf.bbl && mv ltrdigest-pdf.bbl ltrdigest.bbl
pdflatex ltrdigest.tex
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imes/utmbi8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfb>></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmsy10.pfb</usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pf
b></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
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>pdflatex ltrharvest.tex
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t/fonts/type1/urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/u
rw/times/utmri8a.pfb>This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian)
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mv readjoiner.aux readjoiner-pdf.aux
test -e readjoiner.bbl && mv readjoiner.bbl readjoiner-pdf.bbl
test -e uniquesub-pdf.aux && mv uniquesub-pdf.aux uniquesub.aux
test -e uniquesub-pdf.bbl && mv uniquesub-pdf.bbl uniquesub.bbl
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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
-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 2.3.2 man-u-ally from \OT1/pcr/m/n/12 ftp://selab.janelia.org/p
ub/software/hmmer/CURRENT/ \OT1/ptm/m/n/12 and

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\OT1/ptm/m/n/12 loaded from $\OT1/pcr/m/n/12 ftp : / / ftp . ensembl . org / pu
b / current _ fasta / homo _ sapiens _ 47 _ 36i /
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\OT1/ptm/m/n/12 trans-po-son it-self (\OT1/pcr/m/n/12 LTR[]retrotransposon \OT1
/ptm/m/n/12 type) and the pre-dicted LTRs (\OT1/pcr/m/n/12 long[]terminal[]repe
at

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[]\OT1/pcr/m/n/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)[] 

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[]\OT1/pcr/m/n/10 # where:                                                     
                                                                               
                # s = starting position                                        
                                                                               
              # e = ending position                                            
                                                                               
            # l = length                                                       
                                                                               
          # m = motif                                                          
                                                                               
        # ret = LTR-retrotransposon                                            
                                                                               
      # lLTR = left LTR                                                        
                                                                               
    # rLTR = right LTR                                                         
                                                                               
  # TSD = target site duplication                                              
                                                                               
# sim = similarity                                                             
                                                                             # 
seq-nr = sequence number[] 
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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/pcr/m/n/12 gt suffixerator -tis -des -dna -ssp -db genome.fas -indexname
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[]\OT1/ptm/m/n/12 We will also as-sume that the HMM files to be used are called
 \OT1/pcr/m/n/12 HMM1.hmm\OT1/ptm/m/n/12 , \OT1/pcr/m/n/12 HMM2.hmm \OT1/ptm/m/
n/12 and \OT1/pcr/m/n/12 HMM3.hmm\OT1/ptm/m/n/12 ,

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\OT1/pcr/m/n/12 -hmms HMM*.hmm -outfileprefix mygenome-ltrs ltrs[]sorted.gff3 g
enome.fas
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/type1/public/amsfonts/cm/cmsy8.pfb>></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pf
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(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty</usr/share/texlive/t
exmf-dist/fonts/type1/urw/times/utmri8a.pfb)
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test -e matstat-pdf.bbl && mv matstat-pdf.bbl matstat.bbl
>pdflatex matstat.tex
)
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(./uniquesub.aux) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ptm.fd)This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012/Debian)
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\OT1/ptm/m/n/12 loaded from $\OT1/pcr/m/n/12 ftp : / / ftp . ensembl . org / pu
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[]$\OT1/pcr/m/n/14.4 http : / / nar . oxfordjournals . org / cgi / content /
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\OT1/ptm/m/n/12 loaded from $\OT1/pcr/m/n/12 ftp : / / ftp . ensembl . org / pu
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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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[]].
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\OT1/ptm/m/n/12 2.3.2 man-u-ally from \OT1/pcr/m/n/12 ftp://selab.janelia.org/p
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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/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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[1
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[]\OT1/pcr/m/n/10.95 BLAST-Filename \OT1/ptm/m/n/12 de-notes the XML for-mat-te
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[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
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>
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>
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# file output/gt-tagerator--q-Q1.gz--maxocc-10--pck-pck-human.out already exists
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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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(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmbxti10.pfb></usr/share/texlive/texmf-dist/fonts/
type1/public/amsfonts/cm/cmcsc10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmitt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmmi8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.pfb></
usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/sh
are/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/te
xlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti12.pfb></usr/share/texlive/
texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on genomediff.pdf (6 pages, 176585 bytes).
Transcript written on genomediff.log.
mv genomediff.aux genomediff-pdf.aux
test -e genomediff.bbl && mv genomediff.bbl genomediff-pdf.bbl
make[3]: Leaving directory `/«PKGBUILDDIR»/doc/manuals'
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
   debian/rules override_dh_auto_test
make[1]: Entering directory `/«PKGBUILDDIR»'
#dh_auto_test -- useshared=yes 64bit=no testthreads=5
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
   dh_installdirs -a -O--parallel
   debian/rules override_dh_auto_install
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_auto_install -- useshared=yes 64bit=no opt=no errorcheck=no prefix=/«PKGBUILDDIR»/debian/tmp/usr
make[2]: Entering directory `/«PKGBUILDDIR»'
[link libgenometools.so]
[compile skproto.o]
[compile custom_stream.o]
[compile gff3sort.o]
[compile gff3validator.o]
[compile noop.o]
[compile sketch_parsed_with_ctrack.o]
[compile sketch_parsed_with_ordering.o]
[link skproto]
[link custom_stream]
[link gff3sort]
[link gff3validator]
[link noop]
[link sketch_parsed_with_ctrack]
[link sketch_parsed_with_ordering]
test -d /«PKGBUILDDIR»/debian/tmp/usr/bin || mkdir -p /«PKGBUILDDIR»/debian/tmp/usr/bin
cp bin/gt /«PKGBUILDDIR»/debian/tmp/usr/bin
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/.so.0 /«PKGBUILDDIR»/debian/tmp/usr/lib/.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 -DLUA_USE_POSIX -DLUA_DL_DLOPEN -DHAVE_CURSES_H -DHAVE_TERM_H -DUSE_TERMINFO -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DCURSES -DHAVE_SQLITE -DSQLITE_THREADSAFE=1!' \
	  -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 -lm -lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 -llua5.1-filesystem -llua5.1-des56 -lncurses -ldl -lpango-1.0 -lgobject-2.0 -lglib-2.0   -lcairo   -lpangocairo-1.0 -lpango-1.0 -lcairo -lgobject-2.0 -lglib-2.0   -lsqlite3 -lpthread -ldl!' -e "s!@VERSION@!`cat VERSION`!" \
	  -e 's!@BUILDSTAMP@!"2013-06-14 14:47:44"!' \
	  -e 's!@SYSTEM@!Linux!' <src/genometools-config.in \
	  >/«PKGBUILDDIR»/debian/tmp/usr/bin/genometools-config
chmod 755 /«PKGBUILDDIR»/debian/tmp/usr/bin/genometools-config
make[2]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_install --sourcedirectory=gtpython --destdir=/«PKGBUILDDIR»/debian/python-genometools
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»'
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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)
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dpkg-deb: building package `genometools-dbg' in `../genometools-dbg_1.5.1-1_armhf.deb'.
dpkg-deb: building package `libgenometools0' in `../libgenometools0_1.5.1-1_armhf.deb'.
dpkg-deb: building package `genometools' in `../genometools_1.5.1-1_armhf.deb'.
dpkg-deb: building package `libgenometools0-dev' in `../libgenometools0-dev_1.5.1-1_armhf.deb'.
dpkg-deb: building package `python-genometools' in `../python-genometools_1.5.1-1_armhf.deb'.
 dpkg-genchanges -B >../genometools_1.5.1-1_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-1.5.1
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20130614-1449

Finished
────────

I: Built successfully

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


genometools_1.5.1-1_armhf.changes:
──────────────────────────────────

Format: 1.8
Date: Thu, 07 Mar 2013 14:08:05 +0100
Source: genometools
Binary: genometools genometools-common libgenometools0 libgenometools0-dev genometools-doc genometools-dbg python-genometools
Architecture: armhf
Version: 1.5.1-1
Distribution: jessie-staging
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
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 (1.5.1-1) unstable; urgency=low
 .
   * New upstream release.
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 bcf3525e0d44aa7dbcd79c6623c0a511 31754 python optional python-genometools_1.5.1-1_armhf.deb

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


genometools_1.5.1-1_armhf.deb
─────────────────────────────

 new debian package, version 2.0.
 size 1959542 bytes: control archive=3478 bytes.
     939 bytes,    16 lines      control              
    7023 bytes,    97 lines      md5sums              
 Package: genometools
 Version: 1.5.1-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 4618
 Depends: libbz2-1.0, libc6 (>= 2.13-28), libcairo2 (>= 1.2.4), libexpat1 (>= 2.0.1), libgcc1 (>= 1:4.4.0), libglib2.0-0 (>= 2.12.0), liblua5.1-0, libncurses5 (>= 5.5-5~), libpango-1.0-0 (>= 1.14.0), libpangocairo-1.0-0 (>= 1.14.0), libsqlite3-0 (>= 3.5.9), libtinfo5, 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 2013-06-14 14:48 ./
drwxr-xr-x root/root         0 2013-06-14 14:47 ./usr/
drwxr-xr-x root/root         0 2013-06-14 14:48 ./usr/bin/
-rwxr-xr-x root/root   4624396 2013-06-14 14:48 ./usr/bin/gt
drwxr-xr-x root/root         0 2013-06-14 14:48 ./usr/share/
drwxr-xr-x root/root         0 2013-06-14 14:47 ./usr/share/doc/
drwxr-xr-x root/root         0 2013-06-14 14:48 ./usr/share/doc/genometools/
-rw-r--r-- root/root      1772 2013-03-07 12:25 ./usr/share/doc/genometools/README
-rw-r--r-- root/root       760 2013-03-07 12:25 ./usr/share/doc/genometools/CONTRIBUTORS
-rw-r--r-- root/root         6 2013-03-07 12:25 ./usr/share/doc/genometools/VERSION
-rw-r--r-- root/root      6607 2013-03-07 13:07 ./usr/share/doc/genometools/copyright
-rw-r--r-- root/root       932 2013-03-07 13:09 ./usr/share/doc/genometools/changelog.Debian.gz
-rw-r--r-- root/root      4081 2013-03-07 12:25 ./usr/share/doc/genometools/changelog.gz
drwxr-xr-x root/root         0 2013-06-14 14:48 ./usr/share/man/
drwxr-xr-x root/root         0 2013-06-14 14:48 ./usr/share/man/man1/
-rw-r--r-- root/root       768 2013-06-14 14:48 ./usr/share/man/man1/gt-bed_to_gff3.1.gz
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-rw-r--r-- root/root       628 2013-06-14 14:48 ./usr/share/man/man1/gt-clean.1.gz
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-rw-r--r-- root/root      1468 2013-06-14 14:48 ./usr/share/man/man1/gt-genomediff.1.gz
-rw-r--r-- root/root      1383 2013-06-14 14:48 ./usr/share/man/man1/gt-gff3.1.gz
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-rw-r--r-- root/root       812 2013-06-14 14:48 ./usr/share/man/man1/gt-ltrclustering.1.gz
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-rw-r--r-- root/root      1291 2013-06-14 14:48 ./usr/share/man/man1/gt-ltrharvest.1.gz
-rw-r--r-- root/root       878 2013-06-14 14:48 ./usr/share/man/man1/gt-matchtool.1.gz
-rw-r--r-- root/root       824 2013-06-14 14:48 ./usr/share/man/man1/gt-matstat.1.gz
-rw-r--r-- root/root       769 2013-06-14 14:48 ./usr/share/man/man1/gt-md5_to_id.1.gz
-rw-r--r-- root/root       708 2013-06-14 14:48 ./usr/share/man/man1/gt-merge.1.gz
-rw-r--r-- root/root       741 2013-06-14 14:48 ./usr/share/man/man1/gt-mergefeat.1.gz
-rw-r--r-- root/root      1180 2013-06-14 14:48 ./usr/share/man/man1/gt-mgth.1.gz
-rw-r--r-- root/root       778 2013-06-14 14:48 ./usr/share/man/man1/gt-mkfeatureindex.1.gz
-rw-r--r-- root/root       793 2013-06-14 14:48 ./usr/share/man/man1/gt-mkfmindex.1.gz
-rw-r--r-- root/root       624 2013-06-14 14:48 ./usr/share/man/man1/gt-mmapandread.1.gz
-rw-r--r-- root/root       878 2013-06-14 14:48 ./usr/share/man/man1/gt-orffinder.1.gz
-rw-r--r-- root/root       773 2013-06-14 14:48 ./usr/share/man/man1/gt-packedindex-chkintegrity.1.gz
-rw-r--r-- root/root      1316 2013-06-14 14:48 ./usr/share/man/man1/gt-packedindex-chksearch.1.gz
-rw-r--r-- root/root       798 2013-06-14 14:48 ./usr/share/man/man1/gt-packedindex-mkctxmap.1.gz
-rw-r--r-- root/root      1579 2013-06-14 14:48 ./usr/share/man/man1/gt-packedindex-mkindex.1.gz
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-rw-r--r-- root/root       721 2013-06-14 14:48 ./usr/share/man/man1/gt-packedindex.1.gz
-rw-r--r-- root/root       688 2013-06-14 14:48 ./usr/share/man/man1/gt-prebwt.1.gz
-rw-r--r-- root/root       724 2013-06-14 14:48 ./usr/share/man/man1/gt-readjoiner-assembly.1.gz
-rw-r--r-- root/root       845 2013-06-14 14:48 ./usr/share/man/man1/gt-readjoiner-overlap.1.gz
-rw-r--r-- root/root       948 2013-06-14 14:48 ./usr/share/man/man1/gt-readjoiner-prefilter.1.gz
-rw-r--r-- root/root       665 2013-06-14 14:48 ./usr/share/man/man1/gt-readjoiner.1.gz
-rw-r--r-- root/root       749 2013-06-14 14:48 ./usr/share/man/man1/gt-repfind.1.gz
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-rw-r--r-- root/root      1708 2013-06-14 14:48 ./usr/share/man/man1/gt-select.1.gz
-rw-r--r-- root/root       909 2013-06-14 14:48 ./usr/share/man/man1/gt-seq.1.gz
-rw-r--r-- root/root       847 2013-06-14 14:48 ./usr/share/man/man1/gt-seqfilter.1.gz
-rw-r--r-- root/root       613 2013-06-14 14:48 ./usr/share/man/man1/gt-seqids.1.gz
-rw-r--r-- root/root      1113 2013-06-14 14:48 ./usr/share/man/man1/gt-seqmutate.1.gz
-rw-r--r-- root/root       719 2013-06-14 14:48 ./usr/share/man/man1/gt-seqorder.1.gz
-rw-r--r-- root/root       814 2013-06-14 14:48 ./usr/share/man/man1/gt-seqstat.1.gz
-rw-r--r-- root/root       831 2013-06-14 14:48 ./usr/share/man/man1/gt-seqtransform.1.gz
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-rw-r--r-- root/root       820 2013-06-14 14:48 ./usr/share/man/man1/gt-sequniq.1.gz
-rw-r--r-- root/root      1245 2013-06-14 14:48 ./usr/share/man/man1/gt-shredder.1.gz
-rw-r--r-- root/root       714 2013-06-14 14:48 ./usr/share/man/man1/gt-shulengthdist.1.gz
-rw-r--r-- root/root       914 2013-06-14 14:48 ./usr/share/man/man1/gt-simreads.1.gz
-rw-r--r-- root/root      1035 2013-06-14 14:48 ./usr/share/man/man1/gt-sketch.1.gz
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-rw-r--r-- root/root      1355 2013-06-14 14:48 ./usr/share/man/man1/gt-splicesiteinfo.1.gz
-rw-r--r-- root/root       797 2013-06-14 14:48 ./usr/share/man/man1/gt-splitfasta.1.gz
-rw-r--r-- root/root       912 2013-06-14 14:48 ./usr/share/man/man1/gt-stat.1.gz
-rw-r--r-- root/root      1378 2013-06-14 14:48 ./usr/share/man/man1/gt-suffixerator.1.gz
-rw-r--r-- root/root      1187 2013-06-14 14:48 ./usr/share/man/man1/gt-tagerator.1.gz
-rw-r--r-- root/root       969 2013-06-14 14:48 ./usr/share/man/man1/gt-tallymer-mkindex.1.gz
-rw-r--r-- root/root       946 2013-06-14 14:48 ./usr/share/man/man1/gt-tallymer-occratio.1.gz
-rw-r--r-- root/root       837 2013-06-14 14:48 ./usr/share/man/man1/gt-tallymer-search.1.gz
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-rw-r--r-- root/root      1104 2013-06-14 14:48 ./usr/share/man/man1/gt-uniq.1.gz
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-rw-r--r-- root/root      1240 2013-06-14 14:48 ./usr/share/man/man1/gt.1.gz


libgenometools0_1.5.1-1_armhf.deb
─────────────────────────────────

 new debian package, version 2.0.
 size 1957482 bytes: control archive=1504 bytes.
    1025 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: 1.5.1-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 4822
 Depends: libbz2-1.0, libc6 (>= 2.13-28), libcairo2 (>= 1.2.4), libexpat1 (>= 2.0.1), libgcc1 (>= 1:4.4.0), 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), 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 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 2013-06-14 14:48 ./
drwxr-xr-x root/root         0 2013-06-14 14:47 ./usr/
drwxr-xr-x root/root         0 2013-06-14 14:48 ./usr/lib/
-rw-r--r-- root/root   4923476 2013-06-14 14:48 ./usr/lib/libgenometools.so.0
drwxr-xr-x root/root         0 2013-06-14 14:47 ./usr/share/
drwxr-xr-x root/root         0 2013-06-14 14:47 ./usr/share/doc/
drwxr-xr-x root/root         0 2013-06-14 14:48 ./usr/share/doc/libgenometools0/
-rw-r--r-- root/root      6607 2013-03-07 13:07 ./usr/share/doc/libgenometools0/copyright
-rw-r--r-- root/root       932 2013-03-07 13:09 ./usr/share/doc/libgenometools0/changelog.Debian.gz
-rw-r--r-- root/root      4081 2013-03-07 12:25 ./usr/share/doc/libgenometools0/changelog.gz


libgenometools0-dev_1.5.1-1_armhf.deb
─────────────────────────────────────

 new debian package, version 2.0.
 size 82926 bytes: control archive=4728 bytes.
     672 bytes,    18 lines      control              
   12257 bytes,   146 lines      md5sums              
 Package: libgenometools0-dev
 Source: genometools
 Version: 1.5.1-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 422
 Depends: libgenometools0 (= 1.5.1-1)
 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 2013-06-14 14:47 ./usr/include/
drwxr-xr-x root/root         0 2013-06-14 14:47 ./usr/include/genometools/
drwxr-xr-x root/root         0 2013-06-14 14:47 ./usr/include/genometools/core/
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-rw-r--r-- root/root      1585 2013-06-14 14:47 ./usr/include/genometools/core/codon_iterator_simple_api.h
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-rw-r--r-- root/root      3095 2013-06-14 14:47 ./usr/include/genometools/core/dlist_api.h
-rw-r--r-- root/root     32357 2013-06-14 14:47 ./usr/include/genometools/core/encseq_api.h
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-rw-r--r-- root/root     10127 2013-06-14 14:47 ./usr/include/genometools/annotationsketch/graphics_api.h
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-rw-r--r-- root/root      3971 2013-06-14 14:47 ./usr/include/genometools/annotationsketch/layout_api.h
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drwxr-xr-x root/root         0 2013-06-14 14:47 ./usr/include/genometools/ltr/
-rw-r--r-- root/root      1476 2013-06-14 14:47 ./usr/include/genometools/ltr/ltr_classify_stream_api.h
-rw-r--r-- root/root      2142 2013-06-14 14:47 ./usr/include/genometools/ltr/ltr_cluster_stream_api.h
-rw-r--r-- root/root      1754 2013-06-14 14:47 ./usr/include/genometools/ltr/ltr_orf_annotator_stream_api.h
-rw-r--r-- root/root      2669 2013-06-14 14:47 ./usr/include/genometools/ltr/ltr_refseq_match_stream_api.h
-rw-r--r-- root/root      2034 2013-06-14 14:47 ./usr/include/genometools/gt_config.h
-rw-r--r-- root/root      6280 2013-06-14 14:47 ./usr/include/genometools/genometools.h
drwxr-xr-x root/root         0 2013-06-14 14:47 ./usr/share/
drwxr-xr-x root/root         0 2013-06-14 14:47 ./usr/share/doc/
drwxr-xr-x root/root         0 2013-06-14 14:48 ./usr/share/doc/libgenometools0-dev/
-rw-r--r-- root/root      6607 2013-03-07 13:07 ./usr/share/doc/libgenometools0-dev/copyright
-rw-r--r-- root/root       932 2013-03-07 13:09 ./usr/share/doc/libgenometools0-dev/changelog.Debian.gz
-rw-r--r-- root/root      4081 2013-03-07 12:25 ./usr/share/doc/libgenometools0-dev/changelog.gz
drwxr-xr-x root/root         0 2013-06-14 14:48 ./usr/lib/
lrwxrwxrwx root/root         0 2013-06-14 14:48 ./usr/lib/libgenometools.so -> libgenometools.so.0


genometools-dbg_1.5.1-1_armhf.deb
─────────────────────────────────

 new debian package, version 2.0.
 size 5158142 bytes: control archive=754 bytes.
     571 bytes,    14 lines      control              
     447 bytes,     5 lines      md5sums              
 Package: genometools-dbg
 Source: genometools
 Version: 1.5.1-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 5912
 Depends: genometools (= 1.5.1-1) | libgenometools0 (= 1.5.1-1)
 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 2013-06-14 14:48 ./
drwxr-xr-x root/root         0 2013-06-14 14:48 ./usr/
drwxr-xr-x root/root         0 2013-06-14 14:47 ./usr/share/
drwxr-xr-x root/root         0 2013-06-14 14:47 ./usr/share/doc/
drwxr-xr-x root/root         0 2013-06-14 14:48 ./usr/share/doc/genometools-dbg/
-rw-r--r-- root/root      6607 2013-03-07 13:07 ./usr/share/doc/genometools-dbg/copyright
-rw-r--r-- root/root       932 2013-03-07 13:09 ./usr/share/doc/genometools-dbg/changelog.Debian.gz
-rw-r--r-- root/root      4081 2013-03-07 12:25 ./usr/share/doc/genometools-dbg/changelog.gz
drwxr-xr-x root/root         0 2013-06-14 14:48 ./usr/lib/
drwxr-xr-x root/root         0 2013-06-14 14:48 ./usr/lib/debug/
drwxr-xr-x root/root         0 2013-06-14 14:48 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2013-06-14 14:48 ./usr/lib/debug/.build-id/64/
-rw-r--r-- root/root   3040627 2013-06-14 14:48 ./usr/lib/debug/.build-id/64/8197783e33136d973316c78e69ec2c6a93f3c4.debug
drwxr-xr-x root/root         0 2013-06-14 14:48 ./usr/lib/debug/.build-id/ac/
-rw-r--r-- root/root   3000445 2013-06-14 14:48 ./usr/lib/debug/.build-id/ac/f351a8fce55627a51b9e8ed421936f60617828.debug


python-genometools_1.5.1-1_armhf.deb
────────────────────────────────────

 new debian package, version 2.0.
 size 31754 bytes: control archive=2420 bytes.
     672 bytes,    15 lines      control              
    4576 bytes,    57 lines      md5sums              
     168 bytes,     9 lines   *  postinst             #!/bin/sh
     273 bytes,    14 lines   *  prerm                #!/bin/sh
 Package: python-genometools
 Source: genometools
 Version: 1.5.1-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 172
 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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│ Post Build                                                                   │
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│ Cleanup                                                                      │
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Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use

┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary                                                                      │
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Build Architecture: armhf
Build-Space: 219928
Build-Time: 533
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 1155
Job: genometools_1.5.1-1
Machine Architecture: armhf
Package: genometools
Package-Time: 1770
Source-Version: 1.5.1-1
Space: 219928
Status: successful
Version: 1.5.1-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20130614-1449
Build needed 00:29:30, 219928k disc space
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Build log for genometools (1.5.1-1) on armhf
