genometools →
1.5.1-2 →
armhf → 2013-11-03 06:00:53
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on testbuildd.raspbian.org
╔══════════════════════════════════════════════════════════════════════════════╗
║ genometools 1.5.1-2 (armhf) 03 Nov 2013 05:28 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: genometools
Version: 1.5.1-2
Source Version: 1.5.1-2
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/genometools-DGakGg/genometools-1.5.1' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/genometools-DGakGg' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-1c636174-96ee-41c4-8a30-8e7a9c6e6d1e' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [6958 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8086 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 15.1 MB in 36s (410 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
─────────
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 1.5.1-2 (dsc) [2029 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main genometools 1.5.1-2 (tar) [12.1 MB]
Get:3 http://172.17.0.1/private/ jessie-staging/main genometools 1.5.1-2 (diff) [70.0 kB]
Fetched 12.2 MB in 7s (1605 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-VoE6w9/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 6 not upgraded.
Need to get 0 B/704 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 ... 12159 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: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), liblua5.1-0-dev, lua-md5-dev, lua-filesystem-dev, lua-lpeg-dev, libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, libncurses5-dev, libsqlite3-dev, libbam-dev, libpango1.0-dev, texlive-latex-base, texlive-latex-extra, texlive-fonts-extra, latex-xcolor, texlive-fonts-recommended, python
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), liblua5.1-0-dev, lua-md5-dev, lua-filesystem-dev, lua-lpeg-dev, libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, libncurses5-dev, libsqlite3-dev, libbam-dev, libpango1.0-dev, 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-IbiXr7/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 file fontconfig fontconfig-config fonts-cabin
fonts-comfortaa fonts-dejavu-core fonts-dejavu-extra fonts-droid
fonts-font-awesome fonts-freefont-otf fonts-freefont-ttf fonts-gfs-artemisia
fonts-gfs-complutum fonts-gfs-didot fonts-gfs-neohellenic fonts-gfs-olga
fonts-gfs-solomos fonts-inconsolata fonts-junicode fonts-lato
fonts-linuxlibertine fonts-oflb-asana-math fonts-sil-gentium
fonts-sil-gentium-basic fonts-stix gettext gettext-base gir1.2-freedesktop
gir1.2-glib-2.0 gir1.2-pango-1.0 groff-base intltool-debian latex-xcolor
libasprintf0c2 libavahi-client3 libavahi-common-data libavahi-common3
libbam-dev libbz2-dev libcairo-gobject2 libcairo-script-interpreter2
libcairo2 libcairo2-dev libcroco3 libcups2 libcupsfilters1 libcupsimage2
libdatrie1 libdrm-dev libdrm-nouveau2 libdrm-omap1 libdrm-radeon1 libdrm2
libegl1-mesa libegl1-mesa-dev libegl1-mesa-drivers libelfg0 libexpat1
libexpat1-dev libffi6 libfontconfig1 libfontconfig1-dev libfreetype6
libfreetype6-dev libgbm1 libgcrypt11 libgirepository-1.0-1 libgl1-mesa-dev
libgl1-mesa-glx libglapi-mesa libglib2.0-0 libglib2.0-bin libglib2.0-data
libglib2.0-dev libgnutls26 libgpg-error0 libgraphite2-3 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 libllvm3.3 liblua5.1-0 liblua5.1-0-dev liblzo2-2
libmagic1 libncurses5-dev libopenjpeg2 libopenvg1-mesa libp11-kit0
libpango-1.0-0 libpango1.0-dev libpangocairo-1.0-0 libpangoft2-1.0-0
libpangoxft-1.0-0 libpaper-utils libpaper1 libpcre3-dev libpcrecpp0
libpipeline1 libpixman-1-0 libpixman-1-dev libpng12-0 libpng12-dev
libpoppler19 libpopt0 libptexenc1 libpthread-stubs0-dev libpython-stdlib
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 libwayland-client0
libwayland-server0 libx11-6 libx11-data libx11-dev libx11-xcb-dev
libx11-xcb1 libxau-dev libxau6 libxaw7 libxcb-dri2-0 libxcb-dri2-0-dev
libxcb-glx0 libxcb-glx0-dev libxcb-render0 libxcb-render0-dev libxcb-shape0
libxcb-shm0 libxcb-shm0-dev libxcb-xfixes0 libxcb1 libxcb1-dev
libxdamage-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6
libxfixes-dev libxfixes3 libxft-dev libxft2 libxml2 libxmu6 libxpm4
libxrender-dev libxrender1 libxt6 libxxf86vm-dev libxxf86vm1 lua-filesystem
lua-filesystem-dev lua-lpeg lua-lpeg-dev lua-md5 lua-md5-dev luatex man-db
mesa-common-dev mime-support 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-fonts-extra
texlive-fonts-recommended texlive-latex-base texlive-latex-extra
texlive-latex-recommended texlive-pictures ttf-dejavu-core ttf-freefont ucf
x11-common x11proto-core-dev x11proto-damage-dev x11proto-dri2-dev
x11proto-fixes-dev x11proto-gl-dev x11proto-input-dev x11proto-kb-dev
x11proto-render-dev x11proto-xext-dev x11proto-xf86vidmode-dev xdg-utils
xorg-sgml-doctools xtrans-dev 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 gv postscript-viewer
perl-tk xpdf-reader pdf-viewer cm-super libfile-which-perl dot2tex
libtcltk-ruby gvfs-bin
Recommended packages:
texlive-xetex curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libgl1-mesa-dri shared-mime-info krb5-locales libtool libx11-doc xml-core
texlive-luatex libmail-sendmail-perl lmodern ruby wish
texlive-fonts-extra-doc tex-gyre texlive-fonts-recommended-doc tipa
texlive-latex-base-doc texlive-latex-extra-doc latex-beamer
texlive-latex-recommended-doc 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 file fontconfig fontconfig-config fonts-cabin
fonts-comfortaa fonts-dejavu-core fonts-dejavu-extra fonts-droid
fonts-font-awesome fonts-freefont-otf fonts-freefont-ttf fonts-gfs-artemisia
fonts-gfs-complutum fonts-gfs-didot fonts-gfs-neohellenic fonts-gfs-olga
fonts-gfs-solomos fonts-inconsolata fonts-junicode fonts-lato
fonts-linuxlibertine fonts-oflb-asana-math fonts-sil-gentium
fonts-sil-gentium-basic fonts-stix gettext gettext-base gir1.2-freedesktop
gir1.2-glib-2.0 gir1.2-pango-1.0 groff-base intltool-debian latex-xcolor
libasprintf0c2 libavahi-client3 libavahi-common-data libavahi-common3
libbam-dev libbz2-dev libcairo-gobject2 libcairo-script-interpreter2
libcairo2 libcairo2-dev libcroco3 libcups2 libcupsfilters1 libcupsimage2
libdatrie1 libdrm-dev libdrm-nouveau2 libdrm-omap1 libdrm-radeon1 libdrm2
libegl1-mesa libegl1-mesa-dev libegl1-mesa-drivers libelfg0 libexpat1
libexpat1-dev libffi6 libfontconfig1 libfontconfig1-dev libfreetype6
libfreetype6-dev libgbm1 libgcrypt11 libgirepository-1.0-1 libgl1-mesa-dev
libgl1-mesa-glx libglapi-mesa libglib2.0-0 libglib2.0-bin libglib2.0-data
libglib2.0-dev libgnutls26 libgpg-error0 libgraphite2-3 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 libllvm3.3 liblua5.1-0 liblua5.1-0-dev liblzo2-2
libmagic1 libncurses5-dev libopenjpeg2 libopenvg1-mesa libp11-kit0
libpango-1.0-0 libpango1.0-dev libpangocairo-1.0-0 libpangoft2-1.0-0
libpangoxft-1.0-0 libpaper-utils libpaper1 libpcre3-dev libpcrecpp0
libpipeline1 libpixman-1-0 libpixman-1-dev libpng12-0 libpng12-dev
libpoppler19 libpopt0 libptexenc1 libpthread-stubs0-dev libpython-stdlib
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 libwayland-client0
libwayland-server0 libx11-6 libx11-data libx11-dev libx11-xcb-dev
libx11-xcb1 libxau-dev libxau6 libxaw7 libxcb-dri2-0 libxcb-dri2-0-dev
libxcb-glx0 libxcb-glx0-dev libxcb-render0 libxcb-render0-dev libxcb-shape0
libxcb-shm0 libxcb-shm0-dev libxcb-xfixes0 libxcb1 libxcb1-dev
libxdamage-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6
libxfixes-dev libxfixes3 libxft-dev libxft2 libxml2 libxmu6 libxpm4
libxrender-dev libxrender1 libxt6 libxxf86vm-dev libxxf86vm1 lua-filesystem
lua-filesystem-dev lua-lpeg lua-lpeg-dev lua-md5 lua-md5-dev luatex man-db
mesa-common-dev 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-fonts-extra texlive-fonts-recommended
texlive-latex-base texlive-latex-extra texlive-latex-recommended
texlive-pictures ttf-dejavu-core ttf-freefont ucf x11-common
x11proto-core-dev x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev
x11proto-gl-dev x11proto-input-dev x11proto-kb-dev x11proto-render-dev
x11proto-xext-dev x11proto-xf86vidmode-dev xdg-utils xorg-sgml-doctools
xtrans-dev zlib1g-dev
0 upgraded, 231 newly installed, 0 to remove and 6 not upgraded.
Need to get 297 MB/297 MB of archives.
After this operation, 823 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.2.4-1 [36.9 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main libpopt0 armhf 1.16-7 [56.5 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main libssl1.0.0 armhf 1.0.1e-3+rpi1 [1039 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-3 [666 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.5-2 [949 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3.1-1 [29.4 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libgpg-error0 armhf 1.12-0.2 [78.9 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libgcrypt11 armhf 1.5.3-2 [296 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libp11-kit0 armhf 0.18.5-3 [110 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main libtasn1-3 armhf 2.14-3 [64.1 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main libgnutls26 armhf 2.12.23-8 [596 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main libkeyutils1 armhf 1.5.6-1 [7900 B]
Get:14 http://172.17.0.1/private/ jessie-staging/main libkrb5support0 armhf 1.11.3+dfsg-3 [55.3 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main libk5crypto3 armhf 1.11.3+dfsg-3 [134 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main libkrb5-3 armhf 1.11.3+dfsg-3 [340 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main libgssapi-krb5-2 armhf 1.11.3+dfsg-3 [146 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main libidn11 armhf 1.28-1 [181 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.14-2 [213 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main libsqlite3-0 armhf 3.8.0.2-1 [397 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-3 [836 kB]
Get:22 http://172.17.0.1/private/ jessie-staging/main libpython2.7-minimal armhf 2.7.5-8+rvt [540 kB]
Get:23 http://172.17.0.1/private/ jessie-staging/main python2.7-minimal armhf 2.7.5-8+rvt [1492 kB]
Get:24 http://172.17.0.1/private/ jessie-staging/main fonts-droid all 1:4.3-1 [3039 kB]
Get:25 http://172.17.0.1/private/ jessie-staging/main fonts-junicode all 0.7.8-1 [1239 kB]
Get:26 http://172.17.0.1/private/ jessie-staging/main fonts-lato all 1.104-4 [244 kB]
Get:27 http://172.17.0.1/private/ jessie-staging/main libavahi-common-data armhf 0.6.31-2 [137 kB]
Get:28 http://172.17.0.1/private/ jessie-staging/main libavahi-common3 armhf 0.6.31-2 [52.6 kB]
Get:29 http://172.17.0.1/private/ jessie-staging/main libavahi-client3 armhf 0.6.31-2 [55.4 kB]
Get:30 http://172.17.0.1/private/ jessie-staging/main libdrm2 armhf 2.4.46-3 [466 kB]
Get:31 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.0.13-4 [19.8 kB]
Get:32 http://172.17.0.1/private/ jessie-staging/main libglapi-mesa armhf 9.2.2-1 [63.2 kB]
Get:33 http://172.17.0.1/private/ jessie-staging/main libllvm3.3 armhf 1:3.3-9 [8354 kB]
Get:34 http://172.17.0.1/private/ jessie-staging/main libwayland-client0 armhf 1.3.0-1 [20.9 kB]
Get:35 http://172.17.0.1/private/ jessie-staging/main libwayland-server0 armhf 1.3.0-1 [25.2 kB]
Get:36 http://172.17.0.1/private/ jessie-staging/main libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:37 http://172.17.0.1/private/ jessie-staging/main libxdmcp6 armhf 1:1.1.1-1 [24.6 kB]
Get:38 http://172.17.0.1/private/ jessie-staging/main libxcb1 armhf 1.9.1-3 [43.3 kB]
Get:39 http://172.17.0.1/private/ jessie-staging/main libxcb-dri2-0 armhf 1.9.1-3 [12.1 kB]
Get:40 http://172.17.0.1/private/ jessie-staging/main libgbm1 armhf 9.2.2-1 [418 kB]
Get:41 http://172.17.0.1/private/ jessie-staging/main libx11-data all 2:1.6.2-1 [125 kB]
Get:42 http://172.17.0.1/private/ jessie-staging/main libx11-6 armhf 2:1.6.2-1 [867 kB]
Get:43 http://172.17.0.1/private/ jessie-staging/main libx11-xcb1 armhf 2:1.6.2-1 [163 kB]
Get:44 http://172.17.0.1/private/ jessie-staging/main libxcb-render0 armhf 1.9.1-3 [16.8 kB]
Get:45 http://172.17.0.1/private/ jessie-staging/main libxcb-shape0 armhf 1.9.1-3 [10.9 kB]
Get:46 http://172.17.0.1/private/ jessie-staging/main libxcb-xfixes0 armhf 1.9.1-3 [13.8 kB]
Get:47 http://172.17.0.1/private/ jessie-staging/main libegl1-mesa armhf 9.2.2-1 [74.6 kB]
Get:48 http://172.17.0.1/private/ jessie-staging/main libexpat1 armhf 2.1.0-4 [117 kB]
Get:49 http://172.17.0.1/private/ jessie-staging/main libfreetype6 armhf 2.4.9-1.1 [401 kB]
Get:50 http://172.17.0.1/private/ jessie-staging/main ucf all 3.0027+nmu1 [70.6 kB]
Get:51 http://172.17.0.1/private/ jessie-staging/main fonts-dejavu-core all 2.33+svn2514-3 [1042 kB]
Get:52 http://172.17.0.1/private/ jessie-staging/main ttf-dejavu-core all 2.33+svn2514-3 [29.8 kB]
Get:53 http://172.17.0.1/private/ jessie-staging/main fonts-freefont-ttf all 20120503-1 [6024 kB]
Get:54 http://172.17.0.1/private/ jessie-staging/main ttf-freefont all 20120503-1 [118 kB]
Get:55 http://172.17.0.1/private/ jessie-staging/main fontconfig-config all 2.11.0-1 [269 kB]
Get:56 http://172.17.0.1/private/ jessie-staging/main libfontconfig1 armhf 2.11.0-1 [330 kB]
Get:57 http://172.17.0.1/private/ jessie-staging/main libxcb-glx0 armhf 1.9.1-3 [27.6 kB]
Get:58 http://172.17.0.1/private/ jessie-staging/main libxfixes3 armhf 1:5.0.1-1 [21.0 kB]
Get:59 http://172.17.0.1/private/ jessie-staging/main libxdamage1 armhf 1:1.1.4-1 [14.6 kB]
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Get:61 http://172.17.0.1/private/ jessie-staging/main libxxf86vm1 armhf 1:1.1.3-1 [20.0 kB]
Get:62 http://172.17.0.1/private/ jessie-staging/main libgl1-mesa-glx armhf 9.2.2-1 [128 kB]
Get:63 http://172.17.0.1/private/ jessie-staging/main libpixman-1-0 armhf 0.30.2-1 [446 kB]
Get:64 http://172.17.0.1/private/ jessie-staging/main libpng12-0 armhf 1.2.49-5 [179 kB]
Get:65 http://172.17.0.1/private/ jessie-staging/main libxcb-shm0 armhf 1.9.1-3 [10.4 kB]
Get:66 http://172.17.0.1/private/ jessie-staging/main libxrender1 armhf 1:0.9.8-1 [30.4 kB]
Get:67 http://172.17.0.1/private/ jessie-staging/main libcairo2 armhf 1.12.16-2 [998 kB]
Get:68 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.36.4-1 [1907 kB]
Get:69 http://172.17.0.1/private/ jessie-staging/main libcairo-gobject2 armhf 1.12.16-2 [540 kB]
Get:70 http://172.17.0.1/private/ jessie-staging/main liblzo2-2 armhf 2.06-1.2 [55.9 kB]
Get:71 http://172.17.0.1/private/ jessie-staging/main libcairo-script-interpreter2 armhf 1.12.16-2 [575 kB]
Get:72 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
Get:73 http://172.17.0.1/private/ jessie-staging/main libcups2 armhf 1.6.3-1+rpi1 [263 kB]
Get:74 http://172.17.0.1/private/ jessie-staging/main libcupsimage2 armhf 1.6.3-1+rpi1 [107 kB]
Get:75 http://172.17.0.1/private/ jessie-staging/main libjpeg8 armhf 8d-1 [132 kB]
Get:76 http://172.17.0.1/private/ jessie-staging/main libjbig0 armhf 2.0-2 [31.5 kB]
Get:77 http://172.17.0.1/private/ jessie-staging/main libtiff4 armhf 3.9.7-2 [188 kB]
Get:78 http://172.17.0.1/private/ jessie-staging/main libcupsfilters1 armhf 1.0.34-3+b1 [82.2 kB]
Get:79 http://172.17.0.1/private/ jessie-staging/main libdatrie1 armhf 0.2.7.1-1 [28.1 kB]
Get:80 http://172.17.0.1/private/ jessie-staging/main libdrm-nouveau2 armhf 2.4.46-3 [460 kB]
Get:81 http://172.17.0.1/private/ jessie-staging/main libdrm-omap1 armhf 2.4.46-3 [451 kB]
Get:82 http://172.17.0.1/private/ jessie-staging/main libdrm-radeon1 armhf 2.4.46-3 [468 kB]
Get:83 http://172.17.0.1/private/ jessie-staging/main libopenvg1-mesa armhf 9.2.2-1 [41.9 kB]
Get:84 http://172.17.0.1/private/ jessie-staging/main libegl1-mesa-drivers armhf 9.2.2-1 [1934 kB]
Get:85 http://172.17.0.1/private/ jessie-staging/main libgraphite2-3 armhf 1.2.3-1 [55.0 kB]
Get:86 http://172.17.0.1/private/ jessie-staging/main libharfbuzz0a armhf 0.9.19-1 [432 kB]
Get:87 http://172.17.0.1/private/ jessie-staging/main libicu48 armhf 4.8.1.1-13+nmu1 [4516 kB]
Get:88 http://172.17.0.1/private/ jessie-staging/main libharfbuzz-icu0 armhf 0.9.19-1 [299 kB]
Get:89 http://172.17.0.1/private/ jessie-staging/main x11-common all 1:7.7+4 [282 kB]
Get:90 http://172.17.0.1/private/ jessie-staging/main libice6 armhf 2:1.0.8-2 [56.2 kB]
Get:91 http://172.17.0.1/private/ jessie-staging/main libjasper1 armhf 1.900.1-14 [141 kB]
Get:92 http://172.17.0.1/private/ jessie-staging/main liblcms1 armhf 1.19.dfsg-1.2 [98.5 kB]
Get:93 http://172.17.0.1/private/ jessie-staging/main liblcms2-2 armhf 2.2+git20110628-2.3 [124 kB]
Get:94 http://172.17.0.1/private/ jessie-staging/main liblua5.1-0 armhf 5.1.5-5 [146 kB]
Get:95 http://172.17.0.1/private/ jessie-staging/main libthai-data all 0.1.19-2 [156 kB]
Get:96 http://172.17.0.1/private/ jessie-staging/main libthai0 armhf 0.1.19-2 [40.5 kB]
Get:97 http://172.17.0.1/private/ jessie-staging/main fontconfig armhf 2.11.0-1 [407 kB]
Get:98 http://172.17.0.1/private/ jessie-staging/main libpango-1.0-0 armhf 1.32.5-5 [251 kB]
Get:99 http://172.17.0.1/private/ jessie-staging/main libpangoft2-1.0-0 armhf 1.32.5-5 [186 kB]
Get:100 http://172.17.0.1/private/ jessie-staging/main libpangocairo-1.0-0 armhf 1.32.5-5 [176 kB]
Get:101 http://172.17.0.1/private/ jessie-staging/main libxft2 armhf 2.3.1-1 [55.4 kB]
Get:102 http://172.17.0.1/private/ jessie-staging/main libpangoxft-1.0-0 armhf 1.32.5-5 [171 kB]
Get:103 http://172.17.0.1/private/ jessie-staging/main libpaper1 armhf 1.1.24+nmu2 [20.9 kB]
Get:104 http://172.17.0.1/private/ jessie-staging/main libpcrecpp0 armhf 1:8.31-2 [125 kB]
Get:105 http://172.17.0.1/private/ jessie-staging/main libopenjpeg2 armhf 1.3+dfsg-4.6 [75.9 kB]
Get:106 http://172.17.0.1/private/ jessie-staging/main libpoppler19 armhf 0.18.4-8 [990 kB]
Get:107 http://172.17.0.1/private/ jessie-staging/main libsm6 armhf 2:1.2.1-2 [32.5 kB]
Get:108 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:109 http://172.17.0.1/private/ jessie-staging/main libxt6 armhf 1:1.1.4-1 [183 kB]
Get:110 http://172.17.0.1/private/ jessie-staging/main libxmu6 armhf 2:1.1.1-1 [59.1 kB]
Get:111 http://172.17.0.1/private/ jessie-staging/main libxpm4 armhf 1:3.5.10-1 [44.9 kB]
Get:112 http://172.17.0.1/private/ jessie-staging/main libxaw7 armhf 2:1.0.11-1 [195 kB]
Get:113 http://172.17.0.1/private/ jessie-staging/main lua-filesystem armhf 1.6.2-1 [11.8 kB]
Get:114 http://172.17.0.1/private/ jessie-staging/main lua-filesystem-dev armhf 1.6.2-1 [25.6 kB]
Get:115 http://172.17.0.1/private/ jessie-staging/main lua-lpeg armhf 0.12-1 [38.8 kB]
Get:116 http://172.17.0.1/private/ jessie-staging/main lua-lpeg-dev armhf 0.12-1 [61.5 kB]
Get:117 http://172.17.0.1/private/ jessie-staging/main lua-md5 armhf 1.1.2+gitdef7fa6-1 [12.9 kB]
Get:118 http://172.17.0.1/private/ jessie-staging/main lua-md5-dev armhf 1.1.2+gitdef7fa6-1 [21.6 kB]
Get:119 http://172.17.0.1/private/ jessie-staging/main poppler-data all 0.4.6-4 [1481 kB]
Get:120 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.14-2 [53.8 kB]
Get:121 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.3.1-1 [136 kB]
Get:122 http://172.17.0.1/private/ jessie-staging/main mime-support all 3.54 [36.4 kB]
Get:123 http://172.17.0.1/private/ jessie-staging/main libpython2.7-stdlib armhf 2.7.5-8+rvt [2477 kB]
Get:124 http://172.17.0.1/private/ jessie-staging/main python2.7 armhf 2.7.5-8+rvt [233 kB]
Get:125 http://172.17.0.1/private/ jessie-staging/main python-minimal armhf 2.7.5-5 [43.1 kB]
Get:126 http://172.17.0.1/private/ jessie-staging/main libpython-stdlib armhf 2.7.5-5 [19.8 kB]
Get:127 http://172.17.0.1/private/ jessie-staging/main python armhf 2.7.5-5 [180 kB]
Get:128 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.3.1-1 [1837 kB]
Get:129 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:130 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:131 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20130921 [688 kB]
Get:132 http://172.17.0.1/private/ jessie-staging/main fonts-cabin all 1.5-2 [139 kB]
Get:133 http://172.17.0.1/private/ jessie-staging/main fonts-comfortaa all 2.003-1 [133 kB]
Get:134 http://172.17.0.1/private/ jessie-staging/main fonts-dejavu-extra all 2.33+svn2514-3 [1758 kB]
Get:135 http://172.17.0.1/private/ jessie-staging/main fonts-font-awesome all 3.2.1~dfsg-2 [244 kB]
Get:136 http://172.17.0.1/private/ jessie-staging/main fonts-freefont-otf all 20120503-1 [4428 kB]
Get:137 http://172.17.0.1/private/ jessie-staging/main fonts-gfs-artemisia all 1.1-5 [259 kB]
Get:138 http://172.17.0.1/private/ jessie-staging/main fonts-gfs-complutum all 1.1-5 [47.9 kB]
Get:139 http://172.17.0.1/private/ jessie-staging/main fonts-gfs-didot all 1.1-5 [371 kB]
Get:140 http://172.17.0.1/private/ jessie-staging/main fonts-gfs-neohellenic all 1.1-4 [282 kB]
Get:141 http://172.17.0.1/private/ jessie-staging/main fonts-gfs-olga all 1.1-3 [36.0 kB]
Get:142 http://172.17.0.1/private/ jessie-staging/main fonts-gfs-solomos all 1.1-5 [40.6 kB]
Get:143 http://172.17.0.1/private/ jessie-staging/main fonts-inconsolata all 001.010-4 [65.6 kB]
Get:144 http://172.17.0.1/private/ jessie-staging/main fonts-linuxlibertine all 5.3.0-2 [1713 kB]
Get:145 http://172.17.0.1/private/ jessie-staging/main fonts-oflb-asana-math all 000.907-4 [297 kB]
Get:146 http://172.17.0.1/private/ jessie-staging/main fonts-sil-gentium all 20081126:1.02-12 [685 kB]
Get:147 http://172.17.0.1/private/ jessie-staging/main fonts-sil-gentium-basic all 1.1-5 [871 kB]
Get:148 http://172.17.0.1/private/ jessie-staging/main libgirepository-1.0-1 armhf 1.36.0-2 [97.0 kB]
Get:149 http://172.17.0.1/private/ jessie-staging/main gir1.2-glib-2.0 armhf 1.36.0-2 [177 kB]
Get:150 http://172.17.0.1/private/ jessie-staging/main gir1.2-freedesktop armhf 1.36.0-2 [20.7 kB]
Get:151 http://172.17.0.1/private/ jessie-staging/main gir1.2-pango-1.0 armhf 1.32.5-5 [178 kB]
Get:152 http://172.17.0.1/private/ jessie-staging/main libijs-0.35 armhf 0.35-8 [19.0 kB]
Get:153 http://172.17.0.1/private/ jessie-staging/main libjbig2dec0 armhf 0.11+20120125-1 [46.4 kB]
Get:154 http://172.17.0.1/private/ jessie-staging/main libgs9-common all 9.05~dfsg-8 [1981 kB]
Get:155 http://172.17.0.1/private/ jessie-staging/main libgs9 armhf 9.05~dfsg-8 [1546 kB]
Get:156 http://172.17.0.1/private/ jessie-staging/main libkpathsea6 armhf 2013.20130729.30972-2 [160 kB]
Get:157 http://172.17.0.1/private/ jessie-staging/main libptexenc1 armhf 2013.20130729.30972-2 [55.7 kB]
Get:158 http://172.17.0.1/private/ jessie-staging/main tex-common all 4.04 [639 kB]
Get:159 http://172.17.0.1/private/ jessie-staging/main texlive-binaries armhf 2013.20130729.30972-2 [5951 kB]
Get:160 http://172.17.0.1/private/ jessie-staging/main libpaper-utils armhf 1.1.24+nmu2 [17.9 kB]
Get:161 http://172.17.0.1/private/ jessie-staging/main xdg-utils all 1.1.0~rc1+git20111210-7 [83.7 kB]
Get:162 http://172.17.0.1/private/ jessie-staging/main luatex armhf 0.76.0-3 [3601 kB]
Get:163 http://172.17.0.1/private/ jessie-staging/main texlive-base all 2013.20131010-2 [16.1 MB]
Get:164 http://172.17.0.1/private/ jessie-staging/main texlive-latex-base all 2013.20131010-2 [854 kB]
Get:165 http://172.17.0.1/private/ jessie-staging/main texlive-latex-recommended all 2013.20131010-2 [7100 kB]
Get:166 http://172.17.0.1/private/ jessie-staging/main latex-xcolor all 2.11-1.1 [610 kB]
Get:167 http://172.17.0.1/private/ jessie-staging/main libbam-dev armhf 0.1.19-1 [110 kB]
Get:168 http://172.17.0.1/private/ jessie-staging/main libbz2-dev armhf 1.0.6-5 [33.8 kB]
Get:169 http://172.17.0.1/private/ jessie-staging/main libexpat1-dev armhf 2.1.0-4 [210 kB]
Get:170 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-1 [212 kB]
Get:171 http://172.17.0.1/private/ jessie-staging/main libfreetype6-dev armhf 2.4.9-1.1 [748 kB]
Get:172 http://172.17.0.1/private/ jessie-staging/main pkg-config armhf 0.26-1 [56.9 kB]
Get:173 http://172.17.0.1/private/ jessie-staging/main libfontconfig1-dev armhf 2.11.0-1 [928 kB]
Get:174 http://172.17.0.1/private/ jessie-staging/main xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:175 http://172.17.0.1/private/ jessie-staging/main x11proto-core-dev all 7.0.24-1 [779 kB]
Get:176 http://172.17.0.1/private/ jessie-staging/main libxau-dev armhf 1:1.0.8-1 [23.0 kB]
Get:177 http://172.17.0.1/private/ jessie-staging/main libxdmcp-dev armhf 1:1.1.1-1 [40.8 kB]
Get:178 http://172.17.0.1/private/ jessie-staging/main x11proto-input-dev all 2.3-1 [177 kB]
Get:179 http://172.17.0.1/private/ jessie-staging/main x11proto-kb-dev all 1.0.6-2 [269 kB]
Get:180 http://172.17.0.1/private/ jessie-staging/main xtrans-dev all 1.2.7-1 [112 kB]
Get:181 http://172.17.0.1/private/ jessie-staging/main libpthread-stubs0-dev armhf 0.3-4 [4042 B]
Get:182 http://172.17.0.1/private/ jessie-staging/main libxcb1-dev armhf 1.9.1-3 [98.5 kB]
Get:183 http://172.17.0.1/private/ jessie-staging/main libx11-dev armhf 2:1.6.2-1 [991 kB]
Get:184 http://172.17.0.1/private/ jessie-staging/main x11proto-render-dev all 2:0.11.1-2 [20.8 kB]
Get:185 http://172.17.0.1/private/ jessie-staging/main libxrender-dev armhf 1:0.9.8-1 [38.8 kB]
Get:186 http://172.17.0.1/private/ jessie-staging/main x11proto-xext-dev all 7.2.1-1 [273 kB]
Get:187 http://172.17.0.1/private/ jessie-staging/main libxext-dev armhf 2:1.3.2-1 [110 kB]
Get:188 http://172.17.0.1/private/ jessie-staging/main libpng12-dev armhf 1.2.49-5 [258 kB]
Get:189 http://172.17.0.1/private/ jessie-staging/main libice-dev armhf 2:1.0.8-2 [65.9 kB]
Get:190 http://172.17.0.1/private/ jessie-staging/main libsm-dev armhf 2:1.2.1-2 [35.6 kB]
Get:191 http://172.17.0.1/private/ jessie-staging/main libpixman-1-dev armhf 0.30.2-1 [477 kB]
Get:192 http://172.17.0.1/private/ jessie-staging/main libxcb-render0-dev armhf 1.9.1-3 [25.2 kB]
Get:193 http://172.17.0.1/private/ jessie-staging/main libxcb-shm0-dev armhf 1.9.1-3 [12.0 kB]
Get:194 http://172.17.0.1/private/ jessie-staging/main libdrm-dev armhf 2.4.46-3 [577 kB]
Get:195 http://172.17.0.1/private/ jessie-staging/main mesa-common-dev armhf 9.2.2-1 [276 kB]
Get:196 http://172.17.0.1/private/ jessie-staging/main libx11-xcb-dev armhf 2:1.6.2-1 [165 kB]
Get:197 http://172.17.0.1/private/ jessie-staging/main libxcb-dri2-0-dev armhf 1.9.1-3 [15.5 kB]
Get:198 http://172.17.0.1/private/ jessie-staging/main libxcb-glx0-dev armhf 1.9.1-3 [45.9 kB]
Get:199 http://172.17.0.1/private/ jessie-staging/main x11proto-fixes-dev all 1:5.0-2 [19.2 kB]
Get:200 http://172.17.0.1/private/ jessie-staging/main libxfixes-dev armhf 1:5.0.1-1 [24.1 kB]
Get:201 http://172.17.0.1/private/ jessie-staging/main x11proto-damage-dev all 1:1.2.1-2 [11.8 kB]
Get:202 http://172.17.0.1/private/ jessie-staging/main libxdamage-dev armhf 1:1.1.4-1 [14.3 kB]
Get:203 http://172.17.0.1/private/ jessie-staging/main x11proto-xf86vidmode-dev all 2.3.1-2 [6114 B]
Get:204 http://172.17.0.1/private/ jessie-staging/main libxxf86vm-dev armhf 1:1.1.3-1 [25.5 kB]
Get:205 http://172.17.0.1/private/ jessie-staging/main x11proto-dri2-dev all 2.8-2 [18.2 kB]
Get:206 http://172.17.0.1/private/ jessie-staging/main x11proto-gl-dev all 1.4.16-2 [32.1 kB]
Get:207 http://172.17.0.1/private/ jessie-staging/main libgl1-mesa-dev armhf 9.2.2-1 [35.1 kB]
Get:208 http://172.17.0.1/private/ jessie-staging/main libegl1-mesa-dev armhf 9.2.2-1 [46.6 kB]
Get:209 http://172.17.0.1/private/ jessie-staging/main libelfg0 armhf 0.8.13-3 [56.5 kB]
Get:210 http://172.17.0.1/private/ jessie-staging/main libglib2.0-data all 2.36.4-1 [1847 kB]
Get:211 http://172.17.0.1/private/ jessie-staging/main libglib2.0-bin armhf 2.36.4-1 [1060 kB]
Get:212 http://172.17.0.1/private/ jessie-staging/main libpcre3-dev armhf 1:8.31-2 [350 kB]
Get:213 http://172.17.0.1/private/ jessie-staging/main libglib2.0-dev armhf 2.36.4-1 [2113 kB]
Get:214 http://172.17.0.1/private/ jessie-staging/main libcairo2-dev armhf 1.12.16-2 [1225 kB]
Get:215 http://172.17.0.1/private/ jessie-staging/main libharfbuzz-dev armhf 0.9.19-1 [311 kB]
Get:216 http://172.17.0.1/private/ jessie-staging/main libtinfo-dev armhf 5.9+20130608-1 [92.5 kB]
Get:217 http://172.17.0.1/private/ jessie-staging/main libreadline6-dev armhf 6.2+dfsg-0.1 [164 kB]
Get:218 http://172.17.0.1/private/ jessie-staging/main libreadline-dev armhf 6.2+dfsg-0.1 [898 B]
Get:219 http://172.17.0.1/private/ jessie-staging/main liblua5.1-0-dev armhf 5.1.5-5 [202 kB]
Get:220 http://172.17.0.1/private/ jessie-staging/main libncurses5-dev armhf 5.9+20130608-1 [201 kB]
Get:221 http://172.17.0.1/private/ jessie-staging/main libxft-dev armhf 2.3.1-1 [68.1 kB]
Get:222 http://172.17.0.1/private/ jessie-staging/main libpango1.0-dev armhf 1.32.5-5 [397 kB]
Get:223 http://172.17.0.1/private/ jessie-staging/main libsqlite3-dev armhf 3.8.0.2-1 [512 kB]
Get:224 http://172.17.0.1/private/ jessie-staging/main preview-latex-style all 11.87-1 [317 kB]
Get:225 http://172.17.0.1/private/ jessie-staging/main fonts-stix all 1.1.0-1 [763 kB]
Get:226 http://172.17.0.1/private/ jessie-staging/main otf-freefont all 20120503-1 [118 kB]
Get:227 http://172.17.0.1/private/ jessie-staging/main texlive-fonts-extra all 2013.20131010-1 [155 MB]
Get:228 http://172.17.0.1/private/ jessie-staging/main texlive-fonts-recommended all 2013.20131010-2 [5425 kB]
Get:229 http://172.17.0.1/private/ jessie-staging/main texlive-pictures all 2013.20131010-2 [2408 kB]
Get:230 http://172.17.0.1/private/ jessie-staging/main texlive-latex-extra all 2013.20131010-1 [7083 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 297 MB in 5min 34s (887 kB/s)
Selecting previously unselected package libpipeline1:armhf.
(Reading database ... 12159 files and directories currently installed.)
Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.4-1_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-3+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) ...
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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No schema files found: doing nothing.
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update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
All runlevel operations denied by policy
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Setting up libice6:armhf (2:1.0.8-2) ...
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Regenerating fonts cache... done.
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Creating config file /etc/papersize with new version
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Setting up tex-common (4.04) ...
Running mktexlsr. This may take some time... done.
texlive-base is not ready, delaying updmap-sys call
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texlive-base is not ready, cannot create formats
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Setting up libfreetype6-dev (2.4.9-1.1) ...
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Setting up libxdmcp-dev:armhf (1:1.1.1-1) ...
Setting up x11proto-input-dev (2.3-1) ...
Setting up x11proto-kb-dev (1.0.6-2) ...
Setting up xtrans-dev (1.2.7-1) ...
Setting up libpthread-stubs0-dev:armhf (0.3-4) ...
Setting up libxcb1-dev:armhf (1.9.1-3) ...
Setting up libx11-dev:armhf (2:1.6.2-1) ...
Setting up x11proto-render-dev (2:0.11.1-2) ...
Setting up libxrender-dev:armhf (1:0.9.8-1) ...
Setting up x11proto-xext-dev (7.2.1-1) ...
Setting up libxext-dev:armhf (2:1.3.2-1) ...
Setting up libpng12-dev (1.2.49-5) ...
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 (0.30.2-1) ...
Setting up libxcb-render0-dev:armhf (1.9.1-3) ...
Setting up libxcb-shm0-dev:armhf (1.9.1-3) ...
Setting up libdrm-dev (2.4.46-3) ...
Setting up mesa-common-dev (9.2.2-1) ...
Setting up libx11-xcb-dev (2:1.6.2-1) ...
Setting up libxcb-dri2-0-dev:armhf (1.9.1-3) ...
Setting up libxcb-glx0-dev:armhf (1.9.1-3) ...
Setting up x11proto-fixes-dev (1:5.0-2) ...
Setting up libxfixes-dev (1:5.0.1-1) ...
Setting up x11proto-damage-dev (1:1.2.1-2) ...
Setting up libxdamage-dev (1:1.1.4-1) ...
Setting up x11proto-xf86vidmode-dev (2.3.1-2) ...
Setting up libxxf86vm-dev:armhf (1:1.1.3-1) ...
Setting up x11proto-dri2-dev (2.8-2) ...
Setting up x11proto-gl-dev (1.4.16-2) ...
Setting up libgl1-mesa-dev (9.2.2-1) ...
Setting up libegl1-mesa-dev (9.2.2-1) ...
Setting up libelfg0 (0.8.13-3) ...
Setting up libglib2.0-data (2.36.4-1) ...
Setting up libglib2.0-bin (2.36.4-1) ...
Setting up libpcre3-dev:armhf (1:8.31-2) ...
Setting up libglib2.0-dev (2.36.4-1) ...
Setting up libcairo2-dev (1.12.16-2) ...
Setting up libharfbuzz-dev (0.9.19-1) ...
Setting up libtinfo-dev:armhf (5.9+20130608-1) ...
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 (5.1.5-5) ...
Setting up libncurses5-dev:armhf (5.9+20130608-1) ...
Setting up libxft-dev (2.3.1-1) ...
Setting up libpango1.0-dev (1.32.5-5) ...
Setting up libsqlite3-dev:armhf (3.8.0.2-1) ...
Setting up preview-latex-style (11.87-1) ...
Setting up fonts-stix (1.1.0-1) ...
Setting up otf-freefont (20120503-1) ...
Setting up libcupsimage2:armhf (1.6.3-1+rpi1) ...
Setting up libcupsfilters1:armhf (1.0.34-3+b1) ...
Setting up libgs9 (9.05~dfsg-8) ...
Setting up texlive-binaries (2013.20130729.30972-2) ...
update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
Building format(s) --refresh.
This may take some time... done.
Setting up texlive-base (2013.20131010-2) ...
/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 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-fonts-extra (2013.20131010-1) ...
Setting up texlive-fonts-recommended (2013.20131010-2) ...
Setting up texlive-pictures (2013.20131010-2) ...
Setting up texlive-latex-base (2013.20131010-2) ...
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 (2013.20131010-2) ...
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 (2013.20131010-1) ...
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) ...
Processing triggers for libc-bin ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.11.0-armv7-x13 armhf (armv7l)
Toolchain package versions: binutils_2.23.90.20130927-1 dpkg-dev_1.16.12 g++-4.6_4.6.4-4+rpi1 g++-4.8_4.8.1-10+rpi1 gcc-4.6_4.6.4-4+rpi1 gcc-4.8_4.8.1-10+rpi1 libc6-dev_2.17-93 libstdc++-4.8-dev_4.8.1-10+rpi1 libstdc++6_4.8.1-10+rpi1 libstdc++6-4.6-dev_4.6.4-4+rpi1 linux-libc-dev_3.10.1-1+rpi1+b2
Package versions: apt_0.9.11.4+rpi1 base-files_7.2+rpi1 base-passwd_3.5.28 bash_4.2+dfsg-1 binutils_2.23.90.20130927-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.5 build-essential_11.6 bzip2_1.0.6-5 coreutils_8.21-1 cpio_2.11+dfsg-1 cpp_4:4.8.1-3 cpp-4.6_4.6.4-4+rpi1 cpp-4.8_4.8.1-10+rpi1 dash_0.5.7-3 debconf_1.5.51 debfoster_2.7-1.2 debhelper_9.20130921 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.16.12 dpkg-dev_1.16.12 e2fslibs_1.42.8-1 e2fsprogs_1.42.8-1 fakeroot_1.18.4-2 file_1:5.14-2 findutils_4.4.2-6 fontconfig_2.11.0-1 fontconfig-config_2.11.0-1 fonts-cabin_1.5-2 fonts-comfortaa_2.003-1 fonts-dejavu-core_2.33+svn2514-3 fonts-dejavu-extra_2.33+svn2514-3 fonts-droid_1:4.3-1 fonts-font-awesome_3.2.1~dfsg-2 fonts-freefont-otf_20120503-1 fonts-freefont-ttf_20120503-1 fonts-gfs-artemisia_1.1-5 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-lato_1.104-4 fonts-linuxlibertine_5.3.0-2 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++_4:4.8.1-3 g++-4.6_4.6.4-4+rpi1 g++-4.8_4.8.1-10+rpi1 gcc_4:4.8.1-3 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.4-4+rpi1 gcc-4.6-base_4.6.4-4+rpi1 gcc-4.7-base_4.7.3-4+rpi1 gcc-4.8_4.8.1-10+rpi1 gcc-4.8-base_4.8.1-10+rpi1 gettext_0.18.3.1-1 gettext-base_0.18.3.1-1 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_1.4.15-1.1 gpgv_1.4.15-1.1 grep_2.14-4 groff-base_1.22.2-3 gzip_1.6-2 hostname_3.14 initramfs-tools_0.114 initscripts_2.88dsf-43 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_2.2.52-1 libapt-pkg4.12_0.9.11.4+rpi1 libarchive-extract-perl_0.68-1 libasan0_4.8.1-10+rpi1 libasprintf0c2_0.18.3.1-1 libatomic1_4.8.1-10+rpi1 libattr1_1:2.4.47-1 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_2.20.1-5.5 libbz2-1.0_1.0.6-5 libbz2-dev_1.0.6-5 libc-bin_2.17-93 libc-dev-bin_2.17-93 libc6_2.17-93 libc6-dev_2.17-93 libcairo-gobject2_1.12.16-2 libcairo-script-interpreter2_1.12.16-2 libcairo2_1.12.16-2 libcairo2-dev_1.12.16-2 libcap2_1:2.22-1.2 libclass-isa-perl_0.36-5 libcloog-isl4_0.18.0-2 libcomerr2_1.42.8-1 libcroco3_0.6.8-2 libcups2_1.6.3-1+rpi1 libcupsfilters1_1.0.34-3+b1 libcupsimage2_1.6.3-1+rpi1 libdatrie1_0.2.7.1-1 libdb5.1_5.1.29-6 libdbus-1-3_1.6.16-1 libdpkg-perl_1.16.12 libdrm-dev_2.4.46-3 libdrm-nouveau2_2.4.46-3 libdrm-omap1_2.4.46-3 libdrm-radeon1_2.4.46-3 libdrm2_2.4.46-3 libegl1-mesa_9.2.2-1 libegl1-mesa-dev_9.2.2-1 libegl1-mesa-drivers_9.2.2-1 libelfg0_0.8.13-3 libexpat1_2.1.0-4 libexpat1-dev_2.1.0-4 libffi6_3.0.13-4 libfontconfig1_2.11.0-1 libfontconfig1-dev_2.11.0-1 libfreetype6_2.4.9-1.1 libfreetype6-dev_2.4.9-1.1 libgbm1_9.2.2-1 libgc1c2_1:7.2d-5 libgcc-4.8-dev_4.8.1-10+rpi1 libgcc1_1:4.8.1-10+rpi1 libgcrypt11_1.5.3-2 libgdbm3_1.8.3-12 libgirepository-1.0-1_1.36.0-2 libgl1-mesa-dev_9.2.2-1 libgl1-mesa-glx_9.2.2-1 libglapi-mesa_9.2.2-1 libglib2.0-0_2.36.4-1 libglib2.0-bin_2.36.4-1 libglib2.0-data_2.36.4-1 libglib2.0-dev_2.36.4-1 libgmp10_2:5.1.2+dfsg-3 libgnutls26_2.12.23-8 libgomp1_4.8.1-10+rpi1 libgpg-error0_1.12-0.2 libgraphite2-3_1.2.3-1 libgs9_9.05~dfsg-8 libgs9-common_9.05~dfsg-8 libgssapi-krb5-2_1.11.3+dfsg-3 libharfbuzz-dev_0.9.19-1 libharfbuzz-icu0_0.9.19-1 libharfbuzz0a_0.9.19-1 libice-dev_2:1.0.8-2 libice6_2:1.0.8-2 libicu48_4.8.1.1-13+nmu1 libidn11_1.28-1 libijs-0.35_0.35-8 libisl10_0.11.2-1 libjasper1_1.900.1-14 libjbig0_2.0-2 libjbig2dec0_0.11+20120125-1 libjpeg8_8d-1 libk5crypto3_1.11.3+dfsg-3 libkeyutils1_1.5.6-1 libklibc_2.0.1-3.1+rpi1 libkmod2_9-3 libkpathsea6_2013.20130729.30972-2 libkrb5-3_1.11.3+dfsg-3 libkrb5support0_1.11.3+dfsg-3 liblcms1_1.19.dfsg-1.2 liblcms2-2_2.2+git20110628-2.3 libllvm3.3_1:3.3-9 liblog-message-simple-perl_0.10-1 liblua5.1-0_5.1.5-5 liblua5.1-0-dev_5.1.5-5 liblzma5_5.1.1alpha+20120614-2 liblzo2-2_2.06-1.2 libmagic1_1:5.14-2 libmodule-pluggable-perl_4.8-1 libmount1_2.20.1-5.5 libmpc2_0.9-4 libmpc3_1.0.1-1 libmpfr4_3.1.1-2 libncurses5_5.9+20130608-1 libncurses5-dev_5.9+20130608-1 libncursesw5_5.9+20130608-1 libopenjpeg2_1.3+dfsg-4.6 libopenvg1-mesa_9.2.2-1 libp11-kit0_0.18.5-3 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 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_1.2.4-1 libpixman-1-0_0.30.2-1 libpixman-1-dev_0.30.2-1 libpng12-0_1.2.49-5 libpng12-dev_1.2.49-5 libpod-latex-perl_0.61-1 libpoppler19_0.18.4-8 libpopt0_1.16-7 libprocps0_1:3.3.4-2 libptexenc1_2013.20130729.30972-2 libpthread-stubs0-dev_0.3-4 libpython-stdlib_2.7.5-5 libpython2.7-minimal_2.7.5-8+rvt libpython2.7-stdlib_2.7.5-8+rvt libreadline-dev_6.2+dfsg-0.1 libreadline6_6.2+dfsg-0.1 libreadline6-dev_6.2+dfsg-0.1 libselinux1_2.1.13-3+rpi1 libsemanage-common_2.1.10-3+rpi1 libsemanage1_2.1.10-3+rpi1 libsepol1_2.1.9-2 libslang2_2.2.4-15 libsm-dev_2:1.2.1-2 libsm6_2:1.2.1-2 libsqlite3-0_3.8.0.2-1 libsqlite3-dev_3.8.0.2-1 libss2_1.42.8-1 libssl1.0.0_1.0.1e-3+rpi1 libstdc++-4.8-dev_4.8.1-10+rpi1 libstdc++6_4.8.1-10+rpi1 libstdc++6-4.6-dev_4.6.4-4+rpi1 libswitch-perl_2.16-2 libtasn1-3_2.14-3 libterm-ui-perl_0.38-1 libthai-data_0.1.19-2 libthai0_0.1.19-2 libtiff4_3.9.7-2 libtimedate-perl_1.2000-1 libtinfo-dev_5.9+20130608-1 libtinfo5_5.9+20130608-1 libudev0_175-7.2 libudev1_204-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.2 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.5 libwayland-client0_1.3.0-1 libwayland-server0_1.3.0-1 libx11-6_2:1.6.2-1 libx11-data_2:1.6.2-1 libx11-dev_2:1.6.2-1 libx11-xcb-dev_2:1.6.2-1 libx11-xcb1_2:1.6.2-1 libxau-dev_1:1.0.8-1 libxau6_1:1.0.8-1 libxaw7_2:1.0.11-1 libxcb-dri2-0_1.9.1-3 libxcb-dri2-0-dev_1.9.1-3 libxcb-glx0_1.9.1-3 libxcb-glx0-dev_1.9.1-3 libxcb-render0_1.9.1-3 libxcb-render0-dev_1.9.1-3 libxcb-shape0_1.9.1-3 libxcb-shm0_1.9.1-3 libxcb-shm0-dev_1.9.1-3 libxcb-xfixes0_1.9.1-3 libxcb1_1.9.1-3 libxcb1-dev_1.9.1-3 libxdamage-dev_1:1.1.4-1 libxdamage1_1:1.1.4-1 libxdmcp-dev_1:1.1.1-1 libxdmcp6_1:1.1.1-1 libxext-dev_2:1.3.2-1 libxext6_2:1.3.2-1 libxfixes-dev_1:5.0.1-1 libxfixes3_1:5.0.1-1 libxft-dev_2.3.1-1 libxft2_2.3.1-1 libxml2_2.9.1+dfsg1-3 libxmu6_2:1.1.1-1 libxpm4_1:3.5.10-1 libxrender-dev_1:0.9.8-1 libxrender1_1:0.9.8-1 libxt6_1:1.1.4-1 libxxf86vm-dev_1:1.1.3-1 libxxf86vm1_1:1.1.3-1 linux-libc-dev_3.10.1-1+rpi1+b2 login_1:4.1.5.1-1 lsb-base_4.1+Debian12+rpi1 lua-filesystem_1.6.2-1 lua-filesystem-dev_1.6.2-1 lua-lpeg_0.12-1 lua-lpeg-dev_0.12-1 lua-md5_1.1.2+gitdef7fa6-1 lua-md5-dev_1.1.2+gitdef7fa6-1 luatex_0.76.0-3 make_3.81-8.2 makedev_2.3.1-93 man-db_2.6.5-2 mawk_1.3.3-17 mesa-common-dev_9.2.2-1 mime-support_3.54 mount_2.20.1-5.5 multiarch-support_2.17-93 ncurses-base_5.9+20130608-1 ncurses-bin_5.9+20130608-1 otf-freefont_20120503-1 passwd_1:4.1.5.1-1 patch_2.7.1-3 perl_5.18.1-4 perl-base_5.18.1-4 perl-modules_5.18.1-4 pkg-config_0.26-1 plymouth_0.8.8-6+deb8u3 po-debconf_1.0.16+nmu2 poppler-data_0.4.6-4 preview-latex-style_11.87-1 procps_1:3.3.4-2 python_2.7.5-5 python-minimal_2.7.5-5 python2.7_2.7.5-8+rvt python2.7-minimal_2.7.5-8+rvt 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_4.2.2-2 sensible-utils_0.0.9 sysv-rc_2.88dsf-43 sysvinit_2.88dsf-43 sysvinit-utils_2.88dsf-43 tar_1.26+dfsg-8 tex-common_4.04 texlive-base_2013.20131010-2 texlive-binaries_2013.20130729.30972-2 texlive-fonts-extra_2013.20131010-1 texlive-fonts-recommended_2013.20131010-2 texlive-latex-base_2013.20131010-2 texlive-latex-extra_2013.20131010-1 texlive-latex-recommended_2013.20131010-2 texlive-pictures_2013.20131010-2 ttf-dejavu-core_2.33+svn2514-3 ttf-freefont_20120503-1 tzdata_2013d-1 ucf_3.0027+nmu1 udev_204-5 util-linux_2.20.1-5.5 x11-common_1:7.7+4 x11proto-core-dev_7.0.24-1 x11proto-damage-dev_1:1.2.1-2 x11proto-dri2-dev_2.8-2 x11proto-fixes-dev_1:5.0-2 x11proto-gl-dev_1.4.16-2 x11proto-input-dev_2.3-1 x11proto-kb-dev_1.0.6-2 x11proto-render-dev_2:0.11.1-2 x11proto-xext-dev_7.2.1-1 x11proto-xf86vidmode-dev_2.3.1-2 xdg-utils_1.1.0~rc1+git20111210-7 xorg-sgml-doctools_1:1.11-1 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 Mon Oct 28 08:03:05 2013 UTC using DSA key ID C09FD35A
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./genometools_1.5.1-2.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_1.5.1-2.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
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=POSIX
LOGNAME=root
LS_OPTIONS=--color=auto
MAIL=/var/mail/root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/root
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-1c636174-96ee-41c4-8a30-8e7a9c6e6d1e
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
SHLVL=1
SSH_CLIENT=192.168.1.2 45410 22
SSH_CONNECTION=192.168.1.2 45410 192.168.1.45 22
SSH_TTY=/dev/pts/0
TERM=xterm
USER=root
XDG_SESSION_COOKIE=106ef489ba27ee071ab233f6518d3bce-1380046912.711892-759150774
_=/etc/init.d/buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package genometools
dpkg-buildpackage: source version 1.5.1-2
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
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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]
case GT_END_OF_FILE:
^
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]
case GT_END_OF_FILE:
^
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]
case GT_END_OF_FILE:
^
[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]
case GT_END_OF_FILE:
^
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]
case GT_END_OF_FILE:
^
[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]
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]
case -1:
^
[compile sfx-bltrie.o]
[compile sfx-copysort.o]
[compile sfx-diffcov.o]
[compile sfx-enumcodes.o]
[compile sfx-lcpvalues.o]
[compile sfx-linlcp.o]
[compile sfx-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 > \
www/genometools.org/htdocs/examples.html; rm -f /tmp/tmp.sed.$$
bin/gt gtscripts/gtdoc.lua -tex /«PKGBUILDDIR» \
> doc/manuals/api_reference.tex
bin/gt gtscripts/gtdoc.lua -lua -tex /«PKGBUILDDIR» \
> doc/manuals/gtscript_reference.tex
make -C /«PKGBUILDDIR»/doc/devguide
make[3]: Entering directory `/«PKGBUILDDIR»/doc/devguide'
while (pdflatex --shell-escape devguide ; \
grep -q "Rerun to get cross" devguide.log ) do true ; \
done
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Transcript written on devguide.log.
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make[3]: Leaving directory `/«PKGBUILDDIR»/doc/devguide'
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\OT1/ptm/m/n/10.95 run by the com-mand line \OT1/cmtt/m/n/10.95 gt gtscripts/sk
etch[]constructed.lua <style[]file> <PNG[]file>\OT1/ptm/m/n/10.95 )
(../../gtscripts/sketch_constructed.lua [22])
(../../gtruby/sketch_constructed.rb [23]) (../../gtpython/sketch_constructed.py
[24]) (./api_reference.tex [25]
Chapter 2.
LaTeX Warning: Reference `GtAddIntronsStream' on page 26 undefined on input lin
e 5.
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LaTeX Warning: Reference `GtAnnoDBGFFlike' on page 26 undefined on input line 9
.
LaTeX Warning: Reference `GtAnnoDBSchema' on page 26 undefined on input line 11
.
LaTeX Warning: Reference `GtArray' on page 26 undefined on input line 13.
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5.
LaTeX Warning: Reference `GtArrayOutStream' on page 26 undefined on input line
17.
LaTeX Warning: Reference `GtBEDInStream' on page 26 undefined on input line 19.
LaTeX Warning: Reference `GtBittab' on page 26 undefined on input line 21.
LaTeX Warning: Reference `GtBlock' on page 26 undefined on input line 23.
LaTeX Warning: Reference `GtCDSStream' on page 26 undefined on input line 25.
LaTeX Warning: Reference `GtCSAStream' on page 26 undefined on input line 27.
LaTeX Warning: Reference `GtCanvas' on page 26 undefined on input line 29.
LaTeX Warning: Reference `GtCanvasCairoContext' on page 26 undefined on input l
ine 31.
LaTeX Warning: Reference `GtCanvasCairoFile' on page 26 undefined on input line
33.
LaTeX Warning: Reference `GtCodonIterator' on page 26 undefined on input line 3
5.
LaTeX Warning: Reference `GtCodonIteratorEncseq' on page 26 undefined on input
line 37.
LaTeX Warning: Reference `GtCodonIteratorSimple' on page 26 undefined on input
line 39.
LaTeX Warning: Reference `GtColor' on page 26 undefined on input line 41.
LaTeX Warning: Reference `GtCommentNode' on page 26 undefined on input line 43.
LaTeX Warning: Reference `GtCstrTable' on page 26 undefined on input line 45.
LaTeX Warning: Reference `GtCustomTrack' on page 26 undefined on input line 47.
LaTeX Warning: Reference `GtCustomTrackGcContent' on page 26 undefined on input
line 49.
LaTeX Warning: Reference `GtCustomTrackScriptWrapper' on page 26 undefined on i
nput line 51.
[26]
LaTeX Warning: Reference `GtDiagram' on page 27 undefined on input line 53.
LaTeX Warning: Reference `GtDiscDistri' on page 27 undefined on input line 55.
LaTeX Warning: Reference `GtDlist' on page 27 undefined on input line 57.
LaTeX Warning: Reference `GtDlistelem' on page 27 undefined on input line 59.
LaTeX Warning: Reference `GtEOFNode' on page 27 undefined on input line 61.
LaTeX Warning: Reference `GtEncseq' on page 27 undefined on input line 63.
LaTeX Warning: Reference `GtEncseqBuilder' on page 27 undefined on input line 6
5.
LaTeX Warning: Reference `GtEncseqEncoder' on page 27 undefined on input line 6
7.
LaTeX Warning: Reference `GtEncseqLoader' on page 27 undefined on input line 69
.
LaTeX Warning: Reference `GtEncseqReader' on page 27 undefined on input line 71
.
LaTeX Warning: Reference `GtError' on page 27 undefined on input line 73.
LaTeX Warning: Reference `GtExtractFeatureStream' on page 27 undefined on input
line 75.
LaTeX Warning: Reference `GtFeatureIndex' on page 27 undefined on input line 77
.
LaTeX Warning: Reference `GtFeatureIndexMemory' on page 27 undefined on input l
ine 79.
LaTeX Warning: Reference `GtFeatureNode' on page 27 undefined on input line 81.
LaTeX Warning: Reference `GtFeatureNodeIterator' on page 27 undefined on input
line 83.
LaTeX Warning: Reference `GtFeatureStream' on page 27 undefined on input line 8
5.
LaTeX Warning: Reference `GtFile' on page 27 undefined on input line 87.
LaTeX Warning: Reference `GtGFF3InStream' on page 27 undefined on input line 89
.
LaTeX Warning: Reference `GtGFF3OutStream' on page 27 undefined on input line 9
1.
LaTeX Warning: Reference `GtGFF3Parser' on page 27 undefined on input line 93.
LaTeX Warning: Reference `GtGFF3Visitor' on page 27 undefined on input line 95.
LaTeX Warning: Reference `GtGTFInStream' on page 27 undefined on input line 97.
LaTeX Warning: Reference `GtGTFOutStream' on page 27 undefined on input line 99
.
LaTeX Warning: Reference `GtGenomeNode' on page 27 undefined on input line 101.
LaTeX Warning: Reference `GtGraphics' on page 27 undefined on input line 103.
LaTeX Warning: Reference `GtHashmap' on page 27 undefined on input line 105.
[27]
LaTeX Warning: Reference `GtIDToMD5Stream' on page 28 undefined on input line 1
07.
LaTeX Warning: Reference `GtImageInfo' on page 28 undefined on input line 109.
LaTeX Warning: Reference `GtInterFeatureStream' on page 28 undefined on input l
ine 111.
LaTeX Warning: Reference `GtIntervalTree' on page 28 undefined on input line 11
3.
LaTeX Warning: Reference `GtIntervalTreeNode' on page 28 undefined on input lin
e 115.
LaTeX Warning: Reference `GtLayout' on page 28 undefined on input line 117.
LaTeX Warning: Reference `GtLogger' on page 28 undefined on input line 119.
LaTeX Warning: Reference `GtMD5Encoder' on page 28 undefined on input line 121.
LaTeX Warning: Reference `GtMD5ToIDStream' on page 28 undefined on input line 1
23.
LaTeX Warning: Reference `GtMatch' on page 28 undefined on input line 125.
LaTeX Warning: Reference `GtMatchBlast' on page 28 undefined on input line 127.
LaTeX Warning: Reference `GtMatchIterator' on page 28 undefined on input line 1
29.
LaTeX Warning: Reference `GtMatchLAST' on page 28 undefined on input line 131.
LaTeX Warning: Reference `GtMatchOpen' on page 28 undefined on input line 133.
LaTeX Warning: Reference `GtMatchSW' on page 28 undefined on input line 135.
LaTeX Warning: Reference `GtMatchVisitor' on page 28 undefined on input line 13
7.
LaTeX Warning: Reference `GtMergeFeatureStream' on page 28 undefined on input l
ine 139.
LaTeX Warning: Reference `GtMergeStream' on page 28 undefined on input line 141
.
LaTeX Warning: Reference `GtMetaNode' on page 28 undefined on input line 143.
LaTeX Warning: Reference `GtMutex' on page 28 undefined on input line 145.
LaTeX Warning: Reference `GtNodeStream' on page 28 undefined on input line 147.
LaTeX Warning: Reference `GtNodeStreamClass' on page 28 undefined on input line
149.
LaTeX Warning: Reference `GtNodeVisitor' on page 28 undefined on input line 151
.
LaTeX Warning: Reference `GtORFIterator' on page 28 undefined on input line 153
.
LaTeX Warning: Reference `GtOption' on page 28 undefined on input line 155.
LaTeX Warning: Reference `GtOptionParser' on page 28 undefined on input line 15
7.
LaTeX Warning: Reference `GtOutputFileInfo' on page 28 undefined on input line
159.
[28]
LaTeX Warning: Reference `GtPhase' on page 29 undefined on input line 161.
LaTeX Warning: Reference `GtQueue' on page 29 undefined on input line 163.
LaTeX Warning: Reference `GtRDBMySQL' on page 29 undefined on input line 165.
LaTeX Warning: Reference `GtRDBSqlite' on page 29 undefined on input line 167.
LaTeX Warning: Reference `GtRDBVisitor' on page 29 undefined on input line 169.
LaTeX Warning: Reference `GtRWLock' on page 29 undefined on input line 171.
LaTeX Warning: Reference `GtRange' on page 29 undefined on input line 173.
LaTeX Warning: Reference `GtReadmode' on page 29 undefined on input line 175.
LaTeX Warning: Reference `GtRecMap' on page 29 undefined on input line 177.
LaTeX Warning: Reference `GtRegionMapping' on page 29 undefined on input line 1
79.
LaTeX Warning: Reference `GtRegionNode' on page 29 undefined on input line 181.
LaTeX Warning: Reference `GtSelectStream' on page 29 undefined on input line 18
3.
LaTeX Warning: Reference `GtSeqIterator' on page 29 undefined on input line 185
.
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e 187.
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input line 189.
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1.
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LaTeX Warning: Reference `GtSplitter' on page 29 undefined on input line 195.
LaTeX Warning: Reference `GtStatStream' on page 29 undefined on input line 197.
LaTeX Warning: Reference `GtStr' on page 29 undefined on input line 199.
LaTeX Warning: Reference `GtStrArray' on page 29 undefined on input line 201.
LaTeX Warning: Reference `GtStrand' on page 29 undefined on input line 203.
LaTeX Warning: Reference `GtStyle' on page 29 undefined on input line 205.
LaTeX Warning: Reference `GtTagValueMap' on page 29 undefined on input line 207
.
LaTeX Warning: Reference `GtTextWidthCalculator' on page 29 undefined on input
line 209.
LaTeX Warning: Reference `GtTextWidthCalculatorCairo' on page 29 undefined on i
nput line 211.
LaTeX Warning: Reference `GtThread' on page 29 undefined on input line 213.
[29]
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.
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227.
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31.
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51.
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9.
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261.
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[30]
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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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[31]
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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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[32] [33] [34]
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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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[38]
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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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[39]
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[40] [41]
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]cds[]stream[]new([]GtNodeStream *in[]st
ream, GtRegionMapping
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\OT1/cmtt/m/n/10.95 *region[]mapping, unsigned int minorflen, const char *sourc
e, bool
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]csa[]stream[]new([]GtNodeStream *in[]st
ream, unsigned long
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[42]
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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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[43]
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[]\OT1/cmtt/m/n/10.95 GtCodonIteratorStatus gt[]codon[]iterator[]next([]GtCodon
Iterator *ci, char
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[44]
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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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[45]
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[46]
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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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[47]
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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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[48]
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[49]
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[50]
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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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[54] [55]
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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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[71]
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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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[72]
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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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[73]
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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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[74]
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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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[75] [76]
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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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[77] [78] [79]
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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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[80]
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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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[81]
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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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[82]
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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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[83]
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[84]
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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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[85]
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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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[86]
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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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[87]
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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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[88]
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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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[111]
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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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[112]
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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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[113]
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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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[115] [116]
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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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[117]
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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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[118]
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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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[119]
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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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[120]
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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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[121]
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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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[122] [123]
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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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[124]
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]visitor[]stream[]new([]GtNodeStream *in
[]stream,
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[125]
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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
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[]\OT1/ptm/m/n/10.95 Return the (es-ti-mated) to-tal size of all files given in
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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
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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
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onst char *end,
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art, const char *end,
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[]\OT1/cmtt/m/n/10.95 void gt[]qsort[]r([]void *a, size[]t n, size[]t es, void
*data,
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[]\OT1/ptm/m/n/10.95 Like \OT1/cmtt/m/n/10.95 qsort(3)\OT1/ptm/m/n/10.95 , but
al-lows an ad-di-tional \OT1/cmtt/m/n/10.95 data \OT1/ptm/m/n/10.95 pointer pas
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ajor, unsigned int
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ar *format, va[]list
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bibtex annotationsketch
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[5]
Chapter 1.
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<../../www/genometools.org/htdocs/images/diagram.pdf, id=831, 1363.36378pt x 59
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www/genometools.org/htdocs/images/dataflow.pdf>] [8 <../../www/genometools.org/
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629.58289pt> <use ../../www/genometools.org/htdocs/images/cnn_large.png>
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<../../www/genometools.org/htdocs/images/callbacks.png, id=942, 602.25pt x 379.
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[12] (/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
<../../www/genometools.org/htdocs/images/example_strandselect.png, id=965, 602.
25pt x 319.1925pt>
<use ../../www/genometools.org/htdocs/images/example_strandselect.png> [13 <../
../www/genometools.org/htdocs/images/example_nocollapse_noselect.png>]
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<../../www/genometools.org/htdocs/images/example_filterselect.png, id=983, 602.
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<use ../../www/genometools.org/htdocs/images/example_filterselect.png> [14 <../
../www/genometools.org/htdocs/images/example_strandselect.png>]
<../../www/genometools.org/htdocs/images/example_ct.png, id=1011, 602.25pt x 55
4.07pt> <use ../../www/genometools.org/htdocs/images/example_ct.png> [15 <../..
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nometools.org/htdocs/images/example_ct.png>]
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(../../src/examples/sketch_parsed.c [18 <../../www/genometools.org/htdocs/image
s/example_ct2.png>] [19 <../../www/genometools.org/htdocs/images/parsed.png>])
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\OT1/ptm/m/n/10.95 the com-mand line \OT1/cmtt/m/n/10.95 gt gtscripts/sketch[]p
arsed.lua <style[]file> <PNG[]file> <GFF3[]file>\OT1/ptm/m/n/10.95 )
(../../gtscripts/sketch_parsed.lua [20]) (../../gtruby/sketch_parsed.rb
[21]) (../../gtpython/sketch_parsed.py [22])
<../../www/genometools.org/htdocs/images/constructed.png, id=1315, 602.25pt x 1
49.55875pt> <use ../../www/genometools.org/htdocs/images/constructed.png>
(../../src/examples/sketch_constructed.c [23 <../../www/genometools.org/htdocs/
images/constructed.png>] [24])
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\OT1/ptm/m/n/10.95 run by the com-mand line \OT1/cmtt/m/n/10.95 gt gtscripts/sk
etch[]constructed.lua <style[]file> <PNG[]file>\OT1/ptm/m/n/10.95 )
(../../gtscripts/sketch_constructed.lua [25])
(../../gtruby/sketch_constructed.rb [26]) (../../gtpython/sketch_constructed.py
[27]) (./api_reference.tex [28]
Chapter 2.
[29] [30] [31] [32] [33]
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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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[34]
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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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[35] [36] [37]
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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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[38] [39]
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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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[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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\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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[46]
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[]\OT1/cmtt/m/n/10.95 GtCodonIteratorStatus gt[]codon[]iterator[]next([]GtCodon
Iterator *ci, char
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[47]
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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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[49]
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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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[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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[57] [58]
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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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[74]
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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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[76]
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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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[77]
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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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[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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[86]
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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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[91]
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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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[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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[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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[115]
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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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[118] [119]
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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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[120]
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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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[121]
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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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[122]
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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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[123]
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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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[124]
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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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[125] [126]
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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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[127]
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]visitor[]stream[]new([]GtNodeStream *in
[]stream,
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[128]
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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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[129]
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[130]
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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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[131]
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Chapter 1.
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Chapter 2.
[29] [30] [31] [32] [33]
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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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[34]
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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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*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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const char
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alphabet, unsigned
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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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[41]
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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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[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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\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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[46]
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[]\OT1/cmtt/m/n/10.95 GtCodonIteratorStatus gt[]codon[]iterator[]next([]GtCodon
Iterator *ci, char
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[47]
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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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[48]
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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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[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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[51]
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[52]
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[53]
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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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[57] [58]
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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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[74]
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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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[76]
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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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[77]
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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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[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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[86]
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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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[91]
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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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[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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[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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[115]
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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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[118] [119]
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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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[120]
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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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[121]
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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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[122]
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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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[123]
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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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[124]
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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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[125] [126]
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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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[127]
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[]\OT1/cmtt/m/n/10.95 GtNodeStream* gt[]visitor[]stream[]new([]GtNodeStream *in
[]stream,
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[128]
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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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[129]
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[130]
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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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[131]
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[132]
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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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[133]
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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
[134]
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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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[135]
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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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[136]
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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)
LaTeX Font Warning: Some font shapes were not available, defaults substituted.
)
(see the transcript file for additional information) </tmp/texfonts/pk/ljfour/p
ublic/cm/cmttb10.864pk> </tmp/texfonts/pk/ljfour/public/cm/cmttb10.480pk>{/usr/
share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-
dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/f
onts/type1/public/amsfonts/cm/cmssbx10.pfb></usr/share/texlive/texmf-dist/fonts
/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1
/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publi
c/amsfonts/cm/cmtt8.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/ut
mb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/
share/texlive/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on annotationsketch.pdf (139 pages, 892788 bytes).
Transcript written on annotationsketch.log.
mv annotationsketch.aux annotationsketch-pdf.aux
test -e annotationsketch.bbl && mv annotationsketch.bbl annotationsketch-pdf.bbl
make[3]: Leaving directory `/«PKGBUILDDIR»/doc/manuals'
make -C /«PKGBUILDDIR»/doc/manuals
make[3]: Entering directory `/«PKGBUILDDIR»/doc/manuals'
test -e readjoiner-pdf.aux && mv readjoiner-pdf.aux readjoiner.aux
test -e hop-pdf.aux && mv hop-pdf.aux hop.aux
make[3]: [readjoiner-pdf.aux] Error 1 (ignored)
pdflatex readjoiner.tex && rm readjoiner.pdf
make[3]: [hop-pdf.aux] Error 1 (ignored)
pdflatex hop.tex && rm hop.pdf
test -e ltrharvest-pdf.aux && mv ltrharvest-pdf.aux ltrharvest.aux
test -e ltrdigest-pdf.aux && mv ltrdigest-pdf.aux ltrdigest.aux
make[3]: [ltrharvest-pdf.aux] Error 1 (ignored)
pdflatex ltrharvest.tex && rm ltrharvest.pdf
make[3]: [ltrdigest-pdf.aux] Error 1 (ignored)
pdflatex ltrdigest.tex && rm ltrdigest.pdf
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[]$\OT1/pcr/m/n/14.4 http : / / nar . oxfordjournals . org / cgi / content /
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[]
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[]\OT1/ptm/m/n/12 The \OT1/ptm/m/it/12 Read-joiner \OT1/ptm/m/n/12 tools are ru
n us-ing the fol-low-ing syn-tax: \OT1/pcr/m/n/12 gt readjoiner <tool> <argumen
ts>\OT1/ptm/m/n/12 ,
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\OT1/ptm/m/n/12 also the sam-tools man-ual page ($\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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[]\OT1/ptm/m/n/12 a single-end li-brary plus an in-ter-leaved
[2]]
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\OT1/ptm/m/n/12 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[]
[9
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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 .
[10]
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[][]
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[]\OT1/pcr/m/n/12 gt suffixerator -tis -des -dna -ssp -db genome.fas -indexname
genome.fas
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[]\OT1/ptm/m/n/12 We will also as-sume that the HMM files to be used are called
\OT1/pcr/m/n/12 HMM1.hmm\OT1/ptm/m/n/12 , \OT1/pcr/m/n/12 HMM2.hmm \OT1/ptm/m/
n/12 and \OT1/pcr/m/n/12 HMM3.hmm\OT1/ptm/m/n/12 ,
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\OT1/pcr/m/n/12 -hmms HMM*.hmm -outfileprefix mygenome-ltrs ltrs[]sorted.gff3 g
enome.fas
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\OT1/ptm/m/it/12 Tools \OT1/ptm/m/n/12 (see [[]] for in-stal-la-tion in-struc-t
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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
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[]\OT1/pcr/m/n/10 gt suffixerator -db repfinf-sample.seq -indexname repidx -dna
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[]\OT1/ptm/m/n/12 Kurtz, S., Choud-huri, J. V., Ohle-busch, E., Schleier-ma-che
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test -e ltrharvest-pdf.aux && mv ltrharvest-pdf.aux ltrharvest.aux
bibtex ltrharvest
entering extended mode
(./genomediff.tex
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)diff hop-pdf.bbl hop.bbl || mv hop.bbl hop-pdf.bbl && rm -f hop.bbl
mv hop.aux hop-pdf.aux
test -e ltrdigest-pdf.aux && mv ltrdigest-pdf.aux ltrdigest.aux
bibtex ltrdigest
)
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test -e uniquesub-pdf.aux && mv uniquesub-pdf.aux uniquesub.aux
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Warning--I didn't find a database entry for "EKW07"
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(There was 1 error message)
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0a1,3
> \begin{thebibliography}{}
>
> \end{thebibliography}
mv ltrdigest.aux ltrdigest-pdf.aux
)
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bibtex repfind
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0a1,21
> \begin{thebibliography}{1}
>
> \bibitem{oai:CiteSeerPSU:481302}
> Paolo Ferragina and Giovanni Manzini.
> \newblock Opportunistic data structures with applications, September~03 2000.
>
> \bibitem{journals/talg/FerraginaMMN07}
> Paolo Ferragina, Giovanni Manzini, Veli M{\"a}kinen, and Gonzalo Navarro.
> \newblock Compressed representations of sequences and full-text indexes.
> \newblock {\em ACM Transactions on Algorithms}, 3(2), 2007.
>
> \bibitem{genometools}
> Gordon Gremme.
> \newblock The \textsc{GenomeTools} genome analysis system.
> \newblock \url{http://genometools.org}.
>
> \bibitem{gttestdata}
> \textsc{GenomeTools} test data set.
> \newblock \url{git://genometools.org/gttestdata.git}.
>
> \end{thebibliography}
mv packedindex.aux packedindex-pdf.aux
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# file output/gt-tallymer-occratio--output-unique-nonunique--mersizes-10-13-17--esa-reads.out already exists
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# file output/gt-tallymer-search--output-qseqnum-qpos-counts-sequence--tyr-tyr-reads--q-U89959.fna.out already exists
test -e readjoiner-pdf.aux && mv readjoiner-pdf.aux readjoiner.aux
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test -e readjoiner-pdf.bbl && mv readjoiner-pdf.bbl readjoiner.bbl
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pdflatex readjoiner.tex
mv repfind.aux repfind-pdf.aux
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}]
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[][][][][][][][][][][][][][][][][][][][][][][][]
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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/tex/latex/psnfss/ot1ptm.fd)></usr/share/texlive/texmf-dist/fo
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[]
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[]\OT1/ptm/m/n/12 The \OT1/ptm/m/it/12 Read-joiner \OT1/ptm/m/n/12 tools are ru
n us-ing the fol-low-ing syn-tax: \OT1/pcr/m/n/12 gt readjoiner <tool> <argumen
ts>\OT1/ptm/m/n/12 ,
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[1]
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[]\OT1/ptm/m/n/12 a single-end li-brary plus an in-ter-leaved
[2] [3]}] [4] [5] [6] [7] (./readjoiner.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmr12.pfbThis is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013/Debian)
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m/cmsy10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb>
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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[]
[2
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\OT1/ptm/m/n/12 The pre-fix added by HOP (in this case \OT1/pcr/m/n/12 hop\OT1/
ptm/m/n/12 , which is the de-fault) can be changed us-ing the \OT1/pcr/m/n/12 -
outprefix
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[]\OT1/pcr/m/n/10 $ gt ltrharvest -index chr02.19970727.fsa -seed 30 -xdrop 5 -
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[]\OT1/ptm/m/n/12 The \OT1/ptm/m/it/12 Read-joiner \OT1/ptm/m/n/12 tools are ru
n us-ing the fol-low-ing syn-tax: \OT1/pcr/m/n/12 gt readjoiner <tool> <argumen
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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[]
[9 [1]]
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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. $\OT1/pcr/m/n/12 http : / / www .
[10]
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mv readjoiner.aux readjoiner-pdf.aux
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pdflatex ltrdigest.tex
}] [1]
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\OT1/ptm/m/n/12 also the sam-tools man-ual page ($\OT1/pcr/m/n/12 http : / / sa
mtools . sourceforge . net / samtools . shtml$\OT1/ptm/m/n/12 ).
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[]\OT1/ptm/m/n/12 It is usu-ally quite easy to pre-pare the map-ping as re-quir
ed. Say the reads to be cor-rected are \OT1/pcr/m/n/12 f[]reads.fastq
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[]\OT1/pcr/m/n/10 > bwa sampe refseq.fas -f map.sam f_reads.sai r_reads.sai f_r
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\OT1/ptm/m/n/12 The pre-fix added by HOP (in this case \OT1/pcr/m/n/12 hop\OT1/
ptm/m/n/12 , which is the de-fault) can be changed us-ing the \OT1/pcr/m/n/12 -
outprefix
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[]$\OT1/pcr/m/n/14.4 http : / / nar . oxfordjournals . org / cgi / content /
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\OT1/ptm/m/n/12 se-quence fea-tures of LTR retro-trans-posons in pre-dicted can
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[]].
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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/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[]
[9)]
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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 .
[10
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\OT1/ptm/m/n/12 trans-po-son it-self (\OT1/pcr/m/n/12 LTR[]retrotransposon \OT1
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\OT1/ptm/m/n/12 loaded from $\OT1/pcr/m/n/12 ftp : / / ftp . ensembl . org / pu
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[]\OT1/pcr/m/n/12 gt suffixerator -tis -des -dna -ssp -db genome.fas -indexname
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[]$\OT1/pcr/m/n/14.4 http : / / nar . oxfordjournals . org / cgi / content /
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\OT1/ptm/m/it/12 Tools \OT1/ptm/m/n/12 (see [[]] for in-stal-la-tion in-struc-t
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[]\OT1/pcr/m/n/12 gt suffixerator -tis -des -dna -ssp -db genome.fas -indexname
genome.fas
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[]\OT1/ptm/m/n/12 We will also as-sume that the HMM files to be used are called
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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-
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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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[]\OT1/ptm/m/n/12 Suppose the in-put se-quence $\OML/cmm/m/it/12 S \OT1/cmr/m/n
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[]\OT1/pcr/m/n/10 gt suffixerator -db repfinf-sample.seq -indexname repidx -dna
-suf -tis -lcp -ssp -pl
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[]\OT1/ptm/m/n/12 Kurtz, S., Choud-huri, J. V., Ohle-busch, E., Schleier-ma-che
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\OT1/ptm/m/it/12 Tools \OT1/ptm/m/n/12 (see [[]] for in-stal-la-tion in-struc-t
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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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ic/amsfonts/cm/cmmi10.pfb]></usr/share/texlive/texmf-dist/fonts/type1/public/ams
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cm/cmmi7.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr1
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LaTeX Warning: There were undefined references.
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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
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[]\OT1/pcr/m/n/10 gt suffixerator -db repfinf-sample.seq -indexname repidx -dna
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[]\OT1/ptm/m/n/12 Kurtz, S., Choud-huri, J. V., Ohle-busch, E., Schleier-ma-che
r, C., Stoye, J., Giegerich,
[4] (./repfind.aux) )
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m/cmr8.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10
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bibtex genomediff
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mv repfind.aux repfind-pdf.aux
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\OT1/ptm/m/n/12 The \OT1/pcr/b/n/12 mkctxmap \OT1/ptm/m/n/12 sub-tool fa-cil-i-
tates late build-ing of a re-verse lookup ta-ble, it can use the \OT1/pcr/m/sl/
12 prefix.suf
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[]\OT1/ptm/m/n/12 First com-pute the \OT1/ptm/m/it/12 packedin-dex \OT1/ptm/m/n
/12 in-dex file (this as-sumes \OT1/pcr/m/sl/12 chr01.19960731.fsa.gz \OT1/ptm/
m/n/12 has been copied/linked
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test -e genomediff-pdf.bbl || touch genomediff-pdf.bbl
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) [60a1,25
> \begin{thebibliography}{1}
>
> \bibitem{HAU:DOM:WIE:2008}
> Bernhard Haubold, Mirjana Domazet-Loso, and Thomas Wiehe.
> \newblock An alignment-free distance measure for closely related genomes.
> \newblock In {\em RECOMB-CG ’08: Proceedings of the international workshop on
> Comparative Genomics}, pages 87--99, Berlin, Heidelberg, 2008.
> Springer-Verlag.
>
> \bibitem{HAU:PFA:DOM:WIE:2009}
> B.~Haubold, P.~Pfaffelhuber, M.~Domazet-Loso, and T.~Wiehe.
> \newblock Estimating mutation distances from unaligned genomes.
> \newblock {\em J. Comput. Biol.}, 16:1487--1500, "Oct" 2009.
>
> \bibitem{HAU:REE:PFA:2011}
> Bernhard Haubold, Floyd~A. Reed, and Peter Pfaffelhuber.
> \newblock Alignment-free estimation of nucleotide diversity.
> \newblock {\em Bioinformatics}, 27(4):449--455, 2011.
>
> \bibitem{genometools}
> Gordon Gremme.
> \newblock The \textsc{GenomeTools} genome analysis system.
> \newblock \url{http://genometools.org}.
>
> \end{thebibliography}
]
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)}</usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi10.pfbtest -e genomediff-pdf.aux && mv genomediff-pdf.aux genomediff.aux
test -e genomediff-pdf.bbl && mv genomediff-pdf.bbl genomediff.bbl
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)>
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r/ucrro8a.pfb)
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[]\OT1/pcr/m/n/8 # computing prefix matches with up to 1 differences and at mos
t 5 occurrences in the subject sequences[]
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ist/fonts/enc/dvips/base/8r.enc}</usr/share/texlive/texmf-dist/fonts/type1/publ
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)
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ist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr12.pfb>></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr8.
pfb</usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmbxti10.pfb>></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb</usr/share/texlive/texmf-dist/fonts/
type1/public/amsfonts/cm/cmcsc10.pfb></
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st/fonts/type1/urw/times/utmb8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmmi12.pfb>></usr/share/texlive/texmf-dist/fonts/type1/public/ams
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urw/times/utmr8a.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/c
m/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/urw/times/utmri
8a.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>
Output written on tagerator-tmp.pdf (5 pages, 112697 bytes).
Transcript written on tagerator-tmp.log.
</
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></usr/sh
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dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on genomediff.pdf (6 pages, 176835 bytes).
Transcript written on genomediff.log.
pdflatex genomediff.tex
This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013/Debian)
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(/usr/share/texlive/texmf-dist/tex/latex/listings/listings.cfg))
(./optionman.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)
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(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(/usr/share/texlive/texmf-dist/tex/latex/listings/lstlang1.sty)
(./genomediff.aux)
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(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmbxti10.pfb></usr/share/texlive/texmf-dist/fonts/
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
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dist/fonts/type1/public/amsfonts/cm/cmtt12.pfb>
Output written on genomediff.pdf (6 pages, 176601 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
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!' \
-e 's!@CPPFLAGS@!-I\\"/«PKGBUILDDIR»/debian/tmp/usr/include\\" -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!' \
-e 's!@LDFLAGS@!-L/«PKGBUILDDIR»/debian/tmp/usr/lib -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@!"2013-11-03 06:00:29"!' \
-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
pyversions: missing X(S)-Python-Version in control file, fall back to debian/pyversions
pyversions: missing debian/pyversions file, fall back to supported versions
running install
running build
running build_py
creating build
creating build/lib.linux-armv7l-2.7
creating build/lib.linux-armv7l-2.7/gt
copying gt/__init__.py -> build/lib.linux-armv7l-2.7/gt
copying gt/dlload.py -> build/lib.linux-armv7l-2.7/gt
copying gt/props.py -> build/lib.linux-armv7l-2.7/gt
creating build/lib.linux-armv7l-2.7/gt/core
copying gt/core/__init__.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/alphabet.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/array.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/encseq.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/error.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/gtrange.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/gtstr.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/readmode.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/str_array.py -> build/lib.linux-armv7l-2.7/gt/core
copying gt/core/warning.py -> build/lib.linux-armv7l-2.7/gt/core
creating build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/__init__.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/block.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/canvas.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/color.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/custom_track.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/custom_track_example.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/diagram.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/feature_index.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/feature_stream.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/graphics.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/image_info.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/layout.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/rec_map.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
copying gt/annotationsketch/style.py -> build/lib.linux-armv7l-2.7/gt/annotationsketch
creating build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/__init__.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/add_introns_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/anno_db.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/comment_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/custom_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/custom_stream_example.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/custom_visitor.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/custom_visitor_example.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/dup_feature_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/eof_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/feature_index.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/feature_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/feature_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/genome_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/genome_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/gff3_in_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/gff3_out_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/gff3_visitor.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/inter_feature_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/merge_feature_stream.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/meta_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/node_visitor.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/rdb.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/region_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/sequence_node.py -> build/lib.linux-armv7l-2.7/gt/extended
copying gt/extended/strand.py -> build/lib.linux-armv7l-2.7/gt/extended
running install_lib
creating /«PKGBUILDDIR»/debian/python-genometools/usr
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
copying build/lib.linux-armv7l-2.7/gt/__init__.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
copying build/lib.linux-armv7l-2.7/gt/dlload.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
copying build/lib.linux-armv7l-2.7/gt/props.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/__init__.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/alphabet.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/array.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/encseq.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/error.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/gtrange.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/gtstr.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/readmode.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/str_array.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
copying build/lib.linux-armv7l-2.7/gt/core/warning.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/core
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/__init__.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/block.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/canvas.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/color.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/custom_track.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/custom_track_example.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/diagram.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/feature_index.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/feature_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/graphics.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/image_info.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/layout.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/rec_map.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
copying build/lib.linux-armv7l-2.7/gt/annotationsketch/style.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/annotationsketch
creating /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/__init__.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/add_introns_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/anno_db.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/comment_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_stream_example.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_visitor.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/custom_visitor_example.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/dup_feature_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/eof_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/feature_index.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/feature_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/feature_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/genome_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/genome_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/gff3_in_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/gff3_out_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/gff3_visitor.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/inter_feature_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/merge_feature_stream.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/meta_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/node_visitor.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/rdb.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/region_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/sequence_node.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
copying build/lib.linux-armv7l-2.7/gt/extended/strand.py -> /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/gt/extended
running install_egg_info
Writing /«PKGBUILDDIR»/debian/python-genometools/usr/lib/python2.7/dist-packages/GenomeTools-0.1.egg-info
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_install -a -O--parallel
dh_installdocs -a -O--parallel
dh_installchangelogs -a -O--parallel
dh_installman -a -O--parallel
dh_python2 -a -O--parallel
dh_perl -a -O--parallel
dh_link -a -O--parallel
dh_compress -a -O--parallel
dh_fixperms -a -O--parallel
debian/rules override_dh_strip
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_strip --dbg-package=genometools-dbg
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_makeshlibs -a -O--parallel
dh_shlibdeps -a -O--parallel
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/genometools/usr/bin/gt was not linked against libncurses.so.5 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/genometools/usr/bin/gt was not linked against libdl.so.2 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/genometools/usr/bin/gt was not linked against libglib-2.0.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: symbol pthread_join used by debian/libgenometools0/usr/lib/libgenometools.so.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol pthread_create used by debian/libgenometools0/usr/lib/libgenometools.so.0 found in none of the libraries
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libgenometools0/usr/lib/libgenometools.so.0 was not linked against libglib-2.0.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libgenometools0/usr/lib/libgenometools.so.0 was not linked against liblua5.1-lpeg.so.2 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libgenometools0/usr/lib/libgenometools.so.0 was not linked against liblua5.1-filesystem.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libgenometools0/usr/lib/libgenometools.so.0 was not linked against liblua5.1-des56.so.0 (it uses none of the library's symbols)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: Depends field of package libgenometools0-dev: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: Depends field of package genometools-dbg: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: Depends field of package python-genometools: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package python-genometools: unused substitution variable ${python:Provides}
dpkg-gencontrol: warning: package python-genometools: unused substitution variable ${python:Versions}
dh_md5sums -a -O--parallel
dh_builddeb -a -O--parallel
dpkg-deb: building package `libgenometools0' in `../libgenometools0_1.5.1-2_armhf.deb'.
dpkg-deb: building package `genometools' in `../genometools_1.5.1-2_armhf.deb'.
dpkg-deb: building package `libgenometools0-dev' in `../libgenometools0-dev_1.5.1-2_armhf.deb'.
dpkg-deb: building package `genometools-dbg' in `../genometools-dbg_1.5.1-2_armhf.deb'.
dpkg-deb: building package `python-genometools' in `../python-genometools_1.5.1-2_armhf.deb'.
dpkg-genchanges -B -mRaspbian nitrogen6x test autobuilder <root@raspbian.org> >../genometools_1.5.1-2_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 20131103-0601
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
genometools_1.5.1-2_armhf.changes:
──────────────────────────────────
Format: 1.8
Date: Mon, 28 Oct 2013 08:17:04 +0100
Source: genometools
Binary: genometools genometools-common libgenometools0 libgenometools0-dev genometools-doc genometools-dbg python-genometools
Architecture: armhf
Version: 1.5.1-2
Distribution: jessie-staging
Urgency: low
Maintainer: Raspbian nitrogen6x test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
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
Closes: 728017
Changes:
genometools (1.5.1-2) unstable; urgency=low
.
* debian/control
- Add myself to Uploaders
- cme fix dpkg-control
- Follow liblua package name transition
Closes: #728017
- Remove depends from virtual package python-ctypes which is provided
by python
* provide symbols file
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Files:
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
genometools_1.5.1-2_armhf.deb
─────────────────────────────
new debian package, version 2.0.
size 1964200 bytes: control archive=3464 bytes.
913 bytes, 16 lines control
7023 bytes, 97 lines md5sums
Package: genometools
Version: 1.5.1-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4554
Depends: libbz2-1.0, libc6 (>= 2.7), libcairo2 (>= 1.2.4), libexpat1 (>= 2.0.1), 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 2013-11-03 06:01 ./
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/bin/
-rwxr-xr-x root/root 4559048 2013-11-03 06:00 ./usr/bin/gt
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/share/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/share/doc/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./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 1100 2013-10-28 07:56 ./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 2013-11-03 06:00 ./usr/share/man/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/share/man/man1/
-rw-r--r-- root/root 768 2013-11-03 06:00 ./usr/share/man/man1/gt-bed_to_gff3.1.gz
-rw-r--r-- root/root 1439 2013-11-03 06:00 ./usr/share/man/man1/gt-cds.1.gz
-rw-r--r-- root/root 1182 2013-11-03 06:00 ./usr/share/man/man1/gt-chain2dim.1.gz
-rw-r--r-- root/root 1002 2013-11-03 06:00 ./usr/share/man/man1/gt-chseqids.1.gz
-rw-r--r-- root/root 628 2013-11-03 06:00 ./usr/share/man/man1/gt-clean.1.gz
-rw-r--r-- root/root 957 2013-11-03 06:00 ./usr/share/man/man1/gt-compreads-compress.1.gz
-rw-r--r-- root/root 858 2013-11-03 06:00 ./usr/share/man/man1/gt-compreads-decompress.1.gz
-rw-r--r-- root/root 1016 2013-11-03 06:00 ./usr/share/man/man1/gt-compreads-refcompress.1.gz
-rw-r--r-- root/root 817 2013-11-03 06:00 ./usr/share/man/man1/gt-compreads-refdecompress.1.gz
-rw-r--r-- root/root 651 2013-11-03 06:00 ./usr/share/man/man1/gt-compreads.1.gz
-rw-r--r-- root/root 717 2013-11-03 06:00 ./usr/share/man/man1/gt-congruence-spacedseed.1.gz
-rw-r--r-- root/root 693 2013-11-03 06:00 ./usr/share/man/man1/gt-congruence.1.gz
-rw-r--r-- root/root 868 2013-11-03 06:00 ./usr/share/man/man1/gt-convertseq.1.gz
-rw-r--r-- root/root 1346 2013-11-03 06:00 ./usr/share/man/man1/gt-csa.1.gz
-rw-r--r-- root/root 747 2013-11-03 06:00 ./usr/share/man/man1/gt-dupfeat.1.gz
-rw-r--r-- root/root 760 2013-11-03 06:00 ./usr/share/man/man1/gt-encseq-bench.1.gz
-rw-r--r-- root/root 774 2013-11-03 06:00 ./usr/share/man/man1/gt-encseq-bitextract.1.gz
-rw-r--r-- root/root 746 2013-11-03 06:00 ./usr/share/man/man1/gt-encseq-check.1.gz
-rw-r--r-- root/root 926 2013-11-03 06:00 ./usr/share/man/man1/gt-encseq-decode.1.gz
-rw-r--r-- root/root 939 2013-11-03 06:00 ./usr/share/man/man1/gt-encseq-encode.1.gz
-rw-r--r-- root/root 787 2013-11-03 06:00 ./usr/share/man/man1/gt-encseq-info.1.gz
-rw-r--r-- root/root 744 2013-11-03 06:00 ./usr/share/man/man1/gt-encseq-md5.1.gz
-rw-r--r-- root/root 678 2013-11-03 06:00 ./usr/share/man/man1/gt-encseq.1.gz
-rw-r--r-- root/root 848 2013-11-03 06:00 ./usr/share/man/man1/gt-encseq2spm.1.gz
-rw-r--r-- root/root 1122 2013-11-03 06:00 ./usr/share/man/man1/gt-eval.1.gz
-rw-r--r-- root/root 1458 2013-11-03 06:00 ./usr/share/man/man1/gt-extractfeat.1.gz
-rw-r--r-- root/root 2017 2013-11-03 06:00 ./usr/share/man/man1/gt-extractseq.1.gz
-rw-r--r-- root/root 797 2013-11-03 06:00 ./usr/share/man/man1/gt-featureindex.1.gz
-rw-r--r-- root/root 1404 2013-11-03 06:00 ./usr/share/man/man1/gt-fingerprint.1.gz
-rw-r--r-- root/root 1468 2013-11-03 06:00 ./usr/share/man/man1/gt-genomediff.1.gz
-rw-r--r-- root/root 1383 2013-11-03 06:00 ./usr/share/man/man1/gt-gff3.1.gz
-rw-r--r-- root/root 716 2013-11-03 06:00 ./usr/share/man/man1/gt-gff3_to_gtf.1.gz
-rw-r--r-- root/root 682 2013-11-03 06:00 ./usr/share/man/man1/gt-gff3validator.1.gz
-rw-r--r-- root/root 740 2013-11-03 06:00 ./usr/share/man/man1/gt-gtf_to_gff3.1.gz
-rw-r--r-- root/root 1893 2013-11-03 06:00 ./usr/share/man/man1/gt-hop.1.gz
-rw-r--r-- root/root 1355 2013-11-03 06:00 ./usr/share/man/man1/gt-id_to_md5.1.gz
-rw-r--r-- root/root 766 2013-11-03 06:00 ./usr/share/man/man1/gt-interfeat.1.gz
-rw-r--r-- root/root 812 2013-11-03 06:00 ./usr/share/man/man1/gt-ltrclustering.1.gz
-rw-r--r-- root/root 1188 2013-11-03 06:00 ./usr/share/man/man1/gt-ltrdigest.1.gz
-rw-r--r-- root/root 1291 2013-11-03 06:00 ./usr/share/man/man1/gt-ltrharvest.1.gz
-rw-r--r-- root/root 878 2013-11-03 06:00 ./usr/share/man/man1/gt-matchtool.1.gz
-rw-r--r-- root/root 824 2013-11-03 06:00 ./usr/share/man/man1/gt-matstat.1.gz
-rw-r--r-- root/root 769 2013-11-03 06:00 ./usr/share/man/man1/gt-md5_to_id.1.gz
-rw-r--r-- root/root 708 2013-11-03 06:00 ./usr/share/man/man1/gt-merge.1.gz
-rw-r--r-- root/root 741 2013-11-03 06:00 ./usr/share/man/man1/gt-mergefeat.1.gz
-rw-r--r-- root/root 1180 2013-11-03 06:00 ./usr/share/man/man1/gt-mgth.1.gz
-rw-r--r-- root/root 778 2013-11-03 06:00 ./usr/share/man/man1/gt-mkfeatureindex.1.gz
-rw-r--r-- root/root 793 2013-11-03 06:00 ./usr/share/man/man1/gt-mkfmindex.1.gz
-rw-r--r-- root/root 624 2013-11-03 06:00 ./usr/share/man/man1/gt-mmapandread.1.gz
-rw-r--r-- root/root 878 2013-11-03 06:00 ./usr/share/man/man1/gt-orffinder.1.gz
-rw-r--r-- root/root 773 2013-11-03 06:00 ./usr/share/man/man1/gt-packedindex-chkintegrity.1.gz
-rw-r--r-- root/root 1316 2013-11-03 06:00 ./usr/share/man/man1/gt-packedindex-chksearch.1.gz
-rw-r--r-- root/root 798 2013-11-03 06:00 ./usr/share/man/man1/gt-packedindex-mkctxmap.1.gz
-rw-r--r-- root/root 1579 2013-11-03 06:00 ./usr/share/man/man1/gt-packedindex-mkindex.1.gz
-rw-r--r-- root/root 1072 2013-11-03 06:00 ./usr/share/man/man1/gt-packedindex-trsuftab.1.gz
-rw-r--r-- root/root 721 2013-11-03 06:00 ./usr/share/man/man1/gt-packedindex.1.gz
-rw-r--r-- root/root 688 2013-11-03 06:00 ./usr/share/man/man1/gt-prebwt.1.gz
-rw-r--r-- root/root 724 2013-11-03 06:00 ./usr/share/man/man1/gt-readjoiner-assembly.1.gz
-rw-r--r-- root/root 845 2013-11-03 06:00 ./usr/share/man/man1/gt-readjoiner-overlap.1.gz
-rw-r--r-- root/root 948 2013-11-03 06:00 ./usr/share/man/man1/gt-readjoiner-prefilter.1.gz
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libgenometools0_1.5.1-2_armhf.deb
─────────────────────────────────
new debian package, version 2.0.
size 1983346 bytes: control archive=27053 bytes.
999 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
163503 bytes, 4396 lines symbols
Package: libgenometools0
Source: genometools
Version: 1.5.1-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4910
Depends: libbz2-1.0, libc6 (>= 2.7), libcairo2 (>= 1.2.4), libexpat1 (>= 2.0.1), libglib2.0-0 (>= 2.12.0), liblua5.1-0, libpango-1.0-0 (>= 1.14.0), libpangocairo-1.0-0 (>= 1.14.0), libsqlite3-0 (>= 3.5.9), 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 2013-11-03 06:01 ./
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/lib/
-rw-r--r-- root/root 4849572 2013-11-03 06:00 ./usr/lib/libgenometools.so.0
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/share/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/share/doc/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./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 1100 2013-10-28 07:56 ./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_1.5.1-2_armhf.deb
─────────────────────────────────────
new debian package, version 2.0.
size 83052 bytes: control archive=4726 bytes.
672 bytes, 18 lines control
12257 bytes, 146 lines md5sums
Package: libgenometools0-dev
Source: genometools
Version: 1.5.1-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 422
Depends: libgenometools0 (= 1.5.1-2)
Section: libdevel
Priority: optional
Homepage: http://genometools.org
Description: development files for GenomeTools
This package contains the GenomeTools static library and necessary
header files.
.
Besides basic bioinformatics data structures, the library contains components
for sequence and annotation handling, sequence compression, index structure
generation and access, efficient matching, annotation visualization and much
more.
drwxr-xr-x root/root 0 2013-11-03 06:01 ./
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-rw-r--r-- root/root 2669 2013-11-03 06:00 ./usr/include/genometools/ltr/ltr_refseq_match_stream_api.h
-rw-r--r-- root/root 1982 2013-11-03 06:00 ./usr/include/genometools/gt_config.h
-rw-r--r-- root/root 6280 2013-11-03 06:00 ./usr/include/genometools/genometools.h
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/share/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/share/doc/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./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 1100 2013-10-28 07:56 ./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 2013-11-03 06:00 ./usr/lib/
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/libgenometools.so -> libgenometools.so.0
genometools-dbg_1.5.1-2_armhf.deb
─────────────────────────────────
new debian package, version 2.0.
size 6166028 bytes: control archive=755 bytes.
571 bytes, 14 lines control
447 bytes, 5 lines md5sums
Package: genometools-dbg
Source: genometools
Version: 1.5.1-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6891
Depends: genometools (= 1.5.1-2) | libgenometools0 (= 1.5.1-2)
Section: debug
Priority: extra
Homepage: http://genometools.org
Description: versatile genome analysis toolkit, with debug symbols
This package contains debug information stripped from the GenomeTools.
You may decide to install it to help identifying issues, typically
to help communication with upstream developers.
drwxr-xr-x root/root 0 2013-11-03 06:01 ./
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/share/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/share/doc/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./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 1100 2013-10-28 07:56 ./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 2013-11-03 06:00 ./usr/lib/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/lib/debug/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/lib/debug/.build-id/44/
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python-genometools_1.5.1-2_armhf.deb
────────────────────────────────────
new debian package, version 2.0.
size 31950 bytes: control archive=2425 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: 1.5.1-2
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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drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/core/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/annotationsketch/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/share/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/share/doc/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/share/doc/python-genometools/
-rw-r--r-- root/root 6607 2013-03-07 13:07 ./usr/share/doc/python-genometools/copyright
-rw-r--r-- root/root 1100 2013-10-28 07:56 ./usr/share/doc/python-genometools/changelog.Debian.gz
-rw-r--r-- root/root 4081 2013-03-07 12:25 ./usr/share/doc/python-genometools/changelog.gz
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/share/pyshared/
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/share/pyshared/gt/
-rw-r--r-- root/root 1292 2013-03-07 12:25 ./usr/share/pyshared/gt/__init__.py
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-rw-r--r-- root/root 17833 2013-03-07 12:25 ./usr/share/pyshared/gt/core/encseq.py
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-rw-r--r-- root/root 1244 2013-03-07 12:25 ./usr/share/pyshared/gt/core/warning.py
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/share/pyshared/gt/annotationsketch/
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-rw-r--r-- root/root 4073 2013-03-07 12:25 ./usr/share/pyshared/gt/annotationsketch/block.py
-rw-r--r-- root/root 4711 2013-03-07 12:25 ./usr/share/pyshared/gt/annotationsketch/canvas.py
-rw-r--r-- root/root 1112 2013-03-07 12:25 ./usr/share/pyshared/gt/annotationsketch/color.py
-rw-r--r-- root/root 3123 2013-03-07 12:25 ./usr/share/pyshared/gt/annotationsketch/custom_track.py
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-rw-r--r-- root/root 11764 2013-03-07 12:25 ./usr/share/pyshared/gt/annotationsketch/graphics.py
-rw-r--r-- root/root 3312 2013-03-07 12:25 ./usr/share/pyshared/gt/annotationsketch/image_info.py
-rw-r--r-- root/root 3412 2013-03-07 12:25 ./usr/share/pyshared/gt/annotationsketch/layout.py
-rw-r--r-- root/root 2808 2013-03-07 12:25 ./usr/share/pyshared/gt/annotationsketch/rec_map.py
-rw-r--r-- root/root 6265 2013-03-07 12:25 ./usr/share/pyshared/gt/annotationsketch/style.py
drwxr-xr-x root/root 0 2013-11-03 06:00 ./usr/share/pyshared/gt/extended/
-rw-r--r-- root/root 1937 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/__init__.py
-rw-r--r-- root/root 1621 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/add_introns_stream.py
-rw-r--r-- root/root 2693 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/anno_db.py
-rw-r--r-- root/root 1649 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/comment_node.py
-rw-r--r-- root/root 2598 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/custom_stream.py
-rw-r--r-- root/root 1894 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/custom_stream_example.py
-rw-r--r-- root/root 5080 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/custom_visitor.py
-rw-r--r-- root/root 1922 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/custom_visitor_example.py
-rw-r--r-- root/root 1633 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/dup_feature_stream.py
-rw-r--r-- root/root 1378 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/eof_node.py
-rw-r--r-- root/root 5780 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/feature_index.py
-rw-r--r-- root/root 8909 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/feature_node.py
-rw-r--r-- root/root 1699 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/feature_stream.py
-rw-r--r-- root/root 4547 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/genome_node.py
-rw-r--r-- root/root 2078 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/genome_stream.py
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-rw-r--r-- root/root 1385 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/gff3_out_stream.py
-rw-r--r-- root/root 1127 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/gff3_visitor.py
-rw-r--r-- root/root 1628 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/inter_feature_stream.py
-rw-r--r-- root/root 1549 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/merge_feature_stream.py
-rw-r--r-- root/root 1896 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/meta_node.py
-rw-r--r-- root/root 1383 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/node_visitor.py
-rw-r--r-- root/root 2131 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/rdb.py
-rw-r--r-- root/root 1582 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/region_node.py
-rw-r--r-- root/root 2334 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/sequence_node.py
-rw-r--r-- root/root 933 2013-03-07 12:25 ./usr/share/pyshared/gt/extended/strand.py
-rw-r--r-- root/root 257 2013-11-03 06:00 ./usr/share/pyshared/GenomeTools-0.1.egg-info
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/core/warning.py -> ../../../../../share/pyshared/gt/core/warning.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/core/str_array.py -> ../../../../../share/pyshared/gt/core/str_array.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/core/readmode.py -> ../../../../../share/pyshared/gt/core/readmode.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/core/gtstr.py -> ../../../../../share/pyshared/gt/core/gtstr.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/core/gtrange.py -> ../../../../../share/pyshared/gt/core/gtrange.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/core/error.py -> ../../../../../share/pyshared/gt/core/error.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/core/encseq.py -> ../../../../../share/pyshared/gt/core/encseq.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/core/array.py -> ../../../../../share/pyshared/gt/core/array.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/core/alphabet.py -> ../../../../../share/pyshared/gt/core/alphabet.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/core/__init__.py -> ../../../../../share/pyshared/gt/core/__init__.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/annotationsketch/style.py -> ../../../../../share/pyshared/gt/annotationsketch/style.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/annotationsketch/rec_map.py -> ../../../../../share/pyshared/gt/annotationsketch/rec_map.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/annotationsketch/layout.py -> ../../../../../share/pyshared/gt/annotationsketch/layout.py
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lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/annotationsketch/graphics.py -> ../../../../../share/pyshared/gt/annotationsketch/graphics.py
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lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/annotationsketch/feature_index.py -> ../../../../../share/pyshared/gt/annotationsketch/feature_index.py
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lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/annotationsketch/custom_track_example.py -> ../../../../../share/pyshared/gt/annotationsketch/custom_track_example.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/annotationsketch/custom_track.py -> ../../../../../share/pyshared/gt/annotationsketch/custom_track.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/annotationsketch/color.py -> ../../../../../share/pyshared/gt/annotationsketch/color.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/annotationsketch/canvas.py -> ../../../../../share/pyshared/gt/annotationsketch/canvas.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/annotationsketch/block.py -> ../../../../../share/pyshared/gt/annotationsketch/block.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/annotationsketch/__init__.py -> ../../../../../share/pyshared/gt/annotationsketch/__init__.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/strand.py -> ../../../../../share/pyshared/gt/extended/strand.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/sequence_node.py -> ../../../../../share/pyshared/gt/extended/sequence_node.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/region_node.py -> ../../../../../share/pyshared/gt/extended/region_node.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/rdb.py -> ../../../../../share/pyshared/gt/extended/rdb.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/node_visitor.py -> ../../../../../share/pyshared/gt/extended/node_visitor.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/meta_node.py -> ../../../../../share/pyshared/gt/extended/meta_node.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/merge_feature_stream.py -> ../../../../../share/pyshared/gt/extended/merge_feature_stream.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/inter_feature_stream.py -> ../../../../../share/pyshared/gt/extended/inter_feature_stream.py
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lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/gff3_out_stream.py -> ../../../../../share/pyshared/gt/extended/gff3_out_stream.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/gff3_in_stream.py -> ../../../../../share/pyshared/gt/extended/gff3_in_stream.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/genome_stream.py -> ../../../../../share/pyshared/gt/extended/genome_stream.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/genome_node.py -> ../../../../../share/pyshared/gt/extended/genome_node.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/feature_stream.py -> ../../../../../share/pyshared/gt/extended/feature_stream.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/feature_node.py -> ../../../../../share/pyshared/gt/extended/feature_node.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/feature_index.py -> ../../../../../share/pyshared/gt/extended/feature_index.py
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lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/custom_visitor.py -> ../../../../../share/pyshared/gt/extended/custom_visitor.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/custom_stream_example.py -> ../../../../../share/pyshared/gt/extended/custom_stream_example.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/custom_stream.py -> ../../../../../share/pyshared/gt/extended/custom_stream.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/comment_node.py -> ../../../../../share/pyshared/gt/extended/comment_node.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/anno_db.py -> ../../../../../share/pyshared/gt/extended/anno_db.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/add_introns_stream.py -> ../../../../../share/pyshared/gt/extended/add_introns_stream.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/extended/__init__.py -> ../../../../../share/pyshared/gt/extended/__init__.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/props.py -> ../../../../share/pyshared/gt/props.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/dlload.py -> ../../../../share/pyshared/gt/dlload.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/gt/__init__.py -> ../../../../share/pyshared/gt/__init__.py
lrwxrwxrwx root/root 0 2013-11-03 06:00 ./usr/lib/python2.7/dist-packages/GenomeTools-0.1.egg-info -> ../../../share/pyshared/GenomeTools-0.1.egg-info
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 230284
Build-Time: 547
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 1359
Job: genometools_1.5.1-2
Machine Architecture: armhf
Package: genometools
Package-Time: 1973
Source-Version: 1.5.1-2
Space: 230284
Status: successful
Version: 1.5.1-2
────────────────────────────────────────────────────────────────────────────────
Finished at 20131103-0601
Build needed 00:32:53, 230284k disc space