Author: plessy Date: 2011-03-13 03:13:38 +0000 (Sun, 13 Mar 2011) New Revision: 6257
Added: trunk/packages/maq/tags/0.7.1-4/ trunk/packages/maq/tags/0.7.1-4/debian/changelog trunk/packages/maq/tags/0.7.1-4/debian/compat trunk/packages/maq/tags/0.7.1-4/debian/control trunk/packages/maq/tags/0.7.1-4/debian/copyright trunk/packages/maq/tags/0.7.1-4/debian/maq.doc-base trunk/packages/maq/tags/0.7.1-4/debian/upstream-metadata.yaml Removed: trunk/packages/maq/tags/0.7.1-4/debian/changelog trunk/packages/maq/tags/0.7.1-4/debian/compat trunk/packages/maq/tags/0.7.1-4/debian/control trunk/packages/maq/tags/0.7.1-4/debian/copyright trunk/packages/maq/tags/0.7.1-4/debian/maq.doc-base Log: [svn-buildpackage] Tagging maq 0.7.1-4 Deleted: trunk/packages/maq/tags/0.7.1-4/debian/changelog =================================================================== --- trunk/packages/maq/trunk/debian/changelog 2011-03-12 22:31:11 UTC (rev 6254) +++ trunk/packages/maq/tags/0.7.1-4/debian/changelog 2011-03-13 03:13:38 UTC (rev 6257) @@ -1,62 +0,0 @@ -maq (0.7.1-4) UNRELEASED; urgency=low - - * Developmemt of Maq stopped in 2008. Its successors are BWA and SAMtools. - - -- Charles Plessy <[email protected]> Mon, 01 Nov 2010 19:10:28 +0900 - -maq (0.7.1-3) unstable; urgency=low - - * Distribute scripts that are not installed by upstream’s - makefile in /usr/share/maq (debian/install). - * Incremented Standards-Version in debian/policy to reflect - conformance with Policy 3.8.2 (no changes needed). - * debian/patch: made headers conformant with current draft of DEP3. - - -- Charles Plessy <[email protected]> Fri, 17 Jul 2009 22:00:02 +0900 - -maq (0.7.1-2) unstable; urgency=low - - * Enable LARGEFILE64_SOURCE to prevent a problem with zlib on - 64bit archs (Thanks to Peter Green <[email protected]> for - the patch) - Closes: #506009 - * Standards-Version: 3.8.1 (no changes needed) - - -- Andreas Tille <[email protected]> Thu, 16 Apr 2009 15:56:09 +0200 - -maq (0.7.1-1) unstable; urgency=low - - * New upstream release 0.7.1 (Closes: 505820) - - Accepts reads shorter than 127 bp (63 bp before). - - .map alignment changes and not backward-compatible. - - Reversion to short reads possible with --enable-shortreads. - * New upstream release 0.6.8 - - New features for the 1000 genome project. - - Error dependency coefficient reduced from 0.93 to 0.85. - - Added mapvalidate command. - - Support generating GLF format. - - The mapcheck command can optionally dump additional information. - * debian/patches: - - 20_perl_path.patch deleted because accepted upstream. - - 10_prevent_-64_option.patch reorganised to only modify configure.ac - and forwarded upstream. - - 20_prevent_-64_option.patch changes configure and can be regenerated - by running autoreconf. - * debian/control: typo corrected in short description (Closes: #492979) - * debian/reference: BibTeX reference downloaded from - http://genome.cshlp.org/citmgr?gca=genome;18/11/1851 with abstract - removed because it is a copyrighted work. - * debian/README.Sources renamed README.source to comply with Policy. - - -- Charles Plessy <[email protected]> Sun, 16 Nov 2008 22:52:04 +0900 - -maq (0.6.7-1) unstable; urgency=low - - [ Charles Plessy ] - * Initial release (Closes: #489836) - - [ Andreas Tille ] - * Rudely deleted -m64 option from configure because multiarch - building leads to several problems - - -- Andreas Tille <[email protected]> Wed, 16 Jul 2008 12:01:33 +0200 Copied: trunk/packages/maq/tags/0.7.1-4/debian/changelog (from rev 6256, trunk/packages/maq/trunk/debian/changelog) =================================================================== --- trunk/packages/maq/tags/0.7.1-4/debian/changelog (rev 0) +++ trunk/packages/maq/tags/0.7.1-4/debian/changelog 2011-03-13 03:13:38 UTC (rev 6257) @@ -0,0 +1,68 @@ +maq (0.7.1-4) unstable; urgency=low + + * Development of Maq stopped in 2008. Its successors are BWA and SAMtools. + (debian/control, debian/maq.doc-base). + * DEP-5 conformant debian/copyright file, checked with ‘config-edit’. + * Use Debhelper 8 (debian/control, debian/compat). + * Collected various information in debian/upstream-metadata.yaml. + * Incremented Standards-Version in debian/policy to reflect + conformance with Policy 3.9.1 (no changes needed). + + -- Charles Plessy <[email protected]> Sun, 13 Mar 2011 11:35:38 +0900 + +maq (0.7.1-3) unstable; urgency=low + + * Distribute scripts that are not installed by upstream’s + makefile in /usr/share/maq (debian/install). + * Incremented Standards-Version in debian/policy to reflect + conformance with Policy 3.8.2 (no changes needed). + * debian/patch: made headers conformant with current draft of DEP3. + + -- Charles Plessy <[email protected]> Fri, 17 Jul 2009 22:00:02 +0900 + +maq (0.7.1-2) unstable; urgency=low + + * Enable LARGEFILE64_SOURCE to prevent a problem with zlib on + 64bit archs (Thanks to Peter Green <[email protected]> for + the patch) + Closes: #506009 + * Standards-Version: 3.8.1 (no changes needed) + + -- Andreas Tille <[email protected]> Thu, 16 Apr 2009 15:56:09 +0200 + +maq (0.7.1-1) unstable; urgency=low + + * New upstream release 0.7.1 (Closes: 505820) + - Accepts reads shorter than 127 bp (63 bp before). + - .map alignment changes and not backward-compatible. + - Reversion to short reads possible with --enable-shortreads. + * New upstream release 0.6.8 + - New features for the 1000 genome project. + - Error dependency coefficient reduced from 0.93 to 0.85. + - Added mapvalidate command. + - Support generating GLF format. + - The mapcheck command can optionally dump additional information. + * debian/patches: + - 20_perl_path.patch deleted because accepted upstream. + - 10_prevent_-64_option.patch reorganised to only modify configure.ac + and forwarded upstream. + - 20_prevent_-64_option.patch changes configure and can be regenerated + by running autoreconf. + * debian/control: typo corrected in short description (Closes: #492979) + * debian/reference: BibTeX reference downloaded from + http://genome.cshlp.org/citmgr?gca=genome;18/11/1851 with abstract + removed because it is a copyrighted work. + * debian/README.Sources renamed README.source to comply with Policy. + + -- Charles Plessy <[email protected]> Sun, 16 Nov 2008 22:52:04 +0900 + +maq (0.6.7-1) unstable; urgency=low + + [ Charles Plessy ] + * Initial release (Closes: #489836) + + [ Andreas Tille ] + * Rudely deleted -m64 option from configure because multiarch + building leads to several problems + + -- Andreas Tille <[email protected]> Wed, 16 Jul 2008 12:01:33 +0200 Deleted: trunk/packages/maq/tags/0.7.1-4/debian/compat =================================================================== --- trunk/packages/maq/trunk/debian/compat 2011-03-12 22:31:11 UTC (rev 6254) +++ trunk/packages/maq/tags/0.7.1-4/debian/compat 2011-03-13 03:13:38 UTC (rev 6257) @@ -1 +0,0 @@ -7 Copied: trunk/packages/maq/tags/0.7.1-4/debian/compat (from rev 6256, trunk/packages/maq/trunk/debian/compat) =================================================================== --- trunk/packages/maq/tags/0.7.1-4/debian/compat (rev 0) +++ trunk/packages/maq/tags/0.7.1-4/debian/compat 2011-03-13 03:13:38 UTC (rev 6257) @@ -0,0 +1 @@ +8 Deleted: trunk/packages/maq/tags/0.7.1-4/debian/control =================================================================== --- trunk/packages/maq/trunk/debian/control 2011-03-12 22:31:11 UTC (rev 6254) +++ trunk/packages/maq/tags/0.7.1-4/debian/control 2011-03-13 03:13:38 UTC (rev 6257) @@ -1,24 +0,0 @@ -Source: maq -Section: science -Priority: optional -Maintainer: Debian Med Packaging Team <[email protected]> -DM-Upload-Allowed: yes -Uploaders: Andreas Tille <[email protected]>, - Charles Plessy <[email protected]> -Build-Depends: cdbs, debhelper (>= 7), autotools-dev, zlib1g-dev, quilt -Standards-Version: 3.8.2 -Homepage: http://maq.sourceforge.net/ -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/maq/trunk/?rev=0&sc=0 -Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/maq/trunk/ - -Package: maq -Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends} -Description: maps short fixed-length polymorphic DNA sequence reads to reference sequences - Maq (short for Mapping and Assembly with Quality) builds mapping assemblies - from short reads generated by the next-generation sequencing machines. It was - particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has a - preliminary functionality to handle ABI SOLiD data. Maq is previously known as - mapass2. - . - Developmemt of Maq stopped in 2008. Its successors are BWA and SAMtools. Copied: trunk/packages/maq/tags/0.7.1-4/debian/control (from rev 6256, trunk/packages/maq/trunk/debian/control) =================================================================== --- trunk/packages/maq/tags/0.7.1-4/debian/control (rev 0) +++ trunk/packages/maq/tags/0.7.1-4/debian/control 2011-03-13 03:13:38 UTC (rev 6257) @@ -0,0 +1,25 @@ +Source: maq +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Andreas Tille <[email protected]>, + Charles Plessy <[email protected]> +Build-Depends: cdbs, debhelper (>= 8), autotools-dev, zlib1g-dev, quilt +Standards-Version: 3.9.1 +Homepage: http://maq.sourceforge.net/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/maq/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/maq/trunk/ + +Package: maq +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Suggests: bwa, samtools +Description: maps short fixed-length polymorphic DNA sequence reads to reference sequences + Maq (short for Mapping and Assembly with Quality) builds mapping assemblies + from short reads generated by the next-generation sequencing machines. It was + particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has a + preliminary functionality to handle ABI SOLiD data. Maq is previously known as + mapass2. + . + Developmemt of Maq stopped in 2008. Its successors are BWA and SAMtools. Deleted: trunk/packages/maq/tags/0.7.1-4/debian/copyright =================================================================== --- trunk/packages/maq/trunk/debian/copyright 2011-03-12 22:31:11 UTC (rev 6254) +++ trunk/packages/maq/tags/0.7.1-4/debian/copyright 2011-03-13 03:13:38 UTC (rev 6257) @@ -1,50 +0,0 @@ -Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’. - -Name : Maq: Mapping and Assembly with Qualities -Contact : Heng Li <[email protected]> -Source : http://downloads.sourceforge.net/maq/maq-0.7.1.tar.bz2 - -License: GPL3+ -Copyright: 2003-2008, Heng Li <[email protected]> - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. - -On Debian systems, the complete text of the GNU General Public License version -3 can be found in ‘/usr/share/common-licenses/GPL-3’. - -Files: stdaln.* stdhash.hh -Copyright: 2003-2008, Heng Li <[email protected]> -License: LGPL-2.1+ - This library is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public - License as published by the Free Software Foundation; either - version 2.1 of the License, or (at your option) any later version. - - This library is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - Lesser General Public License for more details. - - You should have received a copy of the GNU Lesser General Public - License along with this library; if not, write to the Free Software - Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. - -On Debian systems, the complete text of the GNU Lesser General Public License -version 2.1 can be found in ‘/usr/share/common-licenses/LGPL-2.1’. - -Files: debian/* -Copyright: 2008–2009, Charles Plessy <[email protected]>, - Andreas Tille <[email protected]> -License: Same as Maq itelf - (see above) Copied: trunk/packages/maq/tags/0.7.1-4/debian/copyright (from rev 6255, trunk/packages/maq/trunk/debian/copyright) =================================================================== --- trunk/packages/maq/tags/0.7.1-4/debian/copyright (rev 0) +++ trunk/packages/maq/tags/0.7.1-4/debian/copyright 2011-03-13 03:13:38 UTC (rev 6257) @@ -0,0 +1,45 @@ +Format: http://dep.debian.net/deps/dep5/ +Source: http://downloads.sourceforge.net/maq/maq-0.7.1.tar.bz2 + +Files: * +Copyright: 2003-2008, Heng Li <[email protected]> +License: GPL-3+ + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + . + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + . + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. +Comment: On Debian systems, the complete text of the GNU General Public + License version 3 can be found in ‘/usr/share/common-licenses/GPL-3’. + +Files: stdaln.* stdhash.hh +Copyright: 2003-2008, Heng Li <[email protected]> +License: LGPL-2.1+ + This library is free software; you can redistribute it and/or + modify it under the terms of the GNU Lesser General Public + License as published by the Free Software Foundation; either + version 2.1 of the License, or (at your option) any later version. + . + This library is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + Lesser General Public License for more details. + . + You should have received a copy of the GNU Lesser General Public + License along with this library; if not, write to the Free Software + Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. +Comment: On Debian systems, the complete text of the GNU Lesser General + Public License version 2.1 can be found in ‘/usr/share/common-licenses/LGPL-2.1’. + +Files: debian/* +Copyright: 2008–2011, Charles Plessy <[email protected]>, + Andreas Tille <[email protected]> +License: same-as-upstream + Same as Maq itelf (see above). Deleted: trunk/packages/maq/tags/0.7.1-4/debian/maq.doc-base =================================================================== --- trunk/packages/maq/trunk/debian/maq.doc-base 2011-03-12 22:31:11 UTC (rev 6254) +++ trunk/packages/maq/tags/0.7.1-4/debian/maq.doc-base 2011-03-13 03:13:38 UTC (rev 6257) @@ -1,8 +0,0 @@ -Document: maq -Title: Maq — Mapping and Assembly with Quality -Author: Heng Li <[email protected]> -Abstract: Maq manual page in PDF format -Section: Science/Biology - -Format: PDF -Files: /usr/share/doc/maq/maq.pdf Copied: trunk/packages/maq/tags/0.7.1-4/debian/maq.doc-base (from rev 6256, trunk/packages/maq/trunk/debian/maq.doc-base) =================================================================== --- trunk/packages/maq/tags/0.7.1-4/debian/maq.doc-base (rev 0) +++ trunk/packages/maq/tags/0.7.1-4/debian/maq.doc-base 2011-03-13 03:13:38 UTC (rev 6257) @@ -0,0 +1,10 @@ +Document: maq +Title: Maq — Mapping and Assembly with Quality +Author: Heng Li <[email protected]> +Abstract: Maq manual page in PDF format + Note that Developmemt of Maq stopped in 2008. Its successors are BWA + and SAMtools. +Section: Science/Biology + +Format: PDF +Files: /usr/share/doc/maq/maq.pdf Copied: trunk/packages/maq/tags/0.7.1-4/debian/upstream-metadata.yaml (from rev 6256, trunk/packages/maq/trunk/debian/upstream-metadata.yaml) =================================================================== --- trunk/packages/maq/tags/0.7.1-4/debian/upstream-metadata.yaml (rev 0) +++ trunk/packages/maq/tags/0.7.1-4/debian/upstream-metadata.yaml 2011-03-13 03:13:38 UTC (rev 6257) @@ -0,0 +1,20 @@ +Archive: SourceForge +Contact: Heng Li <[email protected]> +DOI: 10.1101/gr.078212.108 +FAQ: http://maq.sourceforge.net/faq.shtml +Name: Maq +Homepage: http://maq.sourceforge.net/ +PMID: 18714091 +Reference: + author: Li, Heng and Ruan, Jue and Durbin, Richard + title: Mapping short DNA sequencing reads and calling variants using mapping quality scores + journal: Genome Research + volume: 18 + number: 11 + pages: 1851-1858 + doi: 10.1101/gr.078212.108 + year: 2008 + URL: http://genome.cshlp.org/content/18/11/1851.abstract + eprint: http://genome.cshlp.org/content/18/11/1851.full.pdf+html +Watch: | + http://sf.net/maq/maq-([\d\.]+)\.tar\.bz2 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
