Author: plessy Date: 2010-10-27 12:27:54 +0000 (Wed, 27 Oct 2010) New Revision: 5383
Added: trunk/packages/bwa/tags/0.5.8c-1/ trunk/packages/bwa/tags/0.5.8c-1/debian/changelog trunk/packages/bwa/tags/0.5.8c-1/debian/control trunk/packages/bwa/tags/0.5.8c-1/debian/copyright Removed: trunk/packages/bwa/tags/0.5.8c-1/debian/changelog trunk/packages/bwa/tags/0.5.8c-1/debian/control trunk/packages/bwa/tags/0.5.8c-1/debian/copyright Log: [svn-buildpackage] Tagging bwa 0.5.8c-1 Deleted: trunk/packages/bwa/tags/0.5.8c-1/debian/changelog =================================================================== --- trunk/packages/bwa/trunk/debian/changelog 2010-10-27 08:15:22 UTC (rev 5381) +++ trunk/packages/bwa/tags/0.5.8c-1/debian/changelog 2010-10-27 12:27:54 UTC (rev 5383) @@ -1,44 +0,0 @@ -bwa (0.5.8a-1) unstable; urgency=low - - * New upstream release. - * Use the more convenient viewsvn as VCS-Broswer (debian/control). - * Incremented Standards-Version to reflect conformance with - Policy 3.9.0 (debian/control, no changes needed). - - -- Charles Plessy <[email protected]> Wed, 30 Jun 2010 10:44:30 +0900 - -bwa (0.5.7-1) unstable; urgency=low - - * New upstream release. - - -- Charles Plessy <[email protected]> Tue, 02 Mar 2010 23:33:06 +0900 - -bwa (0.5.6-1) unstable; urgency=low - - * New upstream release. - * Incremented Standards-Version to reflect conformance with - Policy 3.8.4 (debian/control). - - -- Charles Plessy <[email protected]> Wed, 17 Feb 2010 12:48:57 +0900 - -bwa (0.5.5-1) unstable; urgency=low - - * New upstream release. - * Using Dpkg source format version ‘3.0 (quilt)’ (debian/source/format). - - -- Charles Plessy <[email protected]> Wed, 11 Nov 2009 23:05:19 +0900 - -bwa (0.5.4-1) unstable; urgency=low - - * New upstream release, see ‘/usr/share/doc/bwa/NEWS.gz’. - * Refreshed debian/copyright. - * Reflected the rename of dBWT-Sw to BWA-SW in the package's description - (debian/control). - - -- Charles Plessy <[email protected]> Mon, 19 Oct 2009 13:59:42 +0900 - -bwa (0.5.3-1) unstable; urgency=low - - * Initial release (Closes: #548719) - - -- Charles Plessy <[email protected]> Thu, 08 Oct 2009 19:20:41 +0900 Copied: trunk/packages/bwa/tags/0.5.8c-1/debian/changelog (from rev 5382, trunk/packages/bwa/trunk/debian/changelog) =================================================================== --- trunk/packages/bwa/tags/0.5.8c-1/debian/changelog (rev 0) +++ trunk/packages/bwa/tags/0.5.8c-1/debian/changelog 2010-10-27 12:27:54 UTC (rev 5383) @@ -0,0 +1,56 @@ +bwa (0.5.8c-1) unstable; urgency=low + + * Bug fix release, reverting the scoring system back to the one used in + 0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not + happen in principle. Such wrong cigars also incur errors in indel calling + when samtools is in use (Closes: #601568). + * Incremented Standards-Version to reflect conformance with Policy 3.9.1 + (debian/control, no changes needed). + * debian/copyright updated and reformatted. + + -- Charles Plessy <[email protected]> Wed, 27 Oct 2010 21:14:34 +0900 + +bwa (0.5.8a-1) unstable; urgency=low + + * New upstream release. + * Use the more convenient viewsvn as VCS-Broswer (debian/control). + * Incremented Standards-Version to reflect conformance with + Policy 3.9.0 (debian/control, no changes needed). + + -- Charles Plessy <[email protected]> Wed, 30 Jun 2010 10:44:30 +0900 + +bwa (0.5.7-1) unstable; urgency=low + + * New upstream release. + + -- Charles Plessy <[email protected]> Tue, 02 Mar 2010 23:33:06 +0900 + +bwa (0.5.6-1) unstable; urgency=low + + * New upstream release. + * Incremented Standards-Version to reflect conformance with + Policy 3.8.4 (debian/control). + + -- Charles Plessy <[email protected]> Wed, 17 Feb 2010 12:48:57 +0900 + +bwa (0.5.5-1) unstable; urgency=low + + * New upstream release. + * Using Dpkg source format version ‘3.0 (quilt)’ (debian/source/format). + + -- Charles Plessy <[email protected]> Wed, 11 Nov 2009 23:05:19 +0900 + +bwa (0.5.4-1) unstable; urgency=low + + * New upstream release, see ‘/usr/share/doc/bwa/NEWS.gz’. + * Refreshed debian/copyright. + * Reflected the rename of dBWT-Sw to BWA-SW in the package's description + (debian/control). + + -- Charles Plessy <[email protected]> Mon, 19 Oct 2009 13:59:42 +0900 + +bwa (0.5.3-1) unstable; urgency=low + + * Initial release (Closes: #548719) + + -- Charles Plessy <[email protected]> Thu, 08 Oct 2009 19:20:41 +0900 Deleted: trunk/packages/bwa/tags/0.5.8c-1/debian/control =================================================================== --- trunk/packages/bwa/trunk/debian/control 2010-10-27 08:15:22 UTC (rev 5381) +++ trunk/packages/bwa/tags/0.5.8c-1/debian/control 2010-10-27 12:27:54 UTC (rev 5383) @@ -1,23 +0,0 @@ -Source: bwa -Section: science -Priority: optional -Maintainer: Debian Med Packaging Team <[email protected]> -DM-Upload-Allowed: yes -Uploaders: Charles Plessy <[email protected]> -Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev -Standards-Version: 3.9.0 -Homepage: http://bio-bwa.sourceforge.net/ -Vcs-Browser: http://svn.debian.org/viewsvn/debian-med/trunk/packages/bwa/trunk/ -Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/bwa/trunk/ - -Package: bwa -Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends} -Suggests: samtools -Description: Burrows-Wheeler Aligner - Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short - nucleotide sequences against a long reference sequence such as the human - genome. It implements two algorithms, bwa-short and BWA-SW. The former works - for query sequences shorter than 200 bp and the latter for longer sequences up - to around 100 kbp. Both algorithms do gapped alignment. They are usually more - accurate and faster on queries with low error rates. Copied: trunk/packages/bwa/tags/0.5.8c-1/debian/control (from rev 5382, trunk/packages/bwa/trunk/debian/control) =================================================================== --- trunk/packages/bwa/tags/0.5.8c-1/debian/control (rev 0) +++ trunk/packages/bwa/tags/0.5.8c-1/debian/control 2010-10-27 12:27:54 UTC (rev 5383) @@ -0,0 +1,23 @@ +Source: bwa +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Charles Plessy <[email protected]> +Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev +Standards-Version: 3.9.1 +Homepage: http://bio-bwa.sourceforge.net/ +Vcs-Browser: http://svn.debian.org/viewsvn/debian-med/trunk/packages/bwa/trunk/ +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/bwa/trunk/ + +Package: bwa +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Suggests: samtools +Description: Burrows-Wheeler Aligner + Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short + nucleotide sequences against a long reference sequence such as the human + genome. It implements two algorithms, bwa-short and BWA-SW. The former works + for query sequences shorter than 200 bp and the latter for longer sequences up + to around 100 kbp. Both algorithms do gapped alignment. They are usually more + accurate and faster on queries with low error rates. Deleted: trunk/packages/bwa/tags/0.5.8c-1/debian/copyright =================================================================== --- trunk/packages/bwa/trunk/debian/copyright 2010-10-27 08:15:22 UTC (rev 5381) +++ trunk/packages/bwa/tags/0.5.8c-1/debian/copyright 2010-10-27 12:27:54 UTC (rev 5383) @@ -1,63 +0,0 @@ -Name : Burrows-Wheeler Aligner -Contact : [email protected] -Source : http://qa.debian.org/watch/sf.php/bio-bwa/bwa-0.5.7.tar.bz2 - -Copyright : © 2008 Genome Research Ltd (GRL) - 2008, by Heng Li <[email protected]> - © 2003-2006, 2008, 2009, by Heng Li <[email protected]> - © 2008, 2009 by attractor <[email protected]> - © 2008 Yuta Mori -License : MIT - - Permission is hereby granted, free of charge, to any person obtaining - a copy of this software and associated documentation files (the - "Software"), to deal in the Software without restriction, including - without limitation the rights to use, copy, modify, merge, publish, - distribute, sublicense, and/or sell copies of the Software, and to - permit persons to whom the Software is furnished to do so, subject to - the following conditions: - - The above copyright notice and this permission notice shall be - included in all copies or substantial portions of the Software. - - THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF - MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND - NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS - BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN - ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN - CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - SOFTWARE. - - -Files : bwt_gen/bwt_gen.* -Copyright : © 2004, Wong Chi Kwong -License : GPL-2+ - - 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 2 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, write to the Free Software Foundation, Inc., - 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. - -On Debian systems, you can find a copy of the GNU General Public License -version 2 in ‘/usr/share/common-licenses/GPL-2’. - - -Files : bwt_gen/QSufSort.* -Copyright : 1999, N. Jesper Larsson -License : - - This software may be used freely for any purpose. However, when distributed, - the original source must be clearly stated, and, when the source code is - distributed, the copyright notice must be retained and any alterations in - the code must be clearly marked. No warranty is given regarding the quality - of this software. Copied: trunk/packages/bwa/tags/0.5.8c-1/debian/copyright (from rev 5382, trunk/packages/bwa/trunk/debian/copyright) =================================================================== --- trunk/packages/bwa/tags/0.5.8c-1/debian/copyright (rev 0) +++ trunk/packages/bwa/tags/0.5.8c-1/debian/copyright 2010-10-27 12:27:54 UTC (rev 5383) @@ -0,0 +1,86 @@ +Format: DEP-5 (beta) +Source: http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.8c.tar.bz2 +Copyright: © 2008 Genome Research Ltd (GRL) + 2008, by Heng Li <[email protected]> + © 2003-2006, 2008, 2009, by Heng Li <[email protected]> + © 2008, 2009 by attractor <[email protected]> + © 2008 Yuta Mori +License: MIT + Permission is hereby granted, free of charge, to any person obtaining + a copy of this software and associated documentation files (the + "Software"), to deal in the Software without restriction, including + without limitation the rights to use, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + . + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + . + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. + +Files: m4/acx_pthread.m4 +Copyright: © 2008 Steven G. Johnson <[email protected]> +License: GPL-3+ with Autoconf exception + 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/>. + . + As a special exception, the respective Autoconf Macro's copyright owner + gives unlimited permission to copy, distribute and modify the configure + scripts that are the output of Autoconf when processing the Macro. You + need not follow the terms of the GNU General Public License when using + or distributing such scripts, even though portions of the text of the + Macro appear in them. The GNU General Public License (GPL) does govern + all other use of the material that constitutes the Autoconf Macro. + . + This special exception to the GPL applies to versions of the Autoconf + Macro released by the Autoconf Archive. When you make and distribute a + modified version of the Autoconf Macro, you may extend this special + exception to the GPL to apply to your modified version as well +Comment: On Debian systems, you can find a copy of the GNU General Public + License version 3 in ‘/usr/share/common-licenses/GPL-3’. + +Files: bwt_gen/bwt_gen.* +Copyright: © 2004, Wong Chi Kwong +License: GPL-2+ + 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 2 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, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. +Comment: On Debian systems, you can find a copy of the GNU General Public + License version 2 in ‘/usr/share/common-licenses/GPL-2’. + +Files: bwt_gen/QSufSort.* +Copyright: 1999, N. Jesper Larsson +License: + This software may be used freely for any purpose. However, when distributed, + the original source must be clearly stated, and, when the source code is + distributed, the copyright notice must be retained and any alterations in + the code must be clearly marked. No warranty is given regarding the quality + of this software. _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
