debian/0000755000000000000000000000000011745777474007215 5ustar debian/upstream0000644000000000000000000000113311726141015010745 0ustar Archive: SourceForge Contact: Heng Li FAQ: http://maq.sourceforge.net/faq.shtml Name: Maq Homepage: http://maq.sourceforge.net/ 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 PMID: 18714091 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/source/0000755000000000000000000000000011745767043010504 5ustar debian/source/format0000644000000000000000000000001411334002506011666 0ustar 3.0 (quilt) debian/docs0000644000000000000000000000002711745767742010064 0ustar README AUTHORS maq.pdf debian/maq.doc-base0000644000000000000000000000044711540066756011362 0ustar Document: maq Title: Maq — Mapping and Assembly with Quality Author: Heng Li 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 debian/copyright0000644000000000000000000000414311745770750011140 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://downloads.sourceforge.net/maq/maq-0.7.1.tar.bz2 Files: * Copyright: 2003-2008, Heng Li 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 . 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 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 , Andreas Tille License: same-as-upstream Same as Maq itelf (see above). debian/compat0000644000000000000000000000000211745767247010410 0ustar 9 debian/install0000644000000000000000000000031611232075311010552 0ustar scripts/asub usr/share/maq scripts/fq_all2std.pl usr/share/maq scripts/maq_post.pl usr/share/maq scripts/maq_sanger.pl usr/share/maq scripts/paf_utils.pl usr/share/maq scripts/solid2fastq.pl usr/share/maq debian/control0000644000000000000000000000212211745767330010603 0ustar Source: maq Section: science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Andreas Tille , Charles Plessy Build-Depends: debhelper (>= 9), autotools-dev, zlib1g-dev, dh-autoreconf Standards-Version: 3.9.3 Homepage: http://maq.sourceforge.net/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/maq/trunk/ Vcs-Svn: svn://svn.debian.org/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. debian/patches/0000755000000000000000000000000011745776533010637 5ustar debian/patches/gcc-4.7.patch0000644000000000000000000000300611745776533012721 0ustar Author: Andreas Tille Date: Wed, 25 Apr 2012 14:20:16 +0200 Bug-Closed: http://bugs.debian.org/667270 Description: Build with g++ version 4.7 Just followed the hint of g++ itself which said: note: use 'this->direct_insert_aux' instead --- maq-0.7.1.orig/stdhash.hh +++ maq-0.7.1/stdhash.hh @@ -412,7 +412,7 @@ inline bool insert(const keytype_t &key) { __lh3_hash_base_class::rehash(); hashint_t i; - int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); + int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); if (ret == 0) return true; if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } else ++(this->n_size); // then ret == 2 @@ -493,7 +493,7 @@ inline bool insert(const keytype_t &key, const valtype_t &val) { rehash(); hashint_t i; - int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); + int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); vals[i] = val; if (ret == 0) return true; if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } @@ -503,7 +503,7 @@ inline bool insert(const keytype_t &key, valtype_t **q) { rehash(); hashint_t i; - int ret = direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); + int ret = this->direct_insert_aux(key, this->n_capacity, this->keys, this->flags, &i); *q = vals + i; if (ret == 0) return true; if (ret == 1) { ++(this->n_size); ++(this->n_occupied); } debian/patches/series0000644000000000000000000000005211745775405012046 0ustar 10_prevent_-64_option.patch gcc-4.7.patch debian/patches/10_prevent_-64_option.patch0000644000000000000000000000165311232075311015577 0ustar Author: Charles Plessy Forwarded: https://sourceforge.net/tracker/index.php?func=detail&aid=2298601&group_id=191815&atid=938895 Reviewed: http://lists.debian.org/debian-mentors/2008/11/msg00189.html Description: Build without -m64. -m64 is not necessary except for building "multiarch" versions, which is probably not the original goal anyway. --- a/configure.ac +++ b/configure.ac @@ -23,10 +23,7 @@ case "${host_cpu}-${host_os}" in AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-m64"], []);; esac;; *) - AC_MSG_CHECKING([if gcc accepts -m64]) - CFLAGS="-m64" - AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-m64"; AC_MSG_RESULT([yes])], - [ext_CFLAGS="-D_FILE_OFFSET_BITS=64"; AC_MSG_RESULT([no])]);; + ext_CFLAGS="-D_FILE_OFFSET_BITS=64";; esac AC_ARG_ENABLE(experimental, [ --enable-experimental enable experimental features], [ext_CFLAGS="${ext_CFLAGS} -DMAQ_SHOW_EXPERIMENTAL"], []) debian/manpages0000644000000000000000000000000611110210477010672 0ustar maq.1 debian/watch0000644000000000000000000000006611110210477010213 0ustar version=3 http://sf.net/maq/maq-([\d\.]+)\.tar\.bz2 debian/maq.lintian-overrides0000644000000000000000000000020411110210477013312 0ustar # Maq ships `maq' and `maq.pl', it is therefore not possible to rename `maq.pl'. maq: script-with-language-extension usr/bin/maq.pl debian/changelog0000644000000000000000000000730711745777341011067 0ustar maq (0.7.1-5) unstable; urgency=low [ Charles Plessy ] * renamed debian/upstream-metadata.yaml to debian/upstream [ Andreas Tille ] * debian/upstream: - Removed duplicated entry DOI - Moved PMID to references * debian/source/format: 3.0 (quilt) * debian/reference: removed because references are kept in debian/upstream (also removed from debian/docs) * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Fixed Vcs fields - Build-Depends: dh-autoreconf - Dropped from Build-Depends: quilt, cdbs * debian/patches/20_prevent_-64_option.patch: Dropped in favour of using dh-autoreconf * debian/rules: converted to dh * debian/copyright: cme fix dpkg-copyright * debian/patches/gcc-4.7.patch: Enable building with g++-4.7 Closes: #667270 * debian/README.source: Removed because there is no point any more to explain how to use quilt -- Andreas Tille Wed, 25 Apr 2012 14:20:16 +0200 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 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 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 for the patch) Closes: #506009 * Standards-Version: 3.8.1 (no changes needed) -- Andreas Tille 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 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 Wed, 16 Jul 2008 12:01:33 +0200 debian/rules0000755000000000000000000000050711745767353010272 0ustar #!/usr/bin/make -f # debian/rules file for maq # (C) Charles Plessy, Andreas Tille # GPL #needed to make the zlib headers behave (they don't like the combination #of _FILE_OFFSET_BITS=64 but not _LARGEFILE64_SOURCE CFLAGS+= -D_LARGEFILE64_SOURCE %: dh $@ --with autoreconf override_dh_compress: dh_compress --exclude=.pdf