maq_0.7.1-5_amd64.deb


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Description

maq - maps short fixed-length polymorphic DNA sequence reads to reference sequences

Distribution: Debian 8 (Jessie)
Repository: Debian Main amd64
Package name: maq
Package version: 0.7.1
Package release: 5
Package architecture: amd64
Package type: deb
Installed size: 559 B
Download size: 313.88 KB
Official Mirror: ftp.br.debian.org
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.

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    Download

    Binary package: maq_0.7.1-5_amd64.deb
    Source package: maq

    Install Howto

    1. Update the package index:
      # sudo apt-get update
    2. Install maq deb package:
      # sudo apt-get install maq

    Files

    • /usr/bin/farm-run.pl
    • /usr/bin/maq
    • /usr/bin/maq.pl
    • /usr/bin/maq_eval.pl
    • /usr/bin/maq_plot.pl
    • /usr/share/doc-base/maq
    • /usr/share/doc/maq/AUTHORS
    • /usr/share/doc/maq/README
    • /usr/share/doc/maq/changelog.Debian.gz
    • /usr/share/doc/maq/changelog.gz
    • /usr/share/doc/maq/copyright
    • /usr/share/doc/maq/maq.pdf
    • /usr/share/lintian/overrides/maq
    • /usr/share/man/man1/maq.1.gz
    • /usr/share/maq/asub
    • /usr/share/maq/fq_all2std.pl
    • /usr/share/maq/maq_post.pl
    • /usr/share/maq/maq_sanger.pl
    • /usr/share/maq/paf_utils.pl
    • /usr/share/maq/solid2fastq.pl

    Changelog

    2012-04-25 - Andreas Tille <tille@debian.org> 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

    2011-03-13 - Charles Plessy <plessy@debian.org> 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).

    2009-07-17 - Charles Plessy <plessy@debian.org> 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.

    2009-04-16 - Andreas Tille <tille@debian.org> maq (0.7.1-2) unstable; urgency=low * Enable LARGEFILE64_SOURCE to prevent a problem with zlib on 64bit archs (Thanks to Peter Green <plugwash@p10link.net> for the patch) Closes: #506009 * Standards-Version: 3.8.1 (no changes needed)

    2008-11-16 - Charles Plessy <plessy@debian.org> 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.

    2008-07-16 - Andreas Tille <tille@debian.org> 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

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