samtools_0.1.19-1ubuntu1_i386.deb


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Description

samtools - processing sequence alignments in SAM and BAM formats

Distribution: Ubuntu 16.04 LTS (Xenial Xerus)
Repository: Ubuntu Universe i386
Package name: samtools
Package version: 0.1.19
Package release: 1ubuntu1
Package architecture: i386
Package type: deb
Installed size: 1.35 KB
Download size: 564.70 KB
Official Mirror: archive.ubuntu.com
Samtools is a set of utilities that manipulate nucleotide sequence alignments in the binary BAM format. It imports from and exports to the ascii SAM (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows to retrieve reads in any regions swiftly. It is designed to work on a stream, and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.

Alternatives

    Download

    Source package: samtools

    Install Howto

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

    Files

    • /etc/bash_completion.d/samtools
    • /usr/bin/bcftools
    • /usr/bin/razip
    • /usr/bin/samtools
    • /usr/lib/samtools/ace2sam
    • /usr/lib/samtools/bamcheck
    • /usr/lib/samtools/maq2sam-long
    • /usr/lib/samtools/maq2sam-short
    • /usr/lib/samtools/md5fa
    • /usr/lib/samtools/md5sum-lite
    • /usr/lib/samtools/wgsim
    • /usr/share/doc/samtools/AUTHORS
    • /usr/share/doc/samtools/NEWS.gz
    • /usr/share/doc/samtools/README.Debian
    • /usr/share/doc/samtools/README.bcftools
    • /usr/share/doc/samtools/changelog.Debian.gz
    • /usr/share/doc/samtools/copyright
    • /usr/share/doc/samtools/reference
    • /usr/share/doc/samtools/examples/00README.txt
    • /usr/share/doc/samtools/examples/ex1.bam
    • /usr/share/doc/samtools/examples/ex1.fa
    • /usr/share/doc/samtools/examples/ex1.sam.gz
    • /usr/share/doc/samtools/examples/toy.fa
    • /usr/share/doc/samtools/examples/toy.sam
    • /usr/share/man/man1/bcftools.1.gz
    • /usr/share/man/man1/razip.1.gz
    • /usr/share/man/man1/samtools.1.gz
    • /usr/share/samtools/blast2sam.pl
    • /usr/share/samtools/bowtie2sam.pl
    • /usr/share/samtools/export2sam.pl
    • /usr/share/samtools/interpolate_sam.pl
    • /usr/share/samtools/novo2sam.pl
    • /usr/share/samtools/plot-bamcheck
    • /usr/share/samtools/psl2sam.pl
    • /usr/share/samtools/r2plot.lua
    • /usr/share/samtools/sam2vcf.pl
    • /usr/share/samtools/samtools.pl
    • /usr/share/samtools/soap2sam.pl
    • /usr/share/samtools/varfilter.py
    • /usr/share/samtools/vcfutils.lua
    • /usr/share/samtools/vcfutils.pl
    • /usr/share/samtools/wgsim_eval.pl
    • /usr/share/samtools/zoom2sam.pl

    Changelog

    2014-09-11 - Matthias Klose <doko@ubuntu.com> samtools (0.1.19-1ubuntu1) utopic; urgency=medium * Apply alignment and endian patches. Closes: #753485.

    2013-03-30 - Charles Plessy <plessy@debian.org> samtools (0.1.19-1) unstable; urgency=low cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua. 2f2d5c5 debian/copyright: collapsed copyright notices from main holders. e194f9e Removed fix_float_tag.patch, corrected upstream. 9c0e543 Refreshed patches. 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch. 8d8550e example/Makefile: pass -lpthread when compiling calDepth. fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS. 6f75b48 debian/control: normalised with cme. e13bb5e debian/control: normalised VCS URLs. a1b1b00 debian/control: deleted DM-Upload-Allowed field. ddcd54e Use NEWS as upstream changelog. 81ad760 Conforms to Policy version 3.9.4.

    2012-12-21 - Dominique Belhachemi <domibel@debian.org> samtools (0.1.18-4) unstable; urgency=low [Charles Plessy] * debian/copyright: Normalised with config-model * added bash completion * Build-depend on Debhelper 9 * Pass build flaggs set by dpkg-buildflags via Debhelper * Moved DOI and PubMed to the Reference namespace * Do not compress the example binary alignment file * Mention ‘SAMtools’ in libbam-dev's description [Andreas Tille] * debian/upstream: replaced BibTeX entry [Dominique Belhachemi] * added patch to fix float tag bug (upstream bug 71)

    2012-07-27 - Dominique Belhachemi <domibel@debian.org> samtools (0.1.18-3) unstable; urgency=low * upload 0.1.18-2 closed the wrong bug, correction: * added patch to fix segfault in mpileup (Closes: #653042) * added patch to fix coverage cap (Closes: #671524)

    2012-07-26 - Dominique Belhachemi <domibel@debian.org> samtools (0.1.18-2) unstable; urgency=low * added patch to fix segfault in mpileup (Closes: #544976) * added patch to fix coverage cap (Closes: #671524)

    2011-09-06 - Charles Plessy <plessy@debian.org> samtools (0.1.18-1) unstable; urgency=low [b990d9d3] New upstream release. [d59366b9] Updated copyright statements. [aa08abe5] Compress binary packages with xz. [9a36c994] Added a DEP 3 header to debian/patches/no-pileup-tests.patch.

    2011-07-11 - Charles Plessy <plessy@debian.org> samtools (0.1.17-1) unstable; urgency=low * New upstream release 0.1.17 (6 July, 2011). * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages). * Patched the example makefile to not use samtools pileup, deprecated. (debian/control, debian/rules, debian/patches/series, debian/patches/no-pileup-tests.patch)

    2011-05-19 - Charles Plessy <plessy@debian.org> samtools (0.1.16-1) unstable; urgency=low * New upstream release, implementing SAM Spec v1.4. * Distribute sam.h and the other headers in /usr/include/samtools. Closes: #625622, #626044, LP: #690997.

    2011-04-12 - Charles Plessy <plessy@debian.org> samtools (0.1.15-1) unstable; urgency=low * New upstream release. * Incremented Standards-Version to reflect conformance with Policy 3.9.2 (debian/control, no changes needed). * debian/watch directly interrogates and downloads froms SourceForge.

    2011-03-29 - Charles Plessy <plessy@debian.org> samtools (0.1.14-1) unstable; urgency=low * New upstream release.

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