samtools_0.1.19-1ubuntu1_i386.deb


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Description

samtools - processing sequence alignments in SAM and BAM formats

Property Value
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

Package Version Architecture Repository
samtools_0.1.19-1ubuntu1_amd64.deb 0.1.19 amd64 Ubuntu Universe
samtools - - -

Requires

Name Value
libc6 >= 2.15
libncurses5 >= 5.5-5~
libtinfo5 -
zlib1g >= 1:1.2.3.3

Download

Type URL
Binary Package samtools_0.1.19-1ubuntu1_i386.deb
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

Path
/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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