staden-io-lib-utils_1.14.6-2_i386.deb


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Description

staden-io-lib-utils - programs for maniuplating DNA sequencing files

Property Value
Distribution Ubuntu 16.04 LTS (Xenial Xerus)
Repository Ubuntu Universe i386
Package name staden-io-lib-utils
Package version 1.14.6
Package release 2
Package architecture i386
Package type deb
Installed size 483 B
Download size 122.40 KB
Official Mirror archive.ubuntu.com
The io_lib from the Staden package is a library of file reading and writing
code to provide a general purpose trace file (and Experiment File) reading
interface. It has been compiled and tested on a variety of unix systems,
MacOS X and MS Windows.
This package contains the programs that are distributed with the Staden io_lib
for manipulating and converting sequencing data files, and in particular files
to maniuplate short reads generated by second and third generation sequencers
and stored in SRF format.

Alternatives

Package Version Architecture Repository
staden-io-lib-utils_1.14.6-2_amd64.deb 1.14.6 amd64 Ubuntu Universe
staden-io-lib-utils - - -

Requires

Name Value
libc6 >= 2.7
libstaden-read11 -

Download

Type URL
Binary Package staden-io-lib-utils_1.14.6-2_i386.deb
Source Package staden-io-lib

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install staden-io-lib-utils deb package:
    # sudo apt-get install staden-io-lib-utils

Files

Path
/usr/bin/append_sff
/usr/bin/convert_trace
/usr/bin/cram_dump
/usr/bin/cram_index
/usr/bin/cram_size
/usr/bin/extract_fastq
/usr/bin/extract_qual
/usr/bin/extract_seq
/usr/bin/get_comment
/usr/bin/hash_exp
/usr/bin/hash_extract
/usr/bin/hash_list
/usr/bin/hash_sff
/usr/bin/hash_tar
/usr/bin/index_tar
/usr/bin/makeSCF
/usr/bin/scf_dump
/usr/bin/scf_info
/usr/bin/scf_update
/usr/bin/scram_flagstat
/usr/bin/scram_merge
/usr/bin/scram_pileup
/usr/bin/scram_test
/usr/bin/scramble
/usr/bin/srf2fasta
/usr/bin/srf2fastq
/usr/bin/srf_dump_all
/usr/bin/srf_extract_hash
/usr/bin/srf_extract_linear
/usr/bin/srf_filter
/usr/bin/srf_index_hash
/usr/bin/srf_info
/usr/bin/srf_list
/usr/bin/trace_dump
/usr/bin/ztr_dump
/usr/share/doc-base/staden-io-lib-hash-file-format
/usr/share/doc-base/staden-io-lib-ztr-format
/usr/share/doc/staden-io-lib-utils/Hash_File_Format
/usr/share/doc/staden-io-lib-utils/README.gz
/usr/share/doc/staden-io-lib-utils/ZTR_format.gz
/usr/share/doc/staden-io-lib-utils/changelog.Debian.gz
/usr/share/doc/staden-io-lib-utils/copyright
/usr/share/man/man1/scramble.1.gz
/usr/share/man/man1/srf2fasta.1.gz
/usr/share/man/man1/srf2fastq.1.gz
/usr/share/man/man1/srf_dump_all.1.gz
/usr/share/man/man1/srf_filter.1.gz
/usr/share/man/man1/srf_index_hash.1.gz
/usr/share/man/man1/srf_info.1.gz
/usr/share/man/man1/srf_list.1.gz

Changelog

2015-11-24 - Andreas Tille <tille@debian.org>
staden-io-lib (1.14.6-2) unstable; urgency=medium
* Enable separate building of arch independet packages
Closes: #806112
* Adapt to latest d-shlibs
2015-11-08 - Andreas Tille <tille@debian.org>
staden-io-lib (1.14.6-1) unstable; urgency=medium
* New upstream version
Closes: #793514
2015-09-22 - Andreas Tille <tille@debian.org>
staden-io-lib (1.14.2-1) unstable; urgency=medium
[ Charles Plessy ]
* Removed debian/libstaden-read1.symbols_old (that is what VCSes
are for). 
[ Andreas Tille ]
* New upstream version
* New soname - so change library package name
2015-07-27 - Andreas Tille <tille@debian.org>
staden-io-lib (1.14.0-1) unstable; urgency=medium
* New upstream version
* Deactivated libstaden-read1.symbols for the moment by renaming
it to libstaden-read1.symbols_old (feel free to maintain this file
but in this form the package does not build)
* d/copyright: remove paragraph about not existing file
2015-07-05 - Andreas Tille <tille@debian.org>
staden-io-lib (1.13.10-1) unstable; urgency=medium
[ Andreas Tille ]
* New upstream version
* cme fix dpkg-control
[ Charles Plessy ]
* Multi-Arch: same. 
* Unfuzzy debian/patches/pathmax.patch.
* Update symbols file.
2014-06-20 - Charles Plessy <plessy@debian.org>
staden-io-lib (1.13.7-1) unstable; urgency=medium
* New upstream release. 
* Removed debian/patches/fix-bam-read.patch, applied upstream.
* debian/libstaden-read1.symbols: updated.  Some symbols are missing but
it is in area of code that are considered beta (in my understanding).
2014-04-24 - Andreas Tille <tille@debian.org>
staden-io-lib (1.13.5-3) unstable; urgency=medium
* debian/rules: fix permissions in arch=all package only when
it is really built
Closes: #745692
2014-04-14 - Andreas Tille <tille@debian.org>
staden-io-lib (1.13.5-2) unstable; urgency=medium
* use dh-autoreconf
Closes: 744664
* Add autopkgtest using new staden-io-lib-examples package
2014-04-01 - Anibal Monsalve Salazar <anibal@debian.org>
staden-io-lib (1.13.5-1.1) unstable; urgency=medium
* Non-maintainer upload.
* Fix io_lib/bam.c read
Patch by Aleksandar Zlicic
Add fix-bam-read.patch
Closes: #736565
2014-03-15 - Charles Plessy <plessy@debian.org>
staden-io-lib (1.13.5-1) unstable; urgency=medium
* New upstream release. 
* debian/libstaden-read1.symbols: updated symbols.
* debian/patches/pathmax.patch: refreshed.
* debian/patches/fix_bufferoverflow.patch: removed (applied upstream).

See Also

Package Description
staden_2.0.0+b10-4ubuntu1_i386.deb DNA sequence assembly (Gap4/Gap5), editing and analysis tools
stalin_0.11-6_i386.deb An extremely aggressive Scheme compiler
stalonetray_0.8.1-1_i386.deb Standalone freedesktop.org and KDE systray implementation
stardata-common_0.8_i386.deb Common framework to manage astronomy packages
stardict-common_3.0.1-9.2ubuntu3_all.deb International dictionary - data files
stardict-czech_20140101-3_all.deb Stardict package for Czech dictionary of foreign words
stardict-gnome_3.0.1-9.2ubuntu3_i386.deb International dictionary for GNOME 2
stardict-gtk_3.0.1-9.2ubuntu3_i386.deb International dictionary written in GTK+ 2.x
stardict-plugin-espeak_3.0.1-9.2ubuntu3_i386.deb International dictionary - eSpeak TTS plugin
stardict-plugin-festival_3.0.1-9.2ubuntu3_i386.deb International dictionary - Festival TTS plugin
stardict-plugin-spell_3.0.1-9.2ubuntu3_i386.deb International dictionary - spell plugin
stardict-plugin_3.0.1-9.2ubuntu3_i386.deb International dictionary - common plugins
stardict-tools_3.0.2-5build1_i386.deb dictionary conversion tools of stardict
stardict-xmlittre_1.0-1_all.deb French Littré dictionary for stardict
stardict_3.0.1-9.2ubuntu3_all.deb International dictionary
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