sci-biology / samtools

Utilities for analysing and manipulating the SAM/BAM alignment formats

Official package sites : http://www.htslib.org/ ·

v1.20 :: 0 :: gentoo

Modified
License
MIT
Keywords
~amd64 ~amd64-linux ~x64-macos ~x86 ~x86-linux

v1.19.2 :: 0 :: gentoo

Modified
License
MIT
Keywords
~amd64 ~amd64-linux ~x64-macos ~x86 ~x86-linux

dev-lang / perl : Larry Wall's Practical Extraction and Report Language

sci-libs / htslib : C library for high-throughput sequencing data formats

sys-libs / ncurses : Console display library

sys-libs / zlib : Standard (de)compression library

dev-lang / perl : Larry Wall's Practical Extraction and Report Language

sci-libs / htslib : C library for high-throughput sequencing data formats

sys-libs / ncurses : Console display library

sys-libs / zlib : Standard (de)compression library

sci-biology / augustus : Eukaryotic gene predictor

Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: add 1.20
Signed-off-by: David Seifert <soap@gentoo.org>
David Seifert · gentoo
sci-biology/samtools: drop 1.17
Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: add 1.19.2
Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: drop 0.1.20-r4
Closes: https://bugs.gentoo.org/862288 Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: drop 1.16.1
Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: add 1.17
Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: drop 1.15.1
Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: add 1.16.1
Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: drop 1.13, 1.15
Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: add 1.15.1
Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: add 1.15
Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: drop 1.10-r1
Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: add 1.13
Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: Add sys-libs/ncurses[unicode(+)]
Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
Sam James · gentoo
sci-biology/samtools: add missing multilib inherit for get_libname
Found using: `grep -rsn -L -e "inherit.*multilib.*" | xargs grep "get_libname"` Signed-off-by: Sam James <sam@gentoo.org> Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: Remove old
Closes: https://bugs.gentoo.org/728018 Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: [QA] Fix UnnecessarySlashStrip
Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: Remove ancient py2 varfilter.py script
Closes: https://bugs.gentoo.org/735444 Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: Bump to version 1.10
Bug: https://bugs.gentoo.org/728018 Package-Manager: Portage-3.0.1, Repoman-2.3.23 Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: Remove python dependency
Closes: https://bugs.gentoo.org/710252 Package-Manager: Portage-2.3.96, Repoman-2.3.22 Signed-off-by: David Seifert <soap@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/samtools: Version bump to 1.9
Bug: https://bugs.gentoo.org/647714 Signed-off-by: David Seifert <soap@gentoo.org> Package-Manager: Portage-2.3.50, Repoman-2.3.11
David Seifert · gentoo
sci-biology/samtools: Remove old
Bug: https://bugs.gentoo.org/show_bug.cgi?id=548170 Bug: https://bugs.gentoo.org/show_bug.cgi?id=620618 Bug: https://bugs.gentoo.org/show_bug.cgi?id=625504 Package-Manager: Portage-2.3.8, Repoman-2.3.3 Closes: https://github.com/gentoo/gentoo/pull/5593
David Seifert · gentoo
sci-biology/samtools: Version bump to 1.5
Package-Manager: Portage-2.3.8, Repoman-2.3.3
David Seifert · gentoo
sci-biology/samtools: [QA] Add missing python metadata variables
Package-Manager: Portage-2.3.5, Repoman-2.3.2
Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
David Seifert · gentoo
sci-biology/samtools: Use 'python-single-r1' instead of 'python-r1'
Package-Manager: portage-2.3.1
David Seifert · gentoo
sci-biology/samtools: Remove lua dep, fix perl shebangs
Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Remove lua dep, fix perl shebangs
Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: version bump to 1.3, to match htslib
* EAPI=6 * Added modern AX_WITH_CURSES that works with pkg-config * Fixed incorrect symlinks for libbam.so Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Move to SLOT="0.1-legacy" for future legacy versions
Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Add elog message discouraging direct use
Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Version bump to 0.1.20
* EAPI=6 * samtools will be slotted with SLOT="legacy", in order to be able to install applications that rely on the old monolithic library. Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Trim DESCRIPTION
* Add sub-slot operator for 'sys-libs/ncurses' dependency Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Trim DESCRIPTION
* Add sub-slot operator for 'sys-libs/ncurses' dependency Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Trim DESCRIPTION
* Add sub-slot operator for 'sys-libs/ncurses' dependency Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Trim DESCRIPTION
* Add sub-slot operator for 'sys-libs/ncurses' dependency Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Trim DESCRIPTION
* Add sub-slot operator for 'sys-libs/ncurses' dependency Package-Manager: portage-2.2.28
David Seifert · gentoo
sci-biology/samtools: Trim DESCRIPTION
Package-Manager: portage-2.2.28
Agostino Sarubbo · gentoo
sci-biology/samtools: amd64 stable wrt bug #525630
Package-Manager: portage-2.2.20.1 RepoMan-Options: --include-arches="amd64"
Robin H. Johnson · gentoo
proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed