./biology/samtools, Tools for manipulating sequence alignment maps

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Branch: CURRENT, Version: 1.12, Package name: samtools-1.12, Maintainer: bacon

Samtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.


Required to run:
[lang/perl5] [biology/htslib] [lang/python37]

Required to build:
[pkgtools/cwrappers]

Master sites:

SHA1: f46eb3a18885fb352d8746d51a206f7f34916232
RMD160: 511ba541e9f3dbbab333d4a24a83f63c628b5b18
Filesize: 4422.324 KB

Version history: (Expand)

CVS history: (Expand)


   2021-03-20 19:17:08 by Jason Bacon | Files touched by this commit (16) | Package updated
Log message:
biology/htslib: Update to 1.12
biology/bcftools: Update to 1.12
biology/samtools: Update to 1.12

Numerous enhancements, performance improvements, and bug fixes since 1.10
Minimized pkgsrc patches in all three packages
Moved htslib to custom tarball since Github-generated distfiles are incomplete
   2020-12-04 21:45:51 by Nia Alarie | Files touched by this commit (456) 
Log message:
Revbump packages with a runtime Python dep but no version prefix.

For the Python 3.8 default switch.
   2020-08-31 20:13:29 by Thomas Klausner | Files touched by this commit (3631) | Package updated
Log message:
*: bump PKGREVISION for perl-5.32.
   2020-07-27 01:30:30 by Jason Bacon | Files touched by this commit (4) 
Log message:
biology/samtools: Upgrade to 1.10

Numerous performance and feature improvements and several bug fixes since 1.9
   2020-01-26 18:32:28 by Roland Illig | Files touched by this commit (981) 
Log message:
all: migrate homepages from http to https

pkglint -r --network --only "migrate"

As a side-effect of migrating the homepages, pkglint also fixed a few
indentations in unrelated lines. These and the new homepages have been
checked manually.
   2019-08-11 15:25:21 by Thomas Klausner | Files touched by this commit (3557) | Package updated
Log message:
Bump PKGREVISIONs for perl 5.30.0
   2019-04-25 09:33:32 by Maya Rashish | Files touched by this commit (620) 
Log message:
PKGREVISION bump for anything using python without a PYPKGPREFIX.

This is a semi-manual PKGREVISION bump.
   2019-03-27 21:47:36 by Jason Bacon | Files touched by this commit (1) 
Log message:
biology/samtools: Add zlib dependency for Linux

Fixes build on CentOS 7 minimal.