Commit graph

10 commits

Author SHA1 Message Date
bacon
b2be005da6 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
2021-03-20 18:17:07 +00:00
nia
f6dd9d2f87 Revbump packages with a runtime Python dep but no version prefix.
For the Python 3.8 default switch.
2020-12-04 20:44:57 +00:00
wiz
00da7815c0 *: bump PKGREVISION for perl-5.32. 2020-08-31 18:06:29 +00:00
bacon
da2db9c4cb biology/bcftools: Upgrade to 1.10.2
Numerous bug fixes, usability improvements and sanity checks were added since
1.9 to prevent common user errors.
2020-07-27 00:29:04 +00:00
rillig
ffe83de7b1 all: migrate several HOMEPAGEs to https
pkglint --only "https instead of http" -r -F

With manual adjustments afterwards since pkglint 19.4.4 fixed a few
indentations in unrelated lines.

This mainly affects projects hosted at SourceForce, as well as
freedesktop.org, CTAN and GNU.
2020-01-18 23:30:05 +00:00
rillig
d93bec131e biology: align variable assignments
pkglint -Wall -F --only aligned --only indent -r
2019-11-02 22:09:00 +00:00
wiz
84e123ddd2 Bump PKGREVISIONs for perl 5.30.0 2019-08-11 13:17:48 +00:00
maya
f34a8c24a3 PKGREVISION bump for anything using python without a PYPKGPREFIX.
This is a semi-manual PKGREVISION bump.
2019-04-25 07:32:34 +00:00
bacon
e2d1b9528f biology/bcftools: Add zlib dependency for Linux
Resolves build failures on CentOS
2019-03-27 15:58:38 +00:00
adam
1d7a39df12 bcftools: added version 1.9
BCFtools is a program for variant calling and manipulating files in the Variant
Call Format (VCF) and its binary counterpart BCF. All commands work
transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
In order to avoid tedious repetion, throughout this document we will use "VCF"
and "BCF" interchangeably, unless specifically noted.

Most commands accept VCF, bgzipped VCF and BCF with filetype detected
automatically even when streaming from a pipe. Indexed VCF and BCF work in all
situations. Unindexed VCF and BCF and streams work in most, but not all
situations. In general, whenever multiple VCFs are read simultaneously, they
must be indexed and therefore also compressed.
2018-11-15 09:21:24 +00:00