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CVS log for pkgsrc/biology/bcftools/Makefile

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Default branch: MAIN


Revision 1.18 / (download) - annotate - [select for diffs], Mon Aug 14 05:23:51 2023 UTC (6 months, 3 weeks ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2023Q4-base, pkgsrc-2023Q4, pkgsrc-2023Q3-base, pkgsrc-2023Q3, HEAD
Changes since 1.17: +2 -1 lines
Diff to previous 1.17 (colored)

*: recursive bump for Python 3.11 as new default

Revision 1.17 / (download) - annotate - [select for diffs], Sat Feb 25 13:56:33 2023 UTC (12 months, 1 week ago) by bacon
Branch: MAIN
CVS Tags: pkgsrc-2023Q2-base, pkgsrc-2023Q2, pkgsrc-2023Q1-base, pkgsrc-2023Q1
Changes since 1.16: +8 -8 lines
Diff to previous 1.16 (colored)

biology/bcftools: Update to 1.17

Numerous enhancements and bug fixes

Changes: https://github.com/samtools/bcftools/releases

Revision 1.16 / (download) - annotate - [select for diffs], Wed Dec 28 15:27:15 2022 UTC (14 months ago) by bacon
Branch: MAIN
Changes since 1.15: +2 -2 lines
Diff to previous 1.15 (colored)

Change MAINTAINER= to OWNER= on mission-critical packages

Revision 1.15 / (download) - annotate - [select for diffs], Thu Jun 30 11:18:04 2022 UTC (20 months ago) by nia
Branch: MAIN
CVS Tags: pkgsrc-2022Q4-base, pkgsrc-2022Q4, pkgsrc-2022Q3-base, pkgsrc-2022Q3
Changes since 1.14: +2 -2 lines
Diff to previous 1.14 (colored)

*: Revbump packages that use Python at runtime without a PKGNAME prefix

Revision 1.14 / (download) - annotate - [select for diffs], Tue Jun 28 11:30:59 2022 UTC (20 months, 1 week ago) by wiz
Branch: MAIN
Changes since 1.13: +2 -1 lines
Diff to previous 1.13 (colored)

*: recursive bump for perl 5.36

Revision 1.13 / (download) - annotate - [select for diffs], Sat Feb 26 23:14:33 2022 UTC (2 years ago) by bacon
Branch: MAIN
CVS Tags: pkgsrc-2022Q2-base, pkgsrc-2022Q2, pkgsrc-2022Q1-base, pkgsrc-2022Q1
Changes since 1.12: +1 -1 lines
Diff to previous 1.12 (colored)

biology/bcftools: Update to 1.15

Several minor enhancements and bug fixes
Changes: https://github.com/samtools/bcftools/tags

Revision 1.12 / (download) - annotate - [select for diffs], Fri Dec 17 15:14:35 2021 UTC (2 years, 2 months ago) by bacon
Branch: MAIN
CVS Tags: pkgsrc-2021Q4-base, pkgsrc-2021Q4
Changes since 1.11: +2 -4 lines
Diff to previous 1.11 (colored)

biology/bcftools: Update to 1.14

Numerous fixes and enhancments since 1.12

Changes: https://github.com/samtools/bcftools/tags

Revision 1.11 / (download) - annotate - [select for diffs], Mon May 24 19:49:10 2021 UTC (2 years, 9 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2021Q3-base, pkgsrc-2021Q3, pkgsrc-2021Q2-base, pkgsrc-2021Q2
Changes since 1.10: +2 -1 lines
Diff to previous 1.10 (colored)

*: recursive bump for perl 5.34

Revision 1.10 / (download) - annotate - [select for diffs], Sat Mar 20 18:17:07 2021 UTC (2 years, 11 months ago) by bacon
Branch: MAIN
CVS Tags: pkgsrc-2021Q1-base, pkgsrc-2021Q1
Changes since 1.9: +2 -3 lines
Diff to previous 1.9 (colored)

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

Revision 1.9 / (download) - annotate - [select for diffs], Fri Dec 4 20:45:00 2020 UTC (3 years, 2 months ago) by nia
Branch: MAIN
CVS Tags: pkgsrc-2020Q4-base, pkgsrc-2020Q4
Changes since 1.8: +2 -2 lines
Diff to previous 1.8 (colored)

Revbump packages with a runtime Python dep but no version prefix.

For the Python 3.8 default switch.

Revision 1.8 / (download) - annotate - [select for diffs], Mon Aug 31 18:06:38 2020 UTC (3 years, 6 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2020Q3-base, pkgsrc-2020Q3
Changes since 1.7: +2 -1 lines
Diff to previous 1.7 (colored)

*: bump PKGREVISION for perl-5.32.

Revision 1.7 / (download) - annotate - [select for diffs], Mon Jul 27 00:29:04 2020 UTC (3 years, 7 months ago) by bacon
Branch: MAIN
Changes since 1.6: +39 -14 lines
Diff to previous 1.6 (colored)

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.

Revision 1.6 / (download) - annotate - [select for diffs], Sat Jan 18 23:30:08 2020 UTC (4 years, 1 month ago) by rillig
Branch: MAIN
CVS Tags: pkgsrc-2020Q2-base, pkgsrc-2020Q2, pkgsrc-2020Q1-base, pkgsrc-2020Q1
Changes since 1.5: +2 -2 lines
Diff to previous 1.5 (colored)

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.

Revision 1.5 / (download) - annotate - [select for diffs], Sat Nov 2 22:09:00 2019 UTC (4 years, 4 months ago) by rillig
Branch: MAIN
CVS Tags: pkgsrc-2019Q4-base, pkgsrc-2019Q4
Changes since 1.4: +2 -2 lines
Diff to previous 1.4 (colored)

biology: align variable assignments

pkglint -Wall -F --only aligned --only indent -r

Revision 1.4 / (download) - annotate - [select for diffs], Sun Aug 11 13:17:59 2019 UTC (4 years, 6 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2019Q3-base, pkgsrc-2019Q3
Changes since 1.3: +2 -2 lines
Diff to previous 1.3 (colored)

Bump PKGREVISIONs for perl 5.30.0

Revision 1.3 / (download) - annotate - [select for diffs], Thu Apr 25 07:32:37 2019 UTC (4 years, 10 months ago) by maya
Branch: MAIN
CVS Tags: pkgsrc-2019Q2-base, pkgsrc-2019Q2
Changes since 1.2: +2 -1 lines
Diff to previous 1.2 (colored)

PKGREVISION bump for anything using python without a PYPKGPREFIX.

This is a semi-manual PKGREVISION bump.

Revision 1.2 / (download) - annotate - [select for diffs], Wed Mar 27 15:58:38 2019 UTC (4 years, 11 months ago) by bacon
Branch: MAIN
CVS Tags: pkgsrc-2019Q1-base, pkgsrc-2019Q1
Changes since 1.1: +3 -2 lines
Diff to previous 1.1 (colored)

biology/bcftools: Add zlib dependency for Linux

Resolves build failures on CentOS

Revision 1.1 / (download) - annotate - [select for diffs], Thu Nov 15 09:21:24 2018 UTC (5 years, 3 months ago) by adam
Branch: MAIN
CVS Tags: pkgsrc-2018Q4-base, pkgsrc-2018Q4

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.

This form allows you to request diff's between any two revisions of a file. You may select a symbolic revision name using the selection box or you may type in a numeric name using the type-in text box.




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