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CVS log for pkgsrc/biology/samtools/Makefile

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Default branch: MAIN

Revision 1.20 / (download) - annotate - [select for diffs], Mon Aug 14 05:23:52 2023 UTC (6 months, 2 weeks ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2023Q4-base, pkgsrc-2023Q4, pkgsrc-2023Q3-base, pkgsrc-2023Q3, HEAD
Changes since 1.19: +2 -1 lines
Diff to previous 1.19 (colored)

*: recursive bump for Python 3.11 as new default

Revision 1.19 / (download) - annotate - [select for diffs], Sat Feb 25 13:52:39 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 1.18: +2 -2 lines
Diff to previous 1.18 (colored)

biology/samtools: Update to 1.17

Numerous enhancements and bug fixes


Revision 1.18 / (download) - annotate - [select for diffs], Wed Dec 28 15:27:17 2022 UTC (14 months ago) by bacon
Branch: MAIN
Changes since 1.17: +2 -2 lines
Diff to previous 1.17 (colored)

Change MAINTAINER= to OWNER= on mission-critical packages

Revision 1.17 / (download) - annotate - [select for diffs], Tue Dec 13 10:28:01 2022 UTC (14 months, 2 weeks ago) by adam
Branch: MAIN
CVS Tags: pkgsrc-2022Q4-base, pkgsrc-2022Q4
Changes since 1.16: +8 -8 lines
Diff to previous 1.16 (colored)

samtools: updated to 1.16.1


Bug fixes:

Fixed a bug with the template-coordinate sort which caused incorrect ordering when using threads, or processing large files that don't fit completely in memory.

Fixed a crash that occurred when trying to use samtools merge in template-coordinate mode.


New work and changes:

samtools reference command added. This subcommand extracts the embedded reference out of a CRAM file.

samtools import now adds grouped by query-name to the header.

Made samtools view read error messages more generic. Former error message would claim that there was a "truncated file or corrupt BAM index file" with no real justification. Also reset errno in stream_view which could lead to confusing error messages.

Make samtools view -p also clear mqual, tlen and cigar.

Add bedcov option -c to report read count.

Add UMI/barcode handling to samtools markdup.

Add a new template coordinate sort order to samtools sort and samtools merge. This is useful when working with unique molecular identifiers (UMIs).

Rename mpileup --ignore-overlaps to --ignore-overlaps-removal or --disable-overlap-removal. The previous name was ambiguous and was often read as an option to enable removal of overlapping bases, while in reality this is on by default and the option turns off the ability to remove overlapping bases.

The dict command can now read BWA's .alt file and add AH:* tags indicating reference sequences that represent alternate loci.

The samtools index command can now accept multiple alignment filenames with the new -M option, and will index each of them separately. (Specifying the output index filename via out.index or the new -o option is currently only applicable when there is only one alignment file to be indexed.)

Allow samtools fastq -T "*". This allows all tags from SAM records to be written to fastq headers. This is a counterpart to samtools import -T "*".

Bug Fixes:

Re-enable --reference option for samtools depth. The reference is not used but this makes the command line usage compatible with older releases.

Fix regex coordinate bug in samtools markdup.

Fix divide by zero in plot-bamstats -m, on unmapped data.

Fix missing RG headers when using samtools merge -r.

Fix a possible unaligned access in samtools reference.


Add documentation on CRAM compression profiles and some of the newer options that appear in CRAM 3.1 and above.

Add sclen filter expression keyword documentation.

Extend FILTER EXPRESSION man page section to match the changes made in HTSlib.

Non user-visible changes and build improvements:

Ensure generated test files are ignored (by git) and cleaned (by make testclean)

Revision 1.16 / (download) - annotate - [select for diffs], Thu Jun 30 11:18:04 2022 UTC (20 months ago) by nia
Branch: MAIN
CVS Tags: pkgsrc-2022Q3-base, pkgsrc-2022Q3
Changes since 1.15: +2 -2 lines
Diff to previous 1.15 (colored)

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

Revision 1.15 / (download) - annotate - [select for diffs], Tue Jun 28 11:31:01 2022 UTC (20 months ago) by wiz
Branch: MAIN
Changes since 1.14: +2 -1 lines
Diff to previous 1.14 (colored)

*: recursive bump for perl 5.36

Revision 1.14 / (download) - annotate - [select for diffs], Sat Feb 26 23:11:43 2022 UTC (2 years ago) by bacon
Branch: MAIN
CVS Tags: pkgsrc-2022Q2-base, pkgsrc-2022Q2, pkgsrc-2022Q1-base, pkgsrc-2022Q1
Changes since 1.13: +1 -1 lines
Diff to previous 1.13 (colored)

biology/samtools: Update to 1.15

Several minor enhancements and bug fixes

Revision 1.13 / (download) - annotate - [select for diffs], Fri Dec 17 15:10:06 2021 UTC (2 years, 2 months ago) by bacon
Branch: MAIN
CVS Tags: pkgsrc-2021Q4-base, pkgsrc-2021Q4
Changes since 1.12: +2 -4 lines
Diff to previous 1.12 (colored)

biology/samtools: Update to 1.14

Numerous fixes and enhancements since 1.12


Revision 1.12 / (download) - annotate - [select for diffs], Mon May 24 19:49:11 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 1.11: +2 -1 lines
Diff to previous 1.11 (colored)

*: recursive bump for perl 5.34

Revision 1.11 / (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 1.10: +3 -4 lines
Diff to previous 1.10 (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 1.10 / (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 1.9: +2 -2 lines
Diff to previous 1.9 (colored)

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

For the Python 3.8 default switch.

Revision 1.9 / (download) - annotate - [select for diffs], Mon Aug 31 18:06:40 2020 UTC (3 years, 6 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2020Q3-base, pkgsrc-2020Q3
Changes since 1.8: +2 -1 lines
Diff to previous 1.8 (colored)

*: bump PKGREVISION for perl-5.32.

Revision 1.8 / (download) - annotate - [select for diffs], Sun Jul 26 23:30:29 2020 UTC (3 years, 7 months ago) by bacon
Branch: MAIN
Changes since 1.7: +26 -13 lines
Diff to previous 1.7 (colored)

biology/samtools: Upgrade to 1.10

Numerous performance and feature improvements and several bug fixes since 1.9

Revision 1.7 / (download) - annotate - [select for diffs], Sun Jan 26 17:30:46 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 1.6: +2 -2 lines
Diff to previous 1.6 (colored)

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.

Revision 1.6 / (download) - annotate - [select for diffs], Sun Aug 11 13:18:01 2019 UTC (4 years, 6 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2019Q4-base, pkgsrc-2019Q4, pkgsrc-2019Q3-base, pkgsrc-2019Q3
Changes since 1.5: +2 -2 lines
Diff to previous 1.5 (colored)

Bump PKGREVISIONs for perl 5.30.0

Revision 1.5 / (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 1.4: +2 -1 lines
Diff to previous 1.4 (colored)

PKGREVISION bump for anything using python without a PYPKGPREFIX.

This is a semi-manual PKGREVISION bump.

Revision 1.4 / (download) - annotate - [select for diffs], Wed Mar 27 20:47:36 2019 UTC (4 years, 11 months ago) by bacon
Branch: MAIN
CVS Tags: pkgsrc-2019Q1-base, pkgsrc-2019Q1
Changes since 1.3: +2 -1 lines
Diff to previous 1.3 (colored)

biology/samtools: Add zlib dependency for Linux

Fixes build on CentOS 7 minimal.

Revision 1.3 / (download) - annotate - [select for diffs], Tue Nov 6 10:49:41 2018 UTC (5 years, 3 months ago) by adam
Branch: MAIN
CVS Tags: pkgsrc-2018Q4-base, pkgsrc-2018Q4
Changes since 1.2: +14 -13 lines
Diff to previous 1.2 (colored)

samtools: updated to 1.9

Release 1.9:

 * Samtools mpileup VCF and BCF output is now deprecated.  It is still
   functional, but will warn.  Please use bcftools mpileup instead.

 * Samtools mpileup now handles the '-d' max_depth option differently.  There
   is no longer an enforced minimum, and '-d 0' is interpreted as limitless
   (no maximum - warning this may be slow).  The default per-file depth is
   now 8000, which matches the value mpileup used to use when processing
   a single sample.  To get the previous default behaviour use the higher
   of 8000 divided by the number of samples across all input files, or 250.

 * Samtools stats new features:

   - The '--remove-overlaps' option discounts overlapping portions of
     templates when computing coverage and mapped base counting.

   - When a target file is in use, the number of bases inside the
     target is printed and the percentage of target bases with coverage
     above a given threshold specified by the '--cov-threshold' option.

   - Split base composition and length statistics by first and last reads.

 * Samtools faidx new features:

   - Now takes long options.

   - Now warns about zero-length and truncated sequences due to the
     requested range being beyond the end of the sequence.

   - Gets a new option (--continue) that allows it to carry on
     when a requested sequence was not in the index.

   - It is now possible to supply the list of regions to output in a text
     file using the new '--region-file' option.

   - New '-i' option to make faidx return the reverse complement of
     the regions requested.

   - faidx now works on FASTQ (returning FASTA) and added a new
     fqidx command to index and return FASTQ.

 * Samtools collate now has a fast option '-f' that only operates on
   primary pairs, dropping secondary and supplementary.  It tries to write
   pairs to the final output file as soon as both reads have been found.

 * Samtools bedcov gets a new '-j' option to make it ignore deletions (D) and
   reference skips (N) when computing coverage.

 * Small speed up to samtools coordinate sort, by converting it to use
   radix sort.

 * Samtools idxstats now works on SAM and CRAM files, however this
   isn't fast due to some information lacking from indices.

 * Compression levels may now be specified with the level=N
   output-fmt-option.  E.g. with -O bam,level=3.

 * Various documentation improvements.

 * Bug-fixes:

   - Improved error reporting in several places.

   - Various test improvements.

   - Fixed failures in the multi-region iterator (view -M) when regions
     provided via BED files include overlaps

   - Samtools stats now counts '=' and 'X' CIGAR operators when
     counting mapped bases.

   - Samtools stats has fixes for insert size filtering (-m, -i).

   - Samtools stats -F now longer negates an earlier -d option.

   - Fix samtools stats crash when using a target region.

   - Samtools sort now keeps to a single thread when the -@ option is absent.
     Previously it would spawn a writer thread, which could cause the CPU
     usage to go slightly over 100%.

   - Fixed samtools phase '-A' option which was incorrectly defined to take
     a parameter.

   - Fixed compilation problems when using C_INCLUDE_PATH.

   - Fixed --version when built from a Git repository.

   - Use noenhanced mode for title in plot-bamstats.  Prevents unwanted
     interpretation of characters like underscore in gnuplot version 5.

   - now reports perfect match hits (no indels or mismatches).

   - Fixed bug in fasta and fastq subcommands where stdout would not be flushed
     correctly if the -0 option was used.

   - Fixed invalid memory access in mpileup and depth on alignment records
     where the sequence is absent.

Revision 1.2 / (download) - annotate - [select for diffs], Wed Aug 22 09:42:59 2018 UTC (5 years, 6 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2018Q3-base, pkgsrc-2018Q3
Changes since 1.1: +2 -1 lines
Diff to previous 1.1 (colored)

Recursive bump for perl5-5.28.0

Revision 1.1 / (download) - annotate - [select for diffs], Mon May 7 18:37:31 2018 UTC (5 years, 9 months ago) by bacon
Branch: MAIN
CVS Tags: pkgsrc-2018Q2-base, pkgsrc-2018Q2

biology/samtools: import samtools-1.8

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.

OK wiz@

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