CVS commit: pkgsrc/biology/samtools

["Adam Ciarcinski" <adam%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   adam
Date:           Tue Dec 13 10:28:01 UTC 2022

Modified Files:
        pkgsrc/biology/samtools: Makefile PLIST distinfo

Log Message:
samtools: updated to 1.16.1

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.

1.16

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.

Documentation:

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)


To generate a diff of this commit:
cvs rdiff -u -r1.16 -r1.17 pkgsrc/biology/samtools/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/samtools/PLIST
cvs rdiff -u -r1.8 -r1.9 pkgsrc/biology/samtools/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/samtools/Makefile
diff -u pkgsrc/biology/samtools/Makefile:1.16 pkgsrc/biology/samtools/Makefile:1.17
--- pkgsrc/biology/samtools/Makefile:1.16       Thu Jun 30 11:18:04 2022
+++ pkgsrc/biology/samtools/Makefile    Tue Dec 13 10:28:01 2022
@@ -1,17 +1,20 @@
-# $NetBSD: Makefile,v 1.16 2022/06/30 11:18:04 nia Exp $
+# $NetBSD: Makefile,v 1.17 2022/12/13 10:28:01 adam Exp $
 
-DISTNAME=      samtools-1.15
-PKGREVISION=   2
+DISTNAME=      samtools-1.16.1
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=samtools/}
+GITHUB_RELEASE=        ${PKGVERSION_NOREV}
+EXTRACT_SUFX=  .tar.bz2
 
 MAINTAINER=    bacon%NetBSD.org@localhost
 HOMEPAGE=      https://www.htslib.org/
 COMMENT=       Tools for manipulating sequence alignment maps
 LICENSE=       mit
 
-USE_TOOLS+=    autoconf automake autoreconf bash gmake perl
-GNU_CONFIGURE= yes
+USE_TOOLS+=            autoconf automake autoreconf bash gmake perl
+GNU_CONFIGURE=         yes
+CONFIGURE_ARGS+=       --with-htslib=system
+TEST_TARGET=           test
 
 SUBST_CLASSES+=                version
 SUBST_STAGE.version=   pre-configure
@@ -29,9 +32,6 @@ REPLACE_PERL+=                test/*.pl
 REPLACE_PERL+=         misc/plot-bamstats misc/plot-ampliconstats
 REPLACE_LUA+=          misc/*.lua
 
-CONFIGURE_ARGS+=       --with-htslib=system
-TEST_TARGET=           test
-
 pre-configure:
        cd ${WRKSRC} && autoreconf -if
 

Index: pkgsrc/biology/samtools/PLIST
diff -u pkgsrc/biology/samtools/PLIST:1.5 pkgsrc/biology/samtools/PLIST:1.6
--- pkgsrc/biology/samtools/PLIST:1.5   Sat Feb 26 23:11:43 2022
+++ pkgsrc/biology/samtools/PLIST       Tue Dec 13 10:28:01 2022
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.5 2022/02/26 23:11:43 bacon Exp $
+@comment $NetBSD: PLIST,v 1.6 2022/12/13 10:28:01 adam Exp $
 bin/ace2sam
 bin/blast2sam.pl
 bin/bowtie2sam.pl
@@ -49,6 +49,7 @@ man/man1/samtools-merge.1
 man/man1/samtools-mpileup.1
 man/man1/samtools-phase.1
 man/man1/samtools-quickcheck.1
+man/man1/samtools-reference.1
 man/man1/samtools-reheader.1
 man/man1/samtools-rmdup.1
 man/man1/samtools-samples.1

Index: pkgsrc/biology/samtools/distinfo
diff -u pkgsrc/biology/samtools/distinfo:1.8 pkgsrc/biology/samtools/distinfo:1.9
--- pkgsrc/biology/samtools/distinfo:1.8        Sat Feb 26 23:11:43 2022
+++ pkgsrc/biology/samtools/distinfo    Tue Dec 13 10:28:01 2022
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.8 2022/02/26 23:11:43 bacon Exp $
+$NetBSD: distinfo,v 1.9 2022/12/13 10:28:01 adam Exp $
 
-BLAKE2s (samtools-1.15.tar.gz) = b37f18ce7134f921f1e8b5ebb087ad88b387934080742f26708bbecf9ddb5df7
-SHA512 (samtools-1.15.tar.gz) = fad213b6d7eb8885b67642ad7235fb35a923238c13fac7fde501f0d8093fa90d49539e895691bc61a94f6d25e8cdfc4e2c4e94ff0ea91ceee248d5140f561cd6
-Size (samtools-1.15.tar.gz) = 4970205 bytes
+BLAKE2s (samtools-1.16.1.tar.bz2) = 45ca326da1c2aa560fde2d582b58150b71f05d72ff996c9ae97427ef22b018a0
+SHA512 (samtools-1.16.1.tar.bz2) = f9d6b8652234c782a1b369f028073ad4a66c44e9620ae60f0ecb35e0874f04ca633713078b692fdc1a1cc4f884ebdbf3ecae6881f11fb3b4fd3d27c5b8da67ba
+Size (samtools-1.16.1.tar.bz2) = 8217689 bytes
 SHA1 (patch-Makefile) = 3fc1f1d67167c8ca8eff1ed17f7a084ec3d4579d