Script 'mail_helper' called by obssrc Hello community, here is the log from the commit of package samtools for openSUSE:Factory checked in at 2022-09-15 22:59:11 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/samtools (Old) and /work/SRC/openSUSE:Factory/.samtools.new.2083 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "samtools" Thu Sep 15 22:59:11 2022 rev:5 rq:1003769 version:1.16.1 Changes: -------- --- /work/SRC/openSUSE:Factory/samtools/samtools.changes 2022-05-04 15:11:02.440163912 +0200 +++ /work/SRC/openSUSE:Factory/.samtools.new.2083/samtools.changes 2022-09-15 23:00:17.753402665 +0200 @@ -1,0 +2,51 @@ +Thu Sep 15 00:59:03 UTC 2022 - Stefan Br??ns <stefan.bru...@rwth-aachen.de> + +- Update to version 1.16.1 + * 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. +- Update to version 1.16.0 + * 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 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. + - Allow samtools fastq -T "*". This allows all tags from SAM + records to be written to fastq headers. + * 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. + + +------------------------------------------------------------------- Old: ---- samtools-1.15.1.tar.bz2 New: ---- samtools-1.16.1.tar.bz2 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ samtools.spec ++++++ --- /var/tmp/diff_new_pack.yCmCuS/_old 2022-09-15 23:00:18.481404720 +0200 +++ /var/tmp/diff_new_pack.yCmCuS/_new 2022-09-15 23:00:18.489404743 +0200 @@ -16,8 +16,10 @@ # +%define htsminversion 1.16 + Name: samtools -Version: 1.15.1 +Version: 1.16.1 Release: 0 Summary: Tools for manipulating next-generation sequencing data License: MIT @@ -26,11 +28,11 @@ Source: https://github.com/samtools/samtools/releases/download/%{version}/samtools-%{version}.tar.bz2 BuildRequires: ncurses-utils BuildRequires: perl -BuildRequires: pkgconfig(htslib) >= %{version} +BuildRequires: pkgconfig(htslib) >= %{htsminversion} BuildRequires: pkgconfig(ncurses) BuildRequires: pkgconfig(zlib) Requires: bgzip -Requires: htsfile >= %{version} +Requires: libhts3 >= %{htsminversion} Requires: perl Requires: tabix ++++++ samtools-1.15.1.tar.bz2 -> samtools-1.16.1.tar.bz2 ++++++ /work/SRC/openSUSE:Factory/samtools/samtools-1.15.1.tar.bz2 /work/SRC/openSUSE:Factory/.samtools.new.2083/samtools-1.16.1.tar.bz2 differ: char 11, line 1
