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Hello community,
here is the log from the commit of package samtools for openSUSE:Factory
checked in at 2022-05-04 15:10:43
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/samtools (Old)
and /work/SRC/openSUSE:Factory/.samtools.new.1538 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "samtools"
Wed May 4 15:10:43 2022 rev:4 rq:974396 version:1.15.1
Changes:
--------
--- /work/SRC/openSUSE:Factory/samtools/samtools.changes 2021-05-18
18:27:12.314764045 +0200
+++ /work/SRC/openSUSE:Factory/.samtools.new.1538/samtools.changes
2022-05-04 15:11:02.440163912 +0200
@@ -1,0 +2,78 @@
+Wed Apr 20 20:13:07 UTC 2022 - Ferdinand Thiessen <r...@fthiessen.de>
+
+- Update to version 1.15.1
+ * Samtools mpileup VCF and BCF output (deprecated in release 1.9)
+ has been removed. Please use bcftools mpileup instead.
+ * Added --min-BQ and --min-MQ options to depth.
+ * Improved automatic file type detection with view -u or
+ view -1.
+ * For markdup optical duplicate marking add regex options for
+ custom coordinates.
+ * New samtools consensus subcommand for generating consensus
+ from SAM, BAM or CRAM files based on the contents of the
+ alignment records.
+ * New samtools view --fetch-pairs option.
+ * New samtools head subcommand for conveniently displaying
+ the headers of a SAM, BAM, or CRAM file.
+ * Bug fixes
+- Update to version 1.14
+ * The legacy samtools API has been removed:
+ libbam.a, bam_endian.h, sam.h and most of bam.h
+ * New samtools samples command to list the samples used in a
+ SAM/BAM/CRAM file.
+ * mpileup now supports base modifications via the SAM Mm/MM
+ auxiliary tag. Please see the --output-mods option.
+ * Added mpileup --output-BP-5 option to output the BP field in
+ 5' to 3' order instead of left to right.
+ * Added samtools view --rf option as an additional FLAG
+ filtering method.
+ * New samtools import -N option to use the second word on
+ a FASTQ header line, matching the SRA/ENA FASTQ variant.
+ * Improve view -x option to simplify specifying multiple tags,
+ and added the reverse --keep-tag option to include rather
+ than exclude.
+ * Switched the processing order of view -x (tag filtering)
+ and -e (expression) handling.
+ * Added filter expression endpos keyword.
+ * samtools view errors now appear after any SAM output,
+ improving their visibility.
+ * Improved samtools sort use of temporary files, both tidying
+ up if it fails and recovery when facing pre-existing
+ temporary files.
+ * Filtering in samtools view now sets the UNMAP BAM flag
+ when given the -p option.
+ * Make CRAM references shared during samtools merge so
+ merging many files has a lower memory usage.
+ * Bug fixes
+- Update to version 1.13
+ * Fixed samtools view FILE REGION, mpileup -r REGION,
+ coverage -r REGION and other region queries
+ * Added options to set and clear flags to samtools view
+ * samtools view now has long option equivalents for most of its
+ single-letter options
+ * A new tool, samtools import, has been added.
+ It reads one or more FASTQ files and converts them into unmapped
+ SAM, BAM or CRAM.
+ * Fixed samtools coverage error message when the target region name#
+ is not present in the file header.
+ * Made samtools coverage ASCII mode produce true ASCII output.
+ * samtools coverage now allows setting the maximum depth,
+ using the -d/--depth option.
+ * samtools flags now accepts any number of command line arguments,
+ allowing multiple SAM flag combinations to be converted at once.
+ * samtools ampliconclip, ampliconstats and plot-ampliconstats now support
+ inputs that list more than one reference.
+ * samtools ampliconclip now accepts the --tolerance option,
+ which allows the user to set the number of bases within which a region
+ is matched.
+ * Fixed negative depth values in ampliconstats output.
+ * samtools addreplacerg now allows for updating (replacing) an
+ existing @RG line in the output header, if a new @RG line is provided
+ in the command line, via the -r argument.
+ * Stopped samtools cat from outputting multiple CRAM EOF markers.
+ * Three new counts have been added to samtools flagstat:
+ primary, mapped primary and duplicate primary.
+ * samtools merge now accepts a -o FILE option specifying the output file,
+ similarly to most other subcommands.
+
+-------------------------------------------------------------------
Old:
----
samtools-1.12.tar.bz2
New:
----
samtools-1.15.1.tar.bz2
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ samtools.spec ++++++
--- /var/tmp/diff_new_pack.hlGHFJ/_old 2022-05-04 15:11:03.104164728 +0200
+++ /var/tmp/diff_new_pack.hlGHFJ/_new 2022-05-04 15:11:03.112164738 +0200
@@ -1,7 +1,7 @@
#
# spec file for package samtools
#
-# Copyright (c) 2021 SUSE LLC
+# Copyright (c) 2022 SUSE LLC
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
@@ -17,7 +17,7 @@
Name: samtools
-Version: 1.12
+Version: 1.15.1
Release: 0
Summary: Tools for manipulating next-generation sequencing data
License: MIT
@@ -40,7 +40,7 @@
with bcftools), and a simple alignment viewer.
%prep
-%setup -q -n %{name}-%{version}
+%setup -q
%build
%configure --with-htslib=system
++++++ samtools-1.12.tar.bz2 -> samtools-1.15.1.tar.bz2 ++++++
/work/SRC/openSUSE:Factory/samtools/samtools-1.12.tar.bz2
/work/SRC/openSUSE:Factory/.samtools.new.1538/samtools-1.15.1.tar.bz2 differ:
char 11, line 1
