Script 'mail_helper' called by obssrc Hello community, here is the log from the commit of package samtools for openSUSE:Factory checked in at 2021-05-18 18:26:51 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/samtools (Old) and /work/SRC/openSUSE:Factory/.samtools.new.2988 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "samtools" Tue May 18 18:26:51 2021 rev:3 rq:893485 version:1.12 Changes: -------- --- /work/SRC/openSUSE:Factory/samtools/samtools.changes 2021-04-21 21:00:16.610284262 +0200 +++ /work/SRC/openSUSE:Factory/.samtools.new.2988/samtools.changes 2021-05-18 18:27:12.314764045 +0200 @@ -1,0 +2,42 @@ +Wed Apr 28 15:57:19 UTC 2021 - Ferdinand Thiessen <[email protected]> + +- Update to version 1.12 + * The legacy samtools API (libbam.a, bam.h, sam.h, etc) is + deprecated and will be removed entirely in a future SAMtools + release. It is recommend coding against the HTSlib API directly. + * I/O errors and record parsing errors during the reading of + SAM/BAM/CRAM files are now always detected. + * samtools --version now displays a summary of the compilation + details and available features, including flags, used libraries + and enabled plugins from HTSlib. + * samtools stats now displays the number of supplementary reads + in the SN section. Also, supplementary reads are no longer + considered when splitting read pairs by orientation. + * samtools stats now counts only the filtered alignments that + overlap target regions, if any are specified. + * samtools view now accepts option -N, which takes a file containing + read names of interest. This allows the output of only the reads + with names contained in the given file. + * samtools view -d option now works without a tag associated value, + which allows it to output all the reads with the given tag. + * samtools view -d and -D options now accept integer and single + character values associated with tags, not just strings. + * samtools view now works with the filtering expressions introduced + by HTSlib. The filtering expression is passed to the program using + the specific option -e or the global long option --input-fmt-option. + * samtools markdup now benefits from an increase in performance + in the situation when a single read has tens or hundreds of + thousands of duplicates. + * A new FASTA/FASTQ sanitizer script (fasta-sanitize.pl) was + added, which corrects the invalid characters in the reference + names. + * Fixed a bug in samtools cat, which prevented the command from + running in multi-threaded mode. + * Fixed a samtools merge segmentation fault when it failed to + merge header @PG records. + * Ampliconclip and ampliconstats now guard against the BED file + containing more than one reference (chromosome) and fail when + found. Adding proper support for multiple references will + appear later. + +------------------------------------------------------------------- Old: ---- samtools-1.11.tar.bz2 New: ---- samtools-1.12.tar.bz2 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ samtools.spec ++++++ --- /var/tmp/diff_new_pack.766g32/_old 2021-05-18 18:27:12.850761722 +0200 +++ /var/tmp/diff_new_pack.766g32/_new 2021-05-18 18:27:12.854761705 +0200 @@ -17,14 +17,13 @@ Name: samtools -Version: 1.11 +Version: 1.12 Release: 0 Summary: Tools for manipulating next-generation sequencing data License: MIT Group: Productivity/Scientific/Other URL: https://github.com/samtools/samtools Source: https://github.com/samtools/samtools/releases/download/%{version}/samtools-%{version}.tar.bz2 -BuildRequires: autoconf BuildRequires: ncurses-utils BuildRequires: perl BuildRequires: pkgconfig(htslib) >= %{version} @@ -44,10 +43,8 @@ %setup -q -n %{name}-%{version} %build -autoheader -autoconf -Wno-syntax %configure --with-htslib=system -make %{?_smp_mflags} +%make_build %install %make_install ++++++ samtools-1.11.tar.bz2 -> samtools-1.12.tar.bz2 ++++++ /work/SRC/openSUSE:Factory/samtools/samtools-1.11.tar.bz2 /work/SRC/openSUSE:Factory/.samtools.new.2988/samtools-1.12.tar.bz2 differ: char 11, line 1
