Script 'mail_helper' called by obssrc Hello community, here is the log from the commit of package samtools for openSUSE:Factory checked in at 2021-04-21 20:59:56 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/samtools (Old) and /work/SRC/openSUSE:Factory/.samtools.new.12324 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "samtools" Wed Apr 21 20:59:56 2021 rev:2 rq:886926 version:1.11 Changes: -------- --- /work/SRC/openSUSE:Factory/samtools/samtools.changes 2020-02-25 16:04:52.128380359 +0100 +++ /work/SRC/openSUSE:Factory/.samtools.new.12324/samtools.changes 2021-04-21 21:00:16.610284262 +0200 @@ -1,0 +2,117 @@ +Fri Mar 19 09:18:00 UTC 2021 - Wang Jun <[email protected]> + +- Update to version 1.11 + * New samtools ampliconclip sub-command for removing primers from + amplicon-based sequencing experiments, including the current + COVID-19 projects. The primers are listed in a BED file and can be + either soft-clipped or hard-clipped. (#1219) + * New samtools ampliconstats sub-command to produce a textual summary + of primer and amplicon usage, in a similar style to "samtools + stats". The misc/plot-ampliconstats script can generate PNG + images based on this text report. (#1227) + * Samtools fixmate, addreplacerg, markdup, ampliconclip and sort now + accept a -u option to enable uncompressed output, which is useful when + sending data over a pipe to another process. Other subcommands which + already support this option for the same purpose are calmd, collate, + merge, view and depad. (#1265) + * samtools stats has a new GCT section, where it reports ACGT content + percentages, similar to GCC but taking into account the read orientation. + (#1274) + * Samtools split now supports splitting by tag content with the -d + option (#1211) + * samtools merge now accepts a BED file as a command line argument (-L) and + does the merging only with reads overlapping the specified regions (#1156) + * Samtools sort now has a minhash collation (-M) to group unmapped + reads with similar sequence together. This can sometimes + significantly reduce the file size. (#1093) + * Samtools bedcov now has -g and -G options to filter-in and + filter-out based on the FLAG field. Also the new -d option adds + an extra column per file counting the number of bases with a depth + greater than or equal to a given threshold. (#1214) + * Fixed samtools bedcov -j option (discard deletions and ref-skips) + with multiple input files (#1212) + * samtools bedcov will now accept BED files with columns separated by + spaces as well as tabs (#1246; #1188 reported by Mary Carmack) + * samtools depth can now include deletions (D) when computing the base + coverage depth, if the user adds the -J option to the command + line (#1163). + * samtools depth will count only the bases of one read, for the overlapping + section of a read pair, if the -s option is used in the command line + (#1241, thanks to Teng Li). + * samtools depth will now write zeros for the entire reference length, + when "samtools depth -aa" is run on a file with no alignments. (#1252; + #1249 reported by Paul Donovan) + * Stopped depth from closing stdout, which triggered test fails + in pysam (#1208, thanks to John Marshall). + * samtools view now accepts remote URIs for FASTA and FAI files. + Furthermore, the reference and index file can be provided in a single + argument, such as + samtools view -T ftp://x.com/ref.fa##idx##ftp://y.com/index.fa.fai a.cram + (#1176; samtools/htslib#933 reported by @uitde007) + * samtools faidx gets new options --fai-idx and --gzi-idx to allow + specification of the locations of the .fai and (if needed) .gzi index + files. (#1283) + * The samtools fasta/fastq '-T' option can now add SAM array (type 'B') tags + to the output header lines. (#1301) + * samtools mpileup can now display MAPQ either as ASCII characters (with + -s/--output-MQ; column now restored to its documented order as in 1.9 and + previous versions) or comma-separated numbers (with --output-extra MAPQ; + in SAM column order alongside other selected --output-extra columns). + When both -s/--output-MQ and -O/--output-BP are used, samtools 1.10 printed + the extra columns in the opposite order. This changes the format produced + by 1.10's --output-extra MAPQ. (#1281, thanks to John Marshall; reported + by Christoffer Flensburg) + * samtools tview now accepts a -w option to set the output width in + text mode (-d T). (#1280) + * The dict command can now add AN tags containing alternative names with + "chr" prefixes added to or removed from each sequence name as appropriate + and listing both "M" and "MT" alternatives for mitochondria. (#1164, + thanks to John Marshall) + * The samtools import command, labelled as obsolete in May 2009 and + removed from all help and documentation later that year, has + finally been removed. Use samtools view instead. (#1185) + * Replaced the remaining usage of the Samtools 0.1 legacy API with + htslib calls. (#1187, thanks to John Marshall) + * Documentation / help improvements (#1154; #1168; #1191; #1199; + #1204; #1313): + - Fixed a few man-page table layout issues + - Added <file>##idx##<index> filename documentation + - Fixed usage statement for samtools addreplacerg + - Miscellaneous spelling and grammar fixes + - Note fixmate/markdup name collated rather than name sorted input + - Note that fastq and fasta inputs should also be name collated + - Reshuffled order of main man-page and added -@ to more sub-pages + - The misc/seq_cache_populate.pl script now gives REF_CACHE guidance + * Additional documentation improvements, thanks to John Marshall (#1181; + #1224; #1248; #1262; #1300) + - Emphasise that samtools index requires a position-sorted file + - Document 2^29 chromosome length limit in BAI indexes + - Numerous typing, spelling and formatting fixes + * Improved the message printed when samtools view fails to read its + input (#1296) + * Added build support for the OpenIndiana OS (#1165, thanks to John Marshall) + * Fixed failing tests on OpenBSD (#1151, thanks to John Marshall) + * The samtools sort tests now use less memory so the test suite works better + on small virtual machines. (#1159) + * Improved markdup's calculation of insert sizes (#1161) + Also improved tests (#1150) and made it run faster when not checking + for optical duplicates or adding 'do' tags (#1308) + * Fixed samtools coverage minor inconsistency vs idxstats (#1205; #1203 + reported by @calliza) + * Fixed samtools coverage quality thresholding options which were the + wrong way round compared to mpileup (-q is the mapping quality threshold + and -Q is base quality). (#1279; #1278 reported by @kaspernie) + * Fixed bug where `samtools fastq -i` would add two copies of the barcode + in the fastq header if both reads in a pair had a "BC:Z" tag (#1309; + #1307 reported by @mattsoup) + * Samtools calmd no longer errors with a SEQ of "*" (#1230; #1229 + reported by Bob Harris) + * Samtools tview now honours $COLUMNS, fixing some CI tests (#1171; #1162 + reported by @cljacobs) + * Fixed a samtools depad overflow condition (#1200) + * Improved curses detection in configure script (#1170, #577, #940) + * Fixed samtools stats integer overflows and added support for long + references (#1174; #1173) + * Fixed a 1-byte undersized memory allocation in samtools merge. (#1302) + +------------------------------------------------------------------- Old: ---- samtools-1.10.tar.bz2 New: ---- samtools-1.11.tar.bz2 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ samtools.spec ++++++ --- /var/tmp/diff_new_pack.5iUWs4/_old 2021-04-21 21:00:17.098285031 +0200 +++ /var/tmp/diff_new_pack.5iUWs4/_new 2021-04-21 21:00:17.098285031 +0200 @@ -1,7 +1,7 @@ # # spec file for package samtools # -# Copyright (c) 2020 SUSE LLC +# Copyright (c) 2021 SUSE LLC # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -17,7 +17,7 @@ Name: samtools -Version: 1.10 +Version: 1.11 Release: 0 Summary: Tools for manipulating next-generation sequencing data License: MIT @@ -56,6 +56,7 @@ perlbin=`which perl` sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/*.pl sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/plot-bamstats +sed -i "s:/usr/bin/env perl:${perlbin}:" %{buildroot}/%{_bindir}/plot-ampliconstats %files %license LICENSE ++++++ samtools-1.10.tar.bz2 -> samtools-1.11.tar.bz2 ++++++ ++++ 250865 lines of diff (skipped)
