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@daviesrob daviesrob released this 16 Dec 15:27
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1.23
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Download the source code here: samtools-1.23.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.)

New work and changes:

  • New reference stats in samtools stats. First line in RFS section gives the total sequence count, count of regions, average GC, min, max, average and total counts. Second line onwards gives regions, lengths, GC and unknown base count. (PR #2224, implements #2139. Requested by Filipe G. Vieira)

  • New, faster Python version of seq_cache_populate to create and update REF_CACHE. (PR #2231. Thanks to Ruben Vorderman)

  • Add a minimum depth (--min-depth) option to samtools coverage. (PR #2235, implements #1563. Requested by Charles Foster)

  • Add an option to exclude reads (--exclude-no-read-group) that have no read group from samtools view when the -r (or -R) options are used. (PR #2271, fixes #2265. Reported by Matt Sexton)

  • Add UMI support to samtools fastq and samtools import. See samtools/htslib#1960. (PR #2270, fixes #2259 amd #2262. Requested by Poshi)

  • Optionally trim soft clips from reads in samtools fastq output. (PR #2233, fixes #1275. Requested by Torsten Seemann)

  • If sam file is sorted by tag, samtools split will output data sequentially to avoid having simultaneous open files. (PR #2281, fixes #2276. Requested by Clint Valentine)

Documentation:

  • In the command help output add a link to the global options in the samtools.1 page on the HTSlib site. (PR #2258, addresses #2236. Reported by Chris Saunders)

  • Add a support section to README.md. This mentions the GitHub issue tracker and an email address for security issues. (PR #2267)

Bug fixes:

  • Prevent samtools coverage from printing a coverage table on failure. (PR #2247, fixes #2242. Reported by Georges Kanaan)

  • Remove deprecated line style commands from plot-bamstats. (PR #2251, fixes #2243. Reported by Suhas Srinivasan)

  • Add missing sam_global_args_free() calls to address (harmless) memory leaks. (PR #2274)

  • Fix samtools consensus crash when used with threads and iterators. See also samtools/htslib#1959 (PR #2269)

Non user-visible changes and build improvements:

  • Ignore and testclean test/stat/*.fa.fai (PR #2241. Thanks to John Marshall)

  • Remove use of C variables starting in _ from bam_consensus.c. (PR #2250, fixes #2248. Reported by Ghanji125)

  • Add Replace RG check exit and add some comments to bam_addrprg.c. (PR #2254. Thanks to Martin Pollard)

Download the source code here: samtools-1.23.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.)

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