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1.3.1
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@jmarshall jmarshall released this 22 Apr 13:53
· 1850 commits to develop since this release
1.3.1
0f298ce
  • Improved error checking and reporting, especially of I/O errors when writing output files (#17, #315, PR #271, PR #317).
  • Build fixes for 32-bit systems; be sure to run configure to enable large file support and access to 2GiB+ files.
  • Numerous VCF parsing fixes (#321, #322, #323, #324, #325; PR #370).
    Particular thanks to Kostya Kortchinsky of the Google Security Team for testing and numerous input parsing bug reports.
  • HTSlib now prints an informational message when initially creating a CRAM reference cache in the default location under your $HOME directory. (No message is printed if you are using $REF_CACHE to specify a location.)
  • Avoided rare race condition when caching downloaded CRAM reference sequence files, by using distinctive names for temporary files (in addition to O_EXCL, which has always been used). Occasional corruption would previously occur when multiple tools were simultaneously caching the same reference sequences on an NFS filesystem that did not support O_EXCL (PR #320).
  • Prevented race condition in file access plugin loading (PR #341).
  • Fixed mpileup memory leak, so no more "[bam_plp_destroy] memory leak […] Continue anyway" warning messages (#299).
  • Various minor CRAM fixes.

The htslib-1.3.1.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they are missing some generated files.

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