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@daviesrob daviesrob released this 15 Apr 15:21
· 110 commits to develop since this release
1.20
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Download the source code here: htslib-1.20.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they are missing some generated files.)

Updates

  • When working on named files, bgzip now sets the modified and access times of the output files it makes to match those of the corresponding input. (PR #1727, feature request #1718. Requested by Gert Hulselmans)

  • It's now possible to use a -o option to specify the output file name in bgzip. (PR #1747, feature request #1726. Requested by Gert Hulselmans)

  • Improved error faidx error messages. (PR #1743, thanks to Nick Moore)

  • Faster reading of SAM array (type "B") tags. These often turn up in ONT and PacBio data. (PR #1741)

  • Improved validity checking of base modification tags. (PR #1749)

  • mpileup overlap removal now works where one read has a deletion. (PR #1751, fixes samtools/samtools#1992. Reported by Long Tian)

  • The S3 plugin can now find buckets via S3 access point aliases. (PR #1756, thanks to Matt Pawelczyk; fixes samtools/samtools#1984. Reported by Albert Li)

  • Added a --threads option (and -@ short option) to tabix. (PR #1755, feature request #1735. Requested by Dan Bolser)

  • tabix can now index Graph Alignment Format (GAF) files. (See https://github.com/lh3/gfatools/blob/master/doc/rGFA.md) (PR #1763, thanks to Adam Novak)

Bug fixes

  • Security fix: Prevent possible heap overflow in cram_encode_aux() on bad RG:Z tags. (PR #1737)

  • Security fix: Prevent attempts to call a NULL pointer if certain URL schemes are used in CRAM @SQ UR: tags. (PR #1757)

  • Security fix: Fixed a bug where following certain AWS S3 redirects could downgrade the connection from TLS (i.e. https://) to unencrypted http://. This could happen when using path-based URLs and AWS_DEFAULT_REGION was set to a region other that the one where the data was stored. (PR #1762, fixes #1760. Reported by andaca)

  • Fixed arithmetic overflow when loading very long references for CRAM. (PR #1738, fixes #1738. Reported by Shane McCarthy)

  • Fixed faidx and CRAM reference look-ups on compressed fasta where the .fai index file was present, but the .gzi index of compressed offsets was not. (PR #1745, fixes #1744. Reported by Theodore Li)

  • Fixed BCF indexing on-the-fly bug which produced invalid indexes when using multiple compression threads. (PR #1742, fixes #1740. Reported by graphenn)

  • Ensure that pileup destructors are called by bam_plp_destroy(), to prevent memory leaks. (PR #1749, PR #1754)

  • Ensure on-the-fly index timestamps are always older than the data file. Previously the files could be closed out of order, leading to warnings being printed when using the index. (PR #1753, fixes #1732. Reported by Gert Hulselmans)

  • To prevent data corruption when reading (strictly invalid) VCF files with duplicated FORMAT tags, all but the first copy of the data associated with the tag are now dropped with a warning. (PR #1752, PR #1761, fixes #1733. Reported by anthakki)

  • Fixed a bug introduced in release 1.19 (PR #1689) which broke variant record data if it tried to remove an over-long tag. (PR #1752, PR #1761)

  • Changed error to warning when complaining about use of the CG tag in SAM or CRAM files. (PR #1758, fixes samtools/samtools#2002)

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