From: Robert D. <rm...@sa...> - 2024-01-22 12:10:44
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Samtools and HTSlib release 1.19.1 are now available from GitHub and SourceForge. This release fixes a regression in version 1.19 that caused written CRAM files to be much bigger than necessary. It also fixes a number of other bugs listed below, including one that could cause crashes or incorrect results when filtering by regions in a BED file. https://github.com/samtools/htslib/releases/tag/1.19.1 https://github.com/samtools/samtools/releases/tag/1.19.1 https://sourceforge.net/projects/samtools/ ------------------------------------------------------------------------------ htslib - changes v1.19.1 ------------------------------------------------------------------------------ * Fixed a regression in release 1.19 that caused all aux records to be stored uncompressed in CRAM files. The resulting files were correctly formatted, but bigger than they needed to be. (PR#1729, fixes samtools#1968. Reported by Clockris) * Fixed possible out-of-bounds reads due to an incorrect check on B tag lengths in cram_encode_aux(). (PR#1725) * Fixed an incorrect check on tag length which could fail to catch a two byte out-of-bounds read in bam_get_aux(). (PR#1728) * Made errors reported by hts_open_format() less confusing when it can't open the reference file. (PR#1724, fixes #1723. Reported by Alex Leonard) * Made hts_close() fail more gracefully if it's passed a NULL pointer (PR#1724) ------------------------------------------------------------------------------ samtools - changes v1.19.1 ------------------------------------------------------------------------------ Bug Fixes: * Fixed a possible array bounds violation when looking up regions in a BED file (e.g. using `samtools view -L`). This could lead to crashes or the return of incomplete results if the BED file contained a large number of entries all referencing low positions on a chromosome. (PR #1962, fixes #1961. Reported by geertvandeweyer) * Fixed a crash in samtools stats that occurred when trying to clean up after it was unable to open a CRAM reference file. (PR #1957, fixes crash reported in samtools/htslib#1723. Reported by Alex Leonard) Documentation: * Fixed inverted logic in the `samtools consensus --show-del` manual page description. (PR #1955, fixes #1951. Reported by Mikhail Schelkunov) * Added a description of the MPC section to the `samtools stats` manual page. (PR #1963, fixes #1954. Reported by litun-fkby) -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA. |