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/
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htslib - changes v1.19.1
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* 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)
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samtools - changes v1.19.1
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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)
--
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