[Samtools-devel] SAMtools and HTSlib release 1.19.1

[Robert D. <rm...@sa...>]

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.