Skip to content
HTSlib release 1.3.1: bug fix release, notably error checking

* 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.

* Fixed documentation problems #348 and #358.