Io_lib 1.13.4 released

Primarily a bug fix release and minor updates to conform to the recent 2.1 CRAM specification update. From the CHANGES file:

Version 1.13.4 (17th February 2014)

  • BAM: Fixed some buffer overruns in BAM decoding.

  • CRAM: Added support for CRAM EOF blocks (new in CRAM v2.1
    specification). Also improved BAM EOF block checking. v2.1 is now
    the default output version.

  • CRAM: Fixed an error causing multi-threading to take longer for the
    first additional thread.

  • CRAM: Improved memory-caching of reference sequences when fetching
    via MD5 path. Also reduced memory used when loading via REF_PATH.

  • CRAM: Experimental / alpha quality code for CRAM version 3.0,
    including new codecs (rANS & arithmetic coders) and CRCs.

  • CRAM: Small improvements to the bzip2 (-j) mode. It now periodically
    tests bzip2 vs gzip and uses whichever is best rather than forcing
    all compression to go via bzip2.

  • CRAM: Fixed crash when handling CRAM files with non-sequential
    reference IDs.

  • Scramble: Now supports 8-way quality binning as an output option.

  • Index_tar: Fixed debian bug #729276 - buffer overflow.

  • Improved Windows building via cross-compilation.

Posted by James Bonfield 2014-02-17

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