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