[Samtools-announce] Picard Release 1.127

[Jason C. <jc...@br...>]

Picard release 1.127

15 December 2014

- CRAM file support
- Make parseOptionsFile public, with a little more control over behavior.
- SamReader conversion of Picard public.
- Added common argument for reference fasta to support CRAM input/output.
- Reference fasta should be optional.
- Use SamReaderFactory makeDefault with reference sequence whenever
possible to allow for CRAM support.
- Added read group tag option, resolves #108 #114
- Various aesthetic tweaks for HTML doc generation.
- Fixed Faked Filter files.  Need them to be of size one element for the
faked filter file to have the same number of elements as other faked types.