Added SAM/BAM/CRAM converter tests. This relies on the jc_cram_changes branch of the htsjdk.
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.
Code review changes.
Code review changes.
Merge pull request #124 from broadinstitute/jc_cram_changes

Added SAM/BAM/CRAM converter tests. This relies on the jc_cram_changes b...