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

...ranch of the htsjdk.

Output CRAM from MarkDuplicates.
Rebase fixes.
SamReader conversion of Picard public.
Deprecation changes.
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.

Rebase changes.

Rebase changes.
It looks like we don't lazily load the header so we should be able to create a utility method to open the SamReader, read the header and then close the SamReader.