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.
indenting?