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.
To line up the param comment starts. Not sure this is common convention but it seems to be the default code style for intellij.