Add option --use_ref_for_cram for using the supplied reference file when reading the reads from a CRAM file.  When True, the reference file given by --ref must be stored on a local POSIX filesystem.
Add option --use_ref_for_cram for using the supplied reference file when
reading the reads from a CRAM file.  When True, the reference file given
by --ref must be stored on a local POSIX filesystem.

PiperOrigin-RevId: 232352755

google/deepvariant,google/deepvariant,google/deepvariant