updated workflow submodule to b723b68
handle svs without crashing
Streamline header filter and appending for Bsmap

The Bsmap aligner module would previously loop over every line of the
aligner generated SAM (in Perl) to create a temporary SAM without
headers. It would then shell out to 'cat' to append the temporary SAM to
the pipeline provided SAM. It now does this in a single step with no
temporary file by shelling out to grep -v -E.
Sort SAM by coordinate in Bsmap aligner module.

Providing a name-sorted SAM to 'samtools fillmd' was causing performance
problems. Hopefully the coordinate-sorted SAM will work correctly.
Add missing subs for sorting in Bsmap module

The sorting subroutine added to the Bsmap aligner module also needs the
_check_db_connection and _disconnect_from_db subroutines for closing the
db handle.
Disabled Mutect test
Merge remote-tracking branch: upstream/master