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.