Initial stable(ish) release

Please see the later releases, an bug was identified in the tests which prevented installation without manual intervention.

Basic tool bam_to_sra_xml.pl for GNOS submission file generation should be stable for use. Some additional output files may be added to aid ID tracking later.

Reference implementation bwa mem in bwa_mem.pl has been updated for 0.7.7 release of bwa.

setup.sh script added to perform installation of all C programs required for any of the tools used in this package.