Devel

[b97pla]

• gzip-compress all vcf files (with GATK) by default (implements #66)
• include the snpEff reference version in version_report.txt
• Fixed typo in version report
• Fixed calls to snpEff (RAM, skip intermediate files, compress output)
• Option to include/exclude OQ, BD and BI tags during bam recalibration
• Option to remove recalibrated bam from final output
• Fixes to processing BAMs when splitting using ParallelShell
• Fixes to handling intermediate files and some un-annotated output files (mostly index files)

[johandahlberg]

The stuff of legends @b97pla! So much good stuff in here.