Rename 'bam_genotype_regions' to 'vcf_to_fasta'.
Fix mistake in synthetic reads format.
Update example data.
Skeleton file for python scripts.
Fixes for handling of unmapped reads.
Fix for read-group argument to BWA sampe/samse for newer version of BWA.
Warn when BWA 0.7.x is used.
Rework safeSAM2BAM for > BWA v0.5.x unmapped reads

Drop attempt at filtering out malformed reads for BWA 0.7.4;
add processing of unmapped reads to ensure that these correspond
to the more strict interpreation of the spec used by Picard, GATK
and other tools, but now followed by BWA.