Add module for 'makefile' parsing/validation.
Add ability to update PG tags to safeSAM2BAM.
Add test for None values.
Reworking of bam_pipeline mkfile format.

Increase the flexibility of the format, allowing arbitrary options
to be passed to Bowtie2 (BWA is TODO), and reduce some previous
inconsistency in the structure. This breaks backwards compatibility!
Improve makefile comments.