Working on callvar. pysam used to access aligned reads, now trying to extract qualities.
First working version.

ReportDRM is now functional, takes a fasta file with protein mutants,
aligns them to protease, RT and integrase and writes a report with
the mutations.
Subtree merged in ReportDRM
First working version of MinVar.

Take as inputs a (possibly gzipped) fastq file, tries to infer subtype, aligns against HXB2,calls variants
with freebayes and parses them in order to write a report in markdown.
Finally, pandoc is called to make a pdf.