Recloned, given x permission
Initial commit
OptimAssembly merged in MinVar
Moving filtering to its own function. Adding universal_newlines=True so that python 3.x would work too.
This produces up to the bam alignment. Now working on translation and codon variant calling.
Working on callvar. pysam used to access aligned reads, now trying to extract qualities.
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.
Improved parsing of matching regions.
Adding a sentence while testing git subtree