now bwa_mem can generate temp file names
refactored how I do the tests to make sure all relevant functions can deal with a None for out_path
updated docs
now for the "sorted bam" stuff
moving shit around
tabix interface
added a command compiler utility, should make things easier for testing.
now has reasonable testing for command compiler
refactored how pileup gets called
now has a way to make snv calls from pileup
added functional test to make sure pileup and bcftools call works properly
a tiny utility function to check whether files are indexed
now has a bcftools merge wrapper. Still need to do some work to make sure input files are in valid formats.
needs to have a '.bam' at the end
that was a pain
simple utility function to write files in tmp files and have python clean up after itself.
now has an annotate
some example regions
Merge branch 'feature/bcftools-interface' into develop