non working stash where I've added MC mate position retrieval from SAMBLASTER v0.19. intended for speed increase
functionally looks for the MC SAM tags, ~25X speedup when present
split reads incorporate mapq info
fixed bug in variable name
fixed bug in auto mean/stdev detection, added dynamic concordant/discordant pair probability. now requires scipy
updated discordant read counting at right breakend
changed priors to 0.1, 0.45, 0.9
colby is an idiot and screwed up order of operations
changed gt priors back to 0.2, 0.4, 0.8
bayes 0.1 0.5 0.9
bayes 0.1 0.4 0.9
changed booster to 1 (no boost)
cleaned up code comments
handles generic multiline breakpoints (sort of)
reversing the transloc thing, since it altered homalt sensitivitiy
increment
test
reinstate logic requiring concordants to be same chrom
decrease in hom sensitivity was due to a bug where splitread_b was not casting var.info['END'] to an int, causing no split reads to be observed at break B
clarified vars