does not require MQ tags in bam file (although it is much faster when they are present
prevent seeking mapq of mate when mate is unmapped
typo
output the scaled depth in the AO,RO, and DP format fields
output integer depth AO, RO
ignore evidence types with no alt reads
source python 2.7
python
proper GQ and GL scores for variants
improved duplication
fixed errors in the way quality is calculated
see what happens if i allow it to genotype variants as 0/0
repaired the reporting of GL likelihoods when no alt read evidence
allow 0/0 gts
revert to non-ref genotypes only
replaced conditionals that I'd removed. these are important because it prevents svtyper from considering reference reads of one type (PE/SR) when only the other type of evidence was detected
revise control for lumpy behavior. one off is only on neg strand reads. this affects sensitivity to split reads in duplications
right side gets incremented with on the + strand
fixed one off things for all SV types (hopefully
broken intermediate commit