Trim mode: remove need for an output filename. Change contains method to remove the smaller bit of sequence flanking the adapter.
Add filters to remove variations that are not somatic, but are prioritized by the p-value when parents are homozygote and the patient is heterozygote.
update test result to reflect introduction of frequency INFO field in somatic format.
Fix a couple of bugs and add tests with mockup for somatic variation calls.
Add unit test to check that issue with homozygous parents, het patient is fixed.
Improve description of changes.