Remove threshold effects when calling genotypes in several samples. Modified the filters to not remove bases in specific samples when the genotype survived filters in at least another sample (previous versions reported these threshold edge effects as differences, which could be confusing, this version simply shows the marginal raw base counts in samples where the genotype could have been filtered by a filter, which makes it easier to compare the strength of the genotype support across samples). This adjustment was done for both base genotype and indel genotypes.
 - LeftOverFilter: now uses minVariationSupport as minimum threshold.
Fix the tests following changes to thresholding behaviour.
Really fix indel thresholding.
Set the count to zero rather than increment it when the base is completely filtered.
really restore counts to value before filter when we determine thresholding can cause problems.
discover-sequence-variants mode: Add ability to associate covariates to samples. See new --covariates option.
discover-sequence-variation mode: Add draft somatic variation format.
IDEA files
removing pom.xml
merge somatic branch
Improve somatic statistics, add test.
restore tests to before thresholding fix.
 - Simpler approach to removing thresholding effects, with JUnit test.
Add draft CommonIndelArtifactFilter.
Print some stats about indels to stdout to help debug.
Print depth at position to stdout.
Print complete depth at site.
Switch to using neural net trained from data.
Add repeat pattern length as feature.
Fix potential NPE.