Refactor code base to keep base counts for forward and reverse strands separately in SampleCountInfo.
Normalize somatic priority score by number of mapped reads, and number of parents and germline samples used in the calculation.
Adjust Change log.
Add strand bias filter.
Fix for minimum number of reads bug.
Make strand bias filter take minimum depth threshold as a parameter (j).
Set parameter j to value used when developing the test.
Add debug assert.
Add debug assert from stable branch.
Add debug assert from stable branch.
Add debug assert from stable branch.
Fix old test, break new one. The problem is with the test rather than recent changes to the code base.
Remove candidate somatic variation that can occur when the germline samples have less coverage than the somatic sample. Now require at least twice the coverage in the somatic sample than the minimum coverage in the germline samples.
Avoid NaN when they are no additional germline samples.
Use somatic base count in the calculation of priority score.
Fix how parentHasGenotype is calculated. Need to consider the bases remaining after failed bases as well.
Improve implementation of SampleCountInfo.baseString. Add method to explain the candidate somatic choices.
Take the max or normalized priority contributions rather than the average.
Add a STRICT_SOMATIC filter.
Fix the calculation of STRICT_SOMATIC filter and the normalization of the priority score.
Fix FDR mode to prevent NPE when a FILTER column is specified.