• Use htsjdk 2.9.0. See htsjdk releases for release notes.
• Add divide method to MathUtil and use it in RnaSeqMetricsCollector. Specifically, take the fiveToThree value zero if the threePrimeCoverage (denominator) is 0. The effect of this change is that instead of dividing by zero, the result is instead zero for histogram-derived values in metrics calculations.
• UpdateVcfSequenceDictionary can now stream the output to stdout. This is a new feature.
• Fix bug in createMetricsDoclet, a gradle task, so that building now generates a document that it did not before. #749
• Cleanup code to remove references to LazyInitializer, which will be deprecated in htsjdk in the near future. #722