- Add metrics to count alignments flagged with the proper pair flag to CollectAlignmentSummaryMetrics (#778). This should be useful towards structural variant discovery workflows. Note that the flag is set differently for BWA MEM alignments versus alignments processed by MergeBamAlignment. See this discussion for an example of how MergeBamAlignment changes the proper pair flag.
- Remove deprecated classes and related tests (#798). The removed classes are CollectWgsMetricsFromQuerySorted, CollectWgsMetricsFromSampledSites, CalculateHsMetrics, and GenotypeReader.