• Fixing up tests in MarkDuplicates so that tests with duplex UMIs are handled properly. (#1404)
• Make crosscheck take a file->sample map input so that we can crosscheck to a un-duplicated vcf. (#1303)
• Improvements to the locus iteration. (#1376)
• • Added in a progress meter to CollectSamErrorMetrics.
• • Added a flag to enable jumping to loci rather than iterating through all variants / loci in order each run.
• Added a test to CollectHsMetrics to harden against future code changes (#1386)
• • Added a test to CollectHsMetrics to harden against future code changes.
• • removed non-working (and unneeded) code in reflectiveCopy
• • added some protection against NPE
• • cleaned-up some code formatting issues.
• • sanitized some sam files.