github broadinstitute/picard 2.21.1
on GitHub

  • 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.
9 months ago