github broadinstitute/picard 2.8.1
on GitHub

  • - removed a O(maxCoverage * nLoci) sanity test which significantly increases run-time for CollectWgsMetrics when the maxCoverage is large, as it is by default for CollectRawWgsMetrics. (#716)
  • Fix to handle overlapped read clipping in MergeBamAlignment when clipping already present (#709)
  • - correcting DUAL_INDEXED adapter sequence according to the documentation (page 17 of http://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences_1000000002694-01.pdf) and also inspection of read sequence from short inserts. (#705)
  • Default output for CreateSequenceDictionary (#712)
  • - remove reference to @Deprecated VariantContextWriterFactory in htsdjk prior to removal from that codebase. (#710)
  • Fix for issues 342 and 138: introduced ALSO_IGNORE_DUPLICATES option (#646)
  • CollectIlluminaBasecallingMetrics supports an alternative barcodes (#702)
  • - use SEQUENCE_REFERENCE when opening files in CheckFingerprints. This should allow fingerprinting CRAM files directly. (#703)
  • Support in-line skips and molecular barcodes. (#697)
  • The molecular indexes should be joined with hyphens rather than (#689)
  • Fix for issue #432 CreateSequenceDictionary stalls indefinitely with large genomes (#687)
3 years ago