github broadinstitute/picard 2.7.0
on GitHub

Changes since the last release:

  • Add logging for loading in dbSNP in CollectVariantCallingMetrics. (#662)
  • fixed format issues
  • added an option to force the file output format when using OUTPUT_BY_READGROUP
  • Small fixups to WgsMetrics missed in #657. (#666)
  • - made index created during test get deleted in the end - tightened TheoreticalHetSensitivity test intervals since it has been made deterministic.
  • QualityYieldMetrics may overflow with many reads. (#665)
  • Total clusers is now a long in GcBiasSummaryMetrics. (#664)
  • Fixing a typo in the usage of FilterVcf.
  • Fixing a number of issues in and add tests for CollectWgsMetricsWithNonZeroCoverage.
  • fix InsertSizeCollection giving bin width trailing zeros when median is not integer; fixed tests as well
  • Rename SetNmAndUqTags and fix #622 (MergeBamAlignment MD tag). (#636)
  • Added options to CollectOxoGMetrics and CollectSequencingArtifactMetrics to include/exclude non-PF reads. (#644)
  • Modified CheckFingerprint to be able to take a VCF as INPUT (as opposed to a SAM/BAM). Added specialized method in FingerprintChecker for that purpose Generalized certain methods to handle VCF vs BAM/SAM as input. Added test cases and test data for FingerprintChecker
  • Fix usage docs: refer to -h instead of --help (#649)
  • UMI Aware Mark Duplicates with rudimentary error correction
  • Revert “Update the NM and MD tags when clipping overlapping inserts in” (#635)
  • Make WgsMetrics mergeable.
  • Added check for REFERENCE_SEQUENCE to avoid NPE in CollectSequencingArtifactMetrics (#639)
  • Added file path to exception message thrown out of BclReader
  • Added the ability to include duplicate reads in CollectSequencingArtifactMetrics. (#633)
  • DuplicationMetrics are now mergeable.
  • The update of the docs for CollectMultipleMetrics. (#626)
  • Using predefined version of MQ (two different kinds) and SA. (#603)
  • Modify documentation to add RNA-seq usage example of READ_NAME_REGEX=null to skip optical duplicate detection.
  • Expose the INCLUDE_UNPAIRED option for CollectSequencingArtifactMetrics in CollectMultipleMetrics.
  • Kt fingerprintchecker fix (#596)
  • Update the NM and MD tags when clipping overlapping inserts in MergeBamAlignment.
  • now relying on getSamReadNameFromFastqHeader in HTSJDK’s SequenceUtil for converting a read name in a FASTQ to a read name in a SAM/BAM file.
3 years ago