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
-hinstead 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.