2.7.0

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.

2.6.0

Picard has switched it's build system from ant to gradle, see the ReadMe for gradle usage instructions.

2.5.0

Release 2.5.0

2.4.1

Release 2.4.1

2.4.0

Release 2.4.0

2.3.0

Release 2.3.0

2.2.4

Release 2.2.4

2.2.3

Release 2.2.3

2.2.2

Release 2.2.2

2.2.1

Release 2.2.1