Release 2.2.0

What's Changed

New Features

• Duplicate marking in GroupReadsByUmi by @tfenne in #940 - GroupReadsByUmi can now optionally also set the pcr_duplicate flag field on all reads while duplicate marking. If duplicate marking mode is engaged then by default secondary, supplementary and mapq=0 reads are passed through to the output BAM
• Addition of threading in GroupReadsByUmi and some other performance optimizations by @tfenne in #950 - threading is designed to help in the specific case where there are very large numbers of UMIs present on reads with the same coordinates (e.g. multiplex PCR with UMIs)
• Add optional validation of kept read ratio to CorrectUmis by @mjhipp in #917
• feat: allow TrimFastq to specify a length per input FASTQ by @nh13 in #928
• feat: add an option to store sample base qualities in the QT for FastqToBam by @nh13 in #933
• adds a barcode option to FastqToBam by @bwlang in #936

Bug Fixes

• Ensure FilterSomaticVcf handles PASS variants correctly by @clintval in #909
• Fix complement of W and S iupac codes. by @tfenne in #912
• Fix pass-QC in output FASTQ read names by @nh13 in #923
• bugfix: ZipperBams should consume any remaining mapped reads by @nh13 in #929

Other Changes

• Update ZipperBams to state the sort is checked in the SAM header by @nh13 in #894
• Improve docs for consensus reads being unaligned by @nh13 in #897
• Fix typos in alignment by @nh13 in #914
• Fix Alignment test by @jacarey in #913
• Update intel gkl to 0.8.10 by @nh13 in #918
• Update broad snapshot artifactory url in build.sbt by @mjhipp in #925
• Fix link in DemuxFastqs.scala by @PeteHaitch in #938
• Suggest fqtk in DemuxFastqs by @nh13 in #939
• Fix reference to transient MI tag in DuplexConsensusCaller by @clintval in #946

New Contributors

• @bwlang made their first contribution in #936
• @PeteHaitch made their first contribution in #938

Full Changelog: 2.1.0...2.2.0