3.0.0

What's Changed

The major change in 3.0 comes in an update to our UMI-based consensus callers, and the inclusion of a new consensus caller for CODEC sequencing data (CallCodecConsensusReads). In addition to the new caller, the following updates were made:

• GroupReadsByUmi now correctly segregates read pairs with the same coordinates and UMIs but where R1 and R2 are swapped
• All consensus callers now support a --rejects option to write reads not used in consensus calling to a BAM file
  • Reads in the BAM files are also tagged with the reason they were rejected in the rr tag
• All consensus callers now support a --stats option which will output a text file with a table of statistics generated during consensus calling
• FilterConsensusReads previous --max-no-call-fraction option has been changed to --max-no-calls and is now interpreted as a fraction if less than 1.0, or as a count of no-call bases if greater than or equal to 1.0.

New Features

• Add support for collections in Metric by @nh13 in #1042
• Remove secondary and supplementary support in GroupReadsByUmi by @nh13
• Merging CODEC work into main by @tfenne in #1092
• Add support for fragment reads to TrimPrimers by @nh13 in #1067
• Add min AD and handle haploid calls for DownsampleVcf by @TedBrookings in #1079

Bug Fixes

• DownsampleVcf test was not using an expected variable by @nh13 in #1054
• AnnotateBamWithUmis did not ignore extra FASTQ records by @nh13 in #1055
• Update the CLI docs of CorrectUmis to be more functionally correct by @yfarjoun in #1082
• Remove primary name if also found in alternate names in CollectAlternateContigNames by @tfenne in #1086

Miscellaneous

• Use strict compiler flags and turn on inlining by @clintval in #1047
• Remove unused variable in AssessPhasing by @nh13 in #1052
• Do not recursively store the pr-preview directory in gh-pages by @nh13 in #1059
• Scaladoc errors to re-enable publishing by @nh13 in #1053
• Fixup sponsors formatting in main README by @clintval in #1063
• Test building with known working versions of the JDK by @clintval in #1061
• Update the skip-missing option doc across update tools by @nh13 in #1064
• Docstring for AlignmentScorer.scoreGap by @ameynert in #1071
• Update GroupReadsByUmi.scala by @cehtolonen in #1076
• Publish to maven central by @nh13 in #1083
• Allow fgbio tools to access meta information about themselves. by @nh13 in #427
• Remove most deprecated code by @nh13 in #1070
• Use a Git cliff TOML for releases by @clintval in #1062

New Contributors

• @ameynert made their first contribution in #1071
• @cehtolonen made their first contribution in #1076

Full Changelog: 2.5.21...3.0.0

2.5.21

Changelog

All notable changes to this project will be documented in this file.

[2.5.21] - 2025-04-05

⚙️ Miscellaneous Tasks

• Change version to 2.5.21-SNAPSHOT
• Debug the release artifact upload
• Release 2.5.21

2.5.20

Changelog

All notable changes to this project will be documented in this file.

[2.5.20] - 2025-04-05

⚙️ Miscellaneous Tasks

• Change version to 2.5.19-SNAPSHOT
• Need to download the JAR artifact before release
• Release 2.5.19
• Change version to 2.5.20-SNAPSHOT
• Fix rebase in github actions for gh-pages
• Release 2.5.20

2.5.17

Changelog

All notable changes to this project will be documented in this file.

[2.5.17] - 2025-04-05

🐛 Bug Fixes

• Do not provide bash args in the retry action

⚙️ Miscellaneous Tasks

• Change version to 2.5.16-SNAPSHOT
• Release 2.5.17

2.5.1

What's Changed

• ci: update actions/cache from v2 to v4 by @nh13 in #1039
• feat: FilterBam optionally writes to a rejects file by @nh13 in #1033
• chore: fix url to unit test status badge by @nh13 in #1041
• feat: add checks to ReviewConsensusVariants for FASTA fai/dict by @nh13 in #1036
• feat: improve error message in consensus calling when base qualities are missing by @nh13 in #1040
• feat: SamSource.query should handle out of range queries by @nh13 in #1028
• Added some tests to the longestDinuc to cover more edge cases by @yfarjoun in #1007
• Add an option to sort by sequence role in CollectAlternateContigNames by @nh13 in #868
• Add DownsampleVcf tool by @TedBrookings in #974
• chore: move unit test cache by @nh13 in #1045
• Add metric builder and sorter by @nh13 in #826
• ci: add preview for gh-pages to each PR by @nh13 in #1044
• ci: add sonatype release to GHA by @nh13 in #1046

New Contributors

• @TedBrookings made their first contribution in #974

Full Changelog: 2.5.0...2.5.1

2.5.0

What's Changed

• Migrate ubuntu-latest to ubuntu-24.04 by @nh13 in #1017
• Update codecov GitHub action to 5.1.1 by @nh13 in #1019
• Update best-practice-consensus-pipeline.md by @eltociear in #1018
• Output umi grouping metrics by @znorgaard in #1021
• Add fulcrum genomics more prominently to github by @nh13 in #1023
• Do not trim reads when both ends are clipped in consensus calling by @nh13 in #1026

New Contributors

• @eltociear made their first contribution in #1018

Full Changelog: 2.4.0...2.5.0

2.4.0

What's Changed

• feat: SequenceMetadata can have name and length looked up by key by @nh13 in #1002
• Fix snapshot releases by @nh13 in #1004
• feat: raise exception if CollectDuplexSeqMetrics run on consensus BAM by @znorgaard in #1003
• Ensure --min-reads is a hard filter in CallDuplexConsensusReads by @clintval in #1010

New Contributors

• @znorgaard made their first contribution in #1003

Full Changelog: 2.3.0...2.4.0

Release 2.3.0

What's Changed

• Add a Zenodo DOI to the README by @nh13 in #955
• PileupBuilder should not report insertions when checking the final mapped base before soft-clipping by @jrm5100 in #956
• fix: ensure that the GroupReadsByUmiTests for marking duplicates are by @nh13 in #962
• fix: mapped header records should overwrite unmapped in ZipperBams by @nh13 in #963
• Fix typo in ExtractUmisFromBam.scala by @nh13 in #966
• ZipperBams to produce mate score ("ms") for samtools markdup by @nh13 in #952
• Make PileupBuilder.includeMapPositionsOutsideFrInsert intuitively correct by @clintval in #981
• doc: update description of consenus tags for duplex by @nh13 in #983
• Update UpdateGffContigNames.scala (typo in docs) by @yfarjoun in #985
• Add conda install instructions to README by @clintval in #988
• Add TemplateCoordinate sort order to the usage of SortBam by @nh13 in #993
• Create CODEOWNERS by @nh13 in #999
• feat: add --umi-prefix to CopyUmiFromReadName by @msto in #958
• Validate IO in SortBam to provide nicer exceptions by @nh13 in #994
• Improve the list of tools in the README.md by @nh13 in #991
• doc: fix duplicate "the" in sequence dictionary docstrings by @nh13 in #1000

New Contributors

• @yfarjoun made their first contribution in #985
• @msto made their first contribution in #958

Full Changelog: 2.2.1...2.3.0

Release 2.2.1

What's Changed

• Allow the PairedAssigner to use UMI pairs where one is absent by @clintval in #954

Full Changelog: 2.2.0...2.2.1

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