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 https://github.com/fulcrumgenomics/fgbio/pull/1042
• Remove secondary and supplementary support in GroupReadsByUmi by @nh13
• Merging CODEC work into main by @tfenne in https://github.com/fulcrumgenomics/fgbio/pull/1092
• Add support for fragment reads to TrimPrimers by @nh13 in https://github.com/fulcrumgenomics/fgbio/pull/1067
• Add min AD and handle haploid calls for DownsampleVcf by @TedBrookings in https://github.com/fulcrumgenomics/fgbio/pull/1079

Bug Fixes

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

Miscellaneous

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

New Contributors

• @ameynert made their first contribution in https://github.com/fulcrumgenomics/fgbio/pull/1071
• @cehtolonen made their first contribution in https://github.com/fulcrumgenomics/fgbio/pull/1076

Full Changelog: https://github.com/fulcrumgenomics/fgbio/compare/2.5.21...3.0.0