Bug Fixes

• Template.fixMateInfo() to set primary mate info before supplementary info (#1114) (da4d2966)
• The consensus RX (UMI) should be called from filtered records only (#1116) (cc3b926e)
• Typos in the consensus caller (#1118) (4a8644b5)
• Improve the numeric stability of the consensus caller (#1120) (e2ccac96)
• Preserve input order in filterToMostCommonAlignment (#1119) (d809e1...

Features

• Speedup CorrectUmis and add a new --revcomp option (#1108) (329763d5)
• Support cell barcodes in consensus calling tools (#1110) (7e51969e)
• Support cell barcodes in ReadStructure and FastqToBam (#1103) (d7b0f042)
• Make it so FastqToBam can stream input (#1098) (8f6efe6d9629b680cdbf89992f4c263c930b89ef)
• Add an entrypoint to SamSource for bytes of SAM/BAM/CRAM (#760) (2ef11...

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 coordinat...

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

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