1 Pull request merged by 1 person

• doc: add fulcrum genomics more prominently to github

  #1023 merged Jan 30, 2025

1 Pull request opened by 1 person

• feature/cached-aligner bugfix

  #1024 opened Jan 30, 2025

4 Issues closed by 1 person

• Compose a `scalafmt` configuration that applies Nils and Tim's preferred conventions

  #1001 closed Jan 31, 2025

• CopyUmiFromReadName should support reverse-complemented UMIs prefixed by "r"

  #957 closed Jan 31, 2025

• FilterConsensusReads --min-reads=1 1 0 requirement failed: Expected the AB-strand to have depth > 0 for read: BJ22CM006291R:2660272 1/2 1b unmapped read

  #847 closed Jan 31, 2025

• CallMolecularConsensusReads vs. CallOverlappingConsensusBases vs. CallDuplexConsensusReads

  #899 closed Jan 31, 2025

14 Unresolved conversations

Sometimes conversations happen on old items that aren’t yet closed. Here is a list of all the Issues and Pull Requests with unresolved conversations.

• UMI Quality

  #1008 commented on Jan 31, 2025 • 0 new comments

• High number of "orphan consensus"

  #1015 commented on Jan 31, 2025 • 0 new comments

• DuplexConsensusReads min-reads and max-reads-per-strand

  #1014 commented on Jan 31, 2025 • 0 new comments

• IUPAC symbol Y

  #1011 commented on Jan 31, 2025 • 0 new comments

• How to specify read structure with variable UMI length?

  #998 commented on Jan 31, 2025 • 0 new comments

• GroupReadsByUmi and optical duplicates

  #1013 commented on Jan 31, 2025 • 0 new comments

• FilterConsensusReads results too little reads compared raw fastq OR uBAM file

  #990 commented on Jan 31, 2025 • 0 new comments

• GroupReadsByUmi duplicate marking may fail when secondary and supplementary alignments are included

  #961 commented on Jan 31, 2025 • 0 new comments

• SetMateInformation should add the MQ tag to any supplementary alignments

  #960 commented on Jan 31, 2025 • 0 new comments

• Allow Bypass of assertCanWriteFile

  #942 commented on Jan 31, 2025 • 0 new comments

• Extend Read Structures operators for reverse-complemented structures

  #949 commented on Jan 31, 2025 • 0 new comments

• SamReader.query() should handle when coordinates are given < 1 or > end of contig

  #943 commented on Jan 31, 2025 • 0 new comments

• question: need to correct MD/NM/UQ tags multiple times on piped commands or not?

  #877 commented on Jan 31, 2025 • 0 new comments

• Filterconsensusreads before vs after mapping

  #887 commented on Jan 31, 2025 • 0 new comments