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feat(codec): warn when CallCodecConsensusReads drops a high fraction of pairs as dovetails

Status: Open.

#1181 In fulcrumgenomics/fgbio;

· nh13 opened on Aug 25, 2026

Investigate calling CODEC duplex consensus across the full unclipped overlap (companion to fulcrumgenomics/fgumi#862)

enhancement

Status: Open.

#1180 In fulcrumgenomics/fgbio;

· nh13 opened on Aug 24, 2026

Remove now-redundant CodecConsensusCaller.isPrimaryFrPair; use SamRecord.isFrPair (htsjdk 5.0.0)

Status: Open.

#1178 In fulcrumgenomics/fgbio;

· nh13 opened on Aug 20, 2026

Consensus read formation silently discards minority alignment families

enhancement

Status: Open.

#1177 In fulcrumgenomics/fgbio;

· fitzlane86 opened on Aug 19, 2026

feature request: customizable UMI tag in CopyUmiFromReadName

Status: Open.

#1175 In fulcrumgenomics/fgbio;

· eboyden opened on Aug 18, 2026

Reads dropped by consensus downsampling are counted as used and never reach --rejects

Status: Open.

#1167 In fulcrumgenomics/fgbio;

· nh13 opened on Aug 7, 2026

Supplementary alignment TLEN is copied from the mate primary (htsjdk #1795)

Status: Open.

#1165 In fulcrumgenomics/fgbio;

· nh13 opened on Jul 31, 2026

Comments on using non-default values in --cell-tag and --raw-umi

question

Status: Open.

#1153 In fulcrumgenomics/fgbio;

· lebelm opened on Mar 31, 2026

Variant Calling on Fgbio processed Bam

Status: Open.

#1144 In fulcrumgenomics/fgbio;

· cnithin7 opened on Mar 9, 2026

Consensus calling the UMI-bases uses hardcoded error rates

Status: Open.

#1124 In fulcrumgenomics/fgbio;

· nh13 opened on Dec 15, 2025

Cache the mate cigar the first time it is parsed on SamRecord

Status: Open.

#1115 In fulcrumgenomics/fgbio;

· clintval opened on Nov 25, 2025

Inonsistent base correction using CallOverlappingConsensusBases

Status: Open.

#1095 In fulcrumgenomics/fgbio;

· jackvwbacon opened on Sep 21, 2025