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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

Update SamRecordClipper's functions to "clip past end of mate" to use distances in query bases, not reference bases

Status: Open.

#1090 In fulcrumgenomics/fgbio;

· tfenne opened on Aug 8, 2025

Add page/section to our wiki on how CODEC consensus calling is done, similar to regular and duplex calling

Status: Open.

#1089 In fulcrumgenomics/fgbio;

· tfenne opened on Aug 8, 2025

Strand not taken into account inside GroupReadsByUmi

Status: Open.

#1084 In fulcrumgenomics/fgbio;

· SPPearce opened on Jul 18, 2025

Generate consensus reads without using UMIs

question

Status: Open.

#1077 In fulcrumgenomics/fgbio;

· SPPearce opened on Jun 6, 2025

Many unit tests for AssessPhasing rely on a broken test fixture

bug

help wanted

Status: Open.

#1050 In fulcrumgenomics/fgbio;

· clintval opened on Apr 18, 2025