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Issues list

Run fgio per chromosome question
#1027 opened Feb 7, 2025 by migrau
@nh13
2
DuplexConsensus - TLEN differences and consensus reads question
#1025 opened Feb 4, 2025 by hrizos
3
Soft clip disappeared after CallMolecularConsensusReads
#1016 opened Dec 2, 2024 by jonghwanyoon
1
@tfenne
2
High number of "orphan consensus" question
#1015 opened Nov 22, 2024 by wiedenhoeft
DuplexConsensusReads min-reads and max-reads-per-strand question
#1014 opened Oct 24, 2024 by saty89
GroupReadsByUmi and optical duplicates question
#1013 opened Oct 14, 2024 by miwalter
1
UMI Quality question
#1008 opened Aug 22, 2024 by prot-devin
@cehtolonen
2
Snapshot releases are broken
#1005 opened Jul 31, 2024 by nh13
How to specify read structure with variable UMI length? question
#998 opened Jul 9, 2024 by bounlu
{readname} did not have a primary R1 record. (GroupReadsByUmi) help wanted question
#995 opened Jun 14, 2024 by xiechangxiao
4
FilterConsensusReads results too little reads compared raw fastq OR uBAM file question
#990 opened May 27, 2024 by teryyoung
@cehtolonen
1
ZipperBams failed. Error: processed all unmapped reads but there are mapped reads remaining to be read. question
#978 opened Apr 10, 2024 by teryyoung
3
feature request: add option to FilterBam to write filtered reads to separate file enhancement help wanted
#971 opened Mar 1, 2024 by eboyden
GroupReadsByUmi duplicate marking may fail when secondary and supplementary alignments are included bug
#961 opened Jan 29, 2024 by nh13
1
@tfenne
2
SetMateInformation should add the MQ tag to any supplementary alignments bug
#960 opened Jan 26, 2024 by msto
1
Extend Read Structures operators for reverse-complemented structures enhancement
#949 opened Nov 13, 2023 by galaxy001
Support NCBI sequence_report.jsonl as input for CollectAlternateContigNames enhancement
#945 opened Oct 19, 2023 by ghuls
4
GroupReadsByUmi long runtime question
#944 opened Oct 19, 2023 by ghost
4
SamReader.query() should handle when coordinates are given < 1 or > end of contig bug
#943 opened Oct 18, 2023 by tfenne
Allow Bypass of assertCanWriteFile enhancement
#942 opened Oct 10, 2023 by greenbagels
@cehtolonen
1
Allow multiple trim lengths or read structure in TrimFastq enhancement
#927 opened Aug 14, 2023 by bkohrn
6
Does CallMolecularConsensusReads handle overlapping fragments? question
#926 opened Aug 7, 2023 by kcibul
1
Build for 2.1.0 fails, but bumping GKL fixes it
#921 opened Jul 12, 2023 by brendes
Retaining secondary and supplementary alignments question
#920 opened Jul 7, 2023 by calcasey
2
Exact UMI from read name question
#908 opened Apr 10, 2023 by xianantwist
2
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