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98 Open 316 Closed
98 Open 316 Closed
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Issues list

Soft clip disappeared after CallMolecularConsensusReads
#1016 opened Dec 2, 2024 by jonghwanyoon
High number of "orphan consensus"
#1015 opened Nov 22, 2024 by wiedenhoeft
DuplexConsensusReads min-reads and max-reads-per-strand
#1014 opened Oct 24, 2024 by saty89
GroupReadsByUmi and optical duplicates
#1013 opened Oct 14, 2024 by miwalter
1
IUPAC symbol Y
#1011 opened Sep 18, 2024 by Liukvr
UMI Quality
#1008 opened Aug 22, 2024 by prot-devin
Make ZipperBams hanlde program name collisions enhancement help wanted
#1006 opened Jul 31, 2024 by bwlang
1
Snapshot releases are broken
#1005 opened Jul 31, 2024 by nh13
Compose a scalafmt configuration that applies Nils and Tim's preferred conventions wontfix
#1001 opened Jul 15, 2024 by msto
@nh13 @tfenne
1
How to specify read structure with variable UMI length?
#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
#990 opened May 27, 2024 by teryyoung
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
GroupReadsByUmi filtered reads number does not cover all filtered reads? question
#972 opened Mar 8, 2024 by milnikol
1
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
#961 opened Jan 29, 2024 by nh13
2
SetMateInformation should add the MQ tag to any supplementary alignments
#960 opened Jan 26, 2024 by msto
1
Documentation for custom SAM tags from CallDuplexConsensusReads question
#959 opened Jan 24, 2024 by BrettLiddell
2
CopyUmiFromReadName should support reverse-complemented UMIs prefixed by "r"
#957 opened Jan 19, 2024 by msto
Extend Read Structures operators for reverse-complemented structures
#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
#943 opened Oct 18, 2023 by tfenne
Allow Bypass of assertCanWriteFile
#942 opened Oct 10, 2023 by greenbagels
Allow multiple trim lengths or read structure in TrimFastq enhancement
#927 opened Aug 14, 2023 by bkohrn
6
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