fulcrumgenomics fgbio issues

fulcrumgenomics / fgbio

Tools for working with genomic and high throughput sequencing data.

http://fulcrumgenomics.github.io/fgbio/

MIT License

308 stars 67 forks source link

issues

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Make ZipperBams hanlde program name collisions

#1006 bwlang opened 2 weeks ago
1
Snapshot releases are broken

#1005 nh13 opened 2 weeks ago
0
Fix snapshot releases

#1004 nh13 closed 2 weeks ago
0
feat: raise exception if CollectDuplexSeqMetrics run on consensus BAM

#1003 znorgaard closed 2 weeks ago
1
feat: SequenceMetadata can have name and length looked up by key

#1002 nh13 closed 1 month ago
1
Compose a `scalafmt` configuration that applies Nils and Tim's preferred conventions

#1001 msto opened 1 month ago
1
doc: fix duplicate "the" in sequence dictionary docstrings

#1000 nh13 closed 1 month ago
1
Create CODEOWNERS

#999 nh13 closed 1 month ago
1
How to specify read structure with variable UMI length?

#998 bounlu opened 1 month ago
0
Update ClipBam.scala

#997 yfarjoun closed 1 month ago
2
Update Bams.scala

#996 yfarjoun closed 1 month ago
4
{readname} did not have a primary R1 record. (GroupReadsByUmi)

#995 xiechangxiao opened 2 months ago
4
Validate IO in SortBam to provide nicer exceptions

#994 nh13 closed 1 month ago
1
Add TemplateCoordinate sort order to the usage of SortBam

#993 nh13 closed 2 months ago
1
Warn or raise an exception when CollectDuplexSeqMetrics is run on a consensus BAM

#992 clintval closed 2 weeks ago
0
Improve the list of tools in the README.md

#991 nh13 closed 1 month ago
1
FilterConsensusReads results too little reads compared raw fastq OR uBAM file

#990 teryyoung opened 2 months ago
0
feat: FastqToBam can extract UMI(s) from the comment in the read name

#989 nh13 opened 3 months ago
1
Add conda install instructions to README

#988 clintval closed 3 months ago
1
Add conda install instructions to homepage

#987 clintval closed 3 months ago
2
The `fgbio` conda package should not require R dependencies

#986 msto closed 3 months ago
2
Update UpdateGffContigNames.scala (typo in docs)

#985 yfarjoun closed 3 months ago
1
Non existent path error when using FastqToBam with links

#984 shashwatsahay closed 3 months ago
1
doc: update description of consenus tags for duplex

#983 nh13 closed 3 months ago
1
Fix codecov not finding the secret token

#982 nh13 closed 3 months ago
0
Make `PileupBuilder.includeMapPositionsOutsideFrInsert` intuitively correct

#981 clintval closed 3 months ago
3
bug: the logic for the PileupBuilder `includeMapPositionsOutsideFrInsert` filter is wrong

#980 jrm5100 closed 3 months ago
6
GroupReadsByUmi groups reads with or without the same end.

#979 jeanquassi closed 3 months ago
2
ZipperBams failed. Error: processed all unmapped reads but there are mapped reads remaining to be read.

#978 teryyoung opened 4 months ago
3
Option to keep MolecularConsensusReads in CallDuplexConsensusReads

#977 karlkashofer closed 4 months ago
3
Add support for multi-allelic variants

#976 jdidion closed 4 months ago
1
Too up-regulated scores after fgbio CallDuplexConsensusReads

#975 VasLem closed 4 months ago
2
Add DownsampleVcf tool

#974 TedBrookings opened 4 months ago
1
CallMolecularConsensus Fails

#973 jmd5596 closed 5 months ago
5
GroupReadsByUmi filtered reads number does not cover all filtered reads?

#972 milnikol opened 5 months ago
1
feature request: add option to FilterBam to write filtered reads to separate file

#971 eboyden opened 5 months ago
0
2 Alignment steps

#970 shashwatsahay closed 5 months ago
1
Samples processed in different lanes

#969 shashwatsahay closed 5 months ago
4
variant calling with paired-end sequencing

#968 emmecola closed 6 months ago
3
heap memory error

#967 subarna-slg closed 6 months ago
1
Fix typo in ExtractUmisFromBam.scala

#966 nh13 closed 6 months ago
1
Missing space in docs

#965 mmterpstra closed 6 months ago
1
GroupReadsByUmi may fail when marking duplicates including secondary/supplementary reads

#964 nh13 opened 6 months ago
1
fix: mapped header records should overwrite unmapped in ZipperBams

#963 nh13 closed 6 months ago
1
fix: ensure that the GroupReadsByUmiTests for marking duplicates are

#962 nh13 closed 6 months ago
1
GroupReadsByUmi duplicate marking may fail when secondary and supplementary alignments are included

#961 nh13 opened 6 months ago
2
SetMateInformation should add the MQ tag to any supplementary alignments

#960 msto opened 6 months ago
1
Documentation for custom SAM tags from CallDuplexConsensusReads

#959 BrettLiddell opened 6 months ago
2
feat: add --umi-prefix to CopyUmiFromReadName

#958 msto closed 1 month ago
1
CopyUmiFromReadName should support reverse-complemented UMIs prefixed by "r"

#957 msto opened 7 months ago
0