fulcrumgenomics/fgbio issues and pull requests

#1008 - UMI Quality

Issue - State: open - Opened by prot-devin 5 months ago

#1007 - Added some tests to the longestDinuc to cover more edge cases

Pull Request - State: open - Opened by yfarjoun 5 months ago - 1 comment

#1006 - Make ZipperBams hanlde program name collisions

Issue - State: open - Opened by bwlang 6 months ago - 1 comment
Labels: enhancement, help wanted

#1005 - Snapshot releases are broken

Issue - State: open - Opened by nh13 6 months ago

#1004 - Fix snapshot releases

Pull Request - State: closed - Opened by nh13 6 months ago

#1003 - feat: raise exception if CollectDuplexSeqMetrics run on consensus BAM

Pull Request - State: closed - Opened by znorgaard 6 months ago - 1 comment

#1002 - feat: SequenceMetadata can have name and length looked up by key

Pull Request - State: closed - Opened by nh13 6 months ago - 1 comment

#1001 - Compose a `scalafmt` configuration that applies Nils and Tim's preferred conventions

Issue - State: open - Opened by msto 6 months ago - 1 comment
Labels: wontfix

#1000 - doc: fix duplicate "the" in sequence dictionary docstrings

Pull Request - State: closed - Opened by nh13 6 months ago - 1 comment

#999 - Create CODEOWNERS

Pull Request - State: closed - Opened by nh13 6 months ago - 1 comment

#998 - How to specify read structure with variable UMI length?

Issue - State: open - Opened by bounlu 6 months ago

#997 - Update ClipBam.scala

Pull Request - State: closed - Opened by yfarjoun 7 months ago - 2 comments

#996 - Update Bams.scala

Pull Request - State: closed - Opened by yfarjoun 7 months ago - 4 comments

#995 - {readname} did not have a primary R1 record. (GroupReadsByUmi)

Issue - State: open - Opened by xiechangxiao 7 months ago - 4 comments
Labels: help wanted, question

#994 - Validate IO in SortBam to provide nicer exceptions

Pull Request - State: closed - Opened by nh13 8 months ago - 1 comment

#993 - Add TemplateCoordinate sort order to the usage of SortBam

Pull Request - State: closed - Opened by nh13 8 months ago - 1 comment

#992 - Warn or raise an exception when CollectDuplexSeqMetrics is run on a consensus BAM

Issue - State: closed - Opened by clintval 8 months ago

#991 - Improve the list of tools in the README.md

Pull Request - State: closed - Opened by nh13 8 months ago - 1 comment

#990 - FilterConsensusReads results too little reads compared raw fastq OR uBAM file

Issue - State: open - Opened by teryyoung 8 months ago

#989 - feat: FastqToBam can extract UMI(s) from the comment in the read name

Pull Request - State: open - Opened by nh13 8 months ago - 1 comment

#988 - Add conda install instructions to README

Pull Request - State: closed - Opened by clintval 8 months ago - 1 comment

#987 - Add conda install instructions to homepage

Pull Request - State: closed - Opened by clintval 8 months ago - 2 comments

#986 - The `fgbio` conda package should not require R dependencies

Issue - State: closed - Opened by msto 8 months ago - 2 comments

#985 - Update UpdateGffContigNames.scala (typo in docs)

Pull Request - State: closed - Opened by yfarjoun 8 months ago - 1 comment

#984 - Non existent path error when using FastqToBam with links

Issue - State: closed - Opened by shashwatsahay 9 months ago - 1 comment

#983 - doc: update description of consenus tags for duplex

Pull Request - State: closed - Opened by nh13 9 months ago - 1 comment

#982 - Fix codecov not finding the secret token

Pull Request - State: closed - Opened by nh13 9 months ago

#981 - Make `PileupBuilder.includeMapPositionsOutsideFrInsert` intuitively correct

Pull Request - State: closed - Opened by clintval 9 months ago - 3 comments

#980 - bug: the logic for the PileupBuilder `includeMapPositionsOutsideFrInsert` filter is wrong

Issue - State: closed - Opened by jrm5100 9 months ago - 6 comments

#979 - GroupReadsByUmi groups reads with or without the same end.

Issue - State: closed - Opened by jeanquassi 9 months ago - 2 comments

#978 - ZipperBams failed. Error: processed all unmapped reads but there are mapped reads remaining to be read.

Issue - State: open - Opened by teryyoung 9 months ago - 3 comments
Labels: question

#977 - Option to keep MolecularConsensusReads in CallDuplexConsensusReads

Issue - State: closed - Opened by karlkashofer 10 months ago - 3 comments

#976 - Add support for multi-allelic variants

Pull Request - State: closed - Opened by jdidion 10 months ago - 1 comment

#975 - Too up-regulated scores after fgbio CallDuplexConsensusReads

Issue - State: closed - Opened by VasLem 10 months ago - 2 comments

#974 - Add DownsampleVcf tool

Pull Request - State: open - Opened by TedBrookings 10 months ago - 1 comment

#973 - CallMolecularConsensus Fails

Issue - State: closed - Opened by jmd5596 10 months ago - 5 comments
Labels: question

#972 - GroupReadsByUmi filtered reads number does not cover all filtered reads?

Issue - State: open - Opened by milnikol 11 months ago - 1 comment
Labels: question

#971 - feature request: add option to FilterBam to write filtered reads to separate file

Issue - State: open - Opened by eboyden 11 months ago
Labels: enhancement, help wanted

#970 - 2 Alignment steps

Issue - State: closed - Opened by shashwatsahay 11 months ago - 1 comment

#969 - Samples processed in different lanes

Issue - State: closed - Opened by shashwatsahay 11 months ago - 4 comments
Labels: question

#968 - variant calling with paired-end sequencing

Issue - State: closed - Opened by emmecola 11 months ago - 3 comments
Labels: question

#967 - heap memory error

Issue - State: closed - Opened by subarna-slg 12 months ago - 1 comment

#966 - Fix typo in ExtractUmisFromBam.scala

Pull Request - State: closed - Opened by nh13 12 months ago - 1 comment

#965 - Missing space in docs

Issue - State: closed - Opened by mmterpstra 12 months ago - 1 comment

#964 - GroupReadsByUmi may fail when marking duplicates including secondary/supplementary reads

Pull Request - State: open - Opened by nh13 12 months ago - 1 comment

#963 - fix: mapped header records should overwrite unmapped in ZipperBams

Pull Request - State: closed - Opened by nh13 12 months ago - 1 comment

#962 - fix: ensure that the GroupReadsByUmiTests for marking duplicates are

Pull Request - State: closed - Opened by nh13 12 months ago - 1 comment

#961 - GroupReadsByUmi duplicate marking may fail when secondary and supplementary alignments are included

Issue - State: open - Opened by nh13 12 months ago - 2 comments

#960 - SetMateInformation should add the MQ tag to any supplementary alignments

Issue - State: open - Opened by msto 12 months ago - 1 comment

#959 - Documentation for custom SAM tags from CallDuplexConsensusReads

Issue - State: open - Opened by BrettLiddell 12 months ago - 2 comments
Labels: question

#958 - feat: add --umi-prefix to CopyUmiFromReadName

Pull Request - State: closed - Opened by msto almost 1 year ago - 1 comment

#957 - CopyUmiFromReadName should support reverse-complemented UMIs prefixed by "r"

Issue - State: open - Opened by msto almost 1 year ago

#956 - PileupBuilder should not report insertions when checking the final mapped base before soft-clipping

Pull Request - State: closed - Opened by jrm5100 about 1 year ago - 1 comment

#955 - Add a Zenodo DOI to the README

Pull Request - State: closed - Opened by nh13 about 1 year ago - 1 comment

#954 - Allow the PairedAssigner to use UMI pairs where one is absent

Pull Request - State: closed - Opened by clintval about 1 year ago - 8 comments

#953 - quality score of masked N bases set to 2

Issue - State: closed - Opened by tobyaicher about 1 year ago - 2 comments

#952 - ZipperBams to produce mate score ("ms") for samtools markdup

Pull Request - State: closed - Opened by nh13 about 1 year ago - 1 comment

#951 - ZipperBams should output the `ms` tag for `samtools markdup`

Issue - State: closed - Opened by nh13 about 1 year ago

#950 - Addition of threading in GroupReadsByUmi and some other performance optimizations.

Pull Request - State: closed - Opened by tfenne about 1 year ago - 1 comment

#949 - Extend Read Structures operators for reverse-complemented structures

Issue - State: open - Opened by galaxy001 about 1 year ago

#948 - Restore consensus calling for pairs with only one mapped read.

Pull Request - State: closed - Opened by tfenne about 1 year ago - 1 comment

#947 - Illegal option: 'ExtractUmisFromBam'

Issue - State: closed - Opened by Neeecolaaaa about 1 year ago - 3 comments

#946 - Fix reference to transient MI tag in DuplexConsensusCaller

Pull Request - State: closed - Opened by clintval about 1 year ago - 2 comments

#945 - Support NCBI sequence_report.jsonl as input for CollectAlternateContigNames

Issue - State: open - Opened by ghuls over 1 year ago - 4 comments
Labels: enhancement

#944 - GroupReadsByUmi long runtime

Issue - State: open - Opened by dps2501 over 1 year ago - 4 comments
Labels: question

#943 - SamReader.query() should handle when coordinates are given < 1 or > end of contig

Issue - State: open - Opened by tfenne over 1 year ago

#942 - Allow Bypass of assertCanWriteFile

Issue - State: open - Opened by greenbagels over 1 year ago

#941 - GroupReadsByUMI sorted input

Issue - State: closed - Opened by FerriolCalvet over 1 year ago - 2 comments
Labels: question

#940 - Alternative PR to add duplicate marking to GroupReadsByUmi

Pull Request - State: closed - Opened by tfenne over 1 year ago - 4 comments

#939 - Suggest fqtk in DemuxFastqs

Pull Request - State: closed - Opened by nh13 over 1 year ago - 1 comment

#938 - Fix link in DemuxFastqs.scala

Pull Request - State: closed - Opened by PeteHaitch over 1 year ago - 3 comments

#937 - Bug Fix - SamRecordClipper.numBasesExtendingPastMate

Pull Request - State: open - Opened by JoeVieira over 1 year ago - 2 comments
Labels: bug, help wanted

#936 - adds a barcode option to FastqToBam

Pull Request - State: closed - Opened by bwlang over 1 year ago - 4 comments

#935 - add --barcode to FastqToBam ?

Issue - State: closed - Opened by bwlang over 1 year ago - 2 comments
Labels: question

#934 - Mark Duplicate Bitflag & include secondary & Supplimentary Reads

Pull Request - State: closed - Opened by JoeVieira over 1 year ago - 3 comments

#933 - feat: add an option to store sample base qualities in the QT for FastqToBam

Pull Request - State: closed - Opened by nh13 over 1 year ago - 1 comment

#932 - New: added Barcode qualities keeping in FastqToBam

Pull Request - State: closed - Opened by galaxy001 over 1 year ago - 6 comments

#931 - Add tag to store barcode quality in sam for FastqToBam

Issue - State: closed - Opened by galaxy001 over 1 year ago - 3 comments
Labels: enhancement, help wanted

#930 - The range of the value in step fgbio FilterConsensusReads

Issue - State: closed - Opened by Xiangnyu over 1 year ago - 3 comments

#929 - bugfix: ZipperBams should consume any remaining mapped reads

Pull Request - State: closed - Opened by nh13 over 1 year ago - 1 comment

#928 - feat: allow TrimFastq to specify a length per input FASTQ

Pull Request - State: closed - Opened by nh13 over 1 year ago
Labels: needs review

#927 - Allow multiple trim lengths or read structure in TrimFastq

Issue - State: open - Opened by bkohrn over 1 year ago - 6 comments
Labels: enhancement

#926 - Does CallMolecularConsensusReads handle overlapping fragments?

Issue - State: open - Opened by kcibul over 1 year ago - 1 comment
Labels: question

#925 - Update broad snapshot artifactory url in build.sbt

Pull Request - State: closed - Opened by mjhipp over 1 year ago

#924 - Broad's Artifactory URL appears to have moved

Issue - State: closed - Opened by brendes over 1 year ago

#923 - Fix pass-QC in output FASTQ read names

Pull Request - State: closed - Opened by nh13 over 1 year ago

#922 - DemuxFastqs --omit-failing-reads opposite expected behavior.

Issue - State: closed - Opened by gouinK over 1 year ago - 3 comments
Labels: bug, help wanted

#921 - Build for 2.1.0 fails, but bumping GKL fixes it

Issue - State: open - Opened by brendes over 1 year ago

#920 - Retaining secondary and supplementary alignments

Issue - State: open - Opened by calcasey over 1 year ago - 2 comments
Labels: question

#919 - families vs groups

Issue - State: closed - Opened by LeilyR over 1 year ago - 1 comment
Labels: question

#918 - Update intel gkl to 0.8.10

Pull Request - State: closed - Opened by nh13 over 1 year ago - 1 comment

#917 - Add optional validation of kept read ratio to CorrectUmis

Pull Request - State: closed - Opened by mjhipp over 1 year ago - 5 comments

#916 - java.lang.OutOfMemoryError on FilterConsensusReads

Issue - State: closed - Opened by LeilyR over 1 year ago - 2 comments
Labels: question

#915 - adding RX tag to bam files, if no fastq available

Issue - State: closed - Opened by LeilyR over 1 year ago - 4 comments
Labels: question

#914 - Fix typos in alignment

Pull Request - State: closed - Opened by nh13 over 1 year ago

#913 - Fix Alignment test

Pull Request - State: closed - Opened by jacarey over 1 year ago - 2 comments

#912 - Fix complement of W and S iupac codes.

Pull Request - State: closed - Opened by tfenne over 1 year ago - 1 comment

#911 - Call consensus reads in a 2*75bp sequencing setting (fwd and reverse do not overlap)

Issue - State: closed - Opened by ktrien over 1 year ago - 3 comments

#910 - Invalid UMI detected in read name with FASTQtoBAM

Issue - State: closed - Opened by sci-kai over 1 year ago - 1 comment

#909 - Ensure FilterSomaticVcf handles PASS variants correctly

Pull Request - State: closed - Opened by clintval almost 2 years ago - 2 comments

GitHub / fulcrumgenomics/fgbio issues and pull requests