Skip to content

Pull requests: fulcrumgenomics/fgbio

New pull request New
34 Open 567 Closed
34 Open 567 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Reviews
Filter by reviews
No reviews Review required Approved review Changes requested
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Pull requests list

WIP: POC of a tool to re-pick primary alignments.
#1012 opened Sep 23, 2024 by tfenne • Draft
1
Added some tests to the longestDinuc to cover more edge cases
#1007 opened Aug 21, 2024 by yfarjoun Loading…
2
feat: FastqToBam can extract UMI(s) from the comment in the read name
#989 opened May 20, 2024 by nh13 Loading…
8
Add DownsampleVcf tool
#974 opened Mar 29, 2024 by TedBrookings Loading…
28
GroupReadsByUmi may fail when marking duplicates including secondary/supplementary reads
#964 opened Jan 30, 2024 by nh13 • Draft
20
Bug Fix - SamRecordClipper.numBasesExtendingPastMate bug help wanted
#937 opened Sep 20, 2023 by JoeVieira Loading…
2
Add option to maintain N in umi needs review
#907 opened Apr 7, 2023 by JoeVieira Loading…
12
Yf coverage unifier
#891 opened Dec 11, 2022 by yfarjoun Loading…
Add an option to skip the mate cigar in EstimateRnaSeqInsertSize needs review
#871 opened Aug 16, 2022 by nh13 Loading…
4
[feat] Add an option to sort by sequence role in CollectAlternateContigNames needs review
#868 opened Jul 31, 2022 by nh13 Loading…
1
Expose chunkSize parameter in CallDuplexConsensusReads
#867 opened Jul 30, 2022 by mjhipp Loading…
@tfenne
22
Remove VariantContexts from most fgbio tools
#836 opened Apr 29, 2022 by kstromhaug Loading…
1
Remove VariantContexts and other HTSJDK classes from HapCutToVcf and tests
#832 opened Apr 25, 2022 by kstromhaug Loading…
3
Add metric builder and sorter
#826 opened Apr 20, 2022 by nh13 Loading…
@tfenne
9
Remove uses of VariantContextSetBuilder in all unit tests
#819 opened Mar 28, 2022 by kstromhaug • Draft
1
Add a github action for generating tool and metrics docs
#811 opened Mar 10, 2022 by nh13 • Draft
1
Add scala implementations for some SamRecord methods
#809 opened Mar 10, 2022 by nh13 Loading…
33
Very rough draft of parallelizing Sorter.
#792 opened Feb 27, 2022 by tfenne • Draft
ErrorRateByReadPosition can ignore intervals
#783 opened Feb 21, 2022 by nh13 • Draft
Add caching to DemuxFastqs
#764 opened Jan 27, 2022 by nh13 • Draft
2
Add an entrypoint to SamSource for bytes of SAM/BAM/CRAM
#760 opened Jan 13, 2022 by clintval Loading…
@nh13
6
Command line tool to produce and print pairwise alignments.
#739 opened Nov 11, 2021 by tfenne Loading…
@tfenne
5
Add source classes for BED and generic Interval types
#665 opened Feb 28, 2021 by clintval Loading…
@tfenne
2
Add support for read groups in EstimatePoolingFractions
#639 opened Dec 12, 2020 by nh13 • Draft
Feature/validate and parse vcf
#636 opened Dec 8, 2020 by nh13 • Draft
ProTip! Adding no:label will show everything without a label.