Skip to content

Pull requests: fulcrumgenomics/fgbio

New pull request New
Clear current search query, filters, and sorts
29 Open 650 Closed
29 Open 650 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
Assigned to nobody Loading
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Pull requests list

Add support for read groups in EstimatePoolingFractions help wanted
#639 opened Dec 12, 2020 by nh13 • Draft
Very rough draft of parallelizing Sorter.
#792 opened Feb 27, 2022 by tfenne • Draft
@tfenne
feat: add a web-page to parse an NCBI assembly report
#1066 opened May 19, 2025 by nh13 • Draft
4 tasks
feat: update to scala 2.13.17 and dependencies
#1111 opened Nov 19, 2025 by nh13 • Draft
Adding some classes to store chain files.
#505 opened Jul 19, 2019 by nh13 • Draft
@nh13
1
WIP: POC of a tool to re-pick primary alignments.
#1012 opened Sep 23, 2024 by tfenne • Draft
1
Remove uses of VariantContextSetBuilder in all unit tests
#819 opened Mar 28, 2022 by kstromhaug • Draft
1
Remove VariantContexts from most fgbio tools help wanted
#836 opened Apr 29, 2022 by kstromhaug Loading…
1
feat: add a a read name filtering writer to the API
#1037 opened Feb 28, 2025 by nh13 • Draft
@nh13
1
feat: add optical duplicate tagging to GroupReadsByUmi
#1029 opened Feb 16, 2025 by yfarjoun • Draft
1
@yfarjoun
1
feat: use an epsilon (2.2204460492503131E-16) when comparing log like…
#1117 opened Nov 30, 2025 by nh13 Loading…
@tfenne @clintval
2
feat: a default base quality may be provided in consensus callers whe… enhancement
#1032 opened Feb 20, 2025 by nh13 • Draft
1
@nh13
2
Add source classes for BED and generic Interval types
#665 opened Feb 28, 2021 by clintval Loading…
@tfenne
2
fix: typos in the consensus caller
#1118 opened Nov 30, 2025 by nh13 Loading…
@tfenne @clintval
2
feat: improve vanilla consenus caller determinism
#1119 opened Nov 30, 2025 by nh13 Loading…
@tfenne @clintval
2
Remove VariantContexts and other HTSJDK classes from HapCutToVcf and tests help wanted
#832 opened Apr 25, 2022 by kstromhaug Loading…
3
Personal tool for computing genotype call rate with a GQ minimum.
#1107 opened Oct 26, 2025 by tfenne Loading…
@yfarjoun
3
Log the JVM maximum runtime memory at startup
#1105 opened Oct 15, 2025 by nh13 Loading…
5
Command line tool to produce and print pairwise alignments.
#739 opened Nov 11, 2021 by tfenne Loading…
@tfenne
5
fix: the consensus RX (UMI) should be called from filtered records only
#1116 opened Nov 29, 2025 by nh13 Loading…
@tfenne @clintval
6
Basic implementation of an adapter for locatable.
#569 opened Mar 5, 2020 by tfenne • Draft
@tfenne
7
Personal tool to split up large intervals in an interval list.
#1100 opened Sep 29, 2025 by tfenne Loading…
@yfarjoun
7
Support variable length umis
#563 opened Jan 21, 2020 by nh13 Loading…
@nh13
8
feat: add a cached version of Aligner
#1060 opened Apr 25, 2025 by nh13 Loading…
@tfenne
8
Often ignore hard clipping when fetching unclipped ends
#1065 opened May 8, 2025 by clintval Loading…
1
@nh13 @tfenne
14
ProTip! no:milestone will show everything without a milestone.