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Pull requests: fulcrumgenomics/fgbio

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Pull requests list

feat!: allow non-terminal + segment in read structures
#1157 opened Apr 23, 2026 by tfenne Member Loading…
6
fix(codec): avoid MatchError on dovetail FR pairs with asymmetric isFrPair bug
#1155 opened Apr 17, 2026 by nh13 Member Loading…
5 tasks done
@tfenne
6
feat: allow variable length UMIs
#1148 opened Mar 24, 2026 by TimD1 Contributor Loading…
23
fix: handle SnappyLoader native library failures gracefully bug
#1128 opened Jan 13, 2026 by nh13 Member Loading…
1
@tfenne
3
fix: remove explicit ref from docs job checkout to support fork PRs
#1126 opened Dec 17, 2025 by nh13 Member Loading…
3
Personal tool for computing genotype call rate with a GQ minimum.
#1107 opened Oct 26, 2025 by tfenne Member Loading…
@yfarjoun
3
Personal tool to split up large intervals in an interval list.
#1100 opened Sep 29, 2025 by tfenne Member Loading…
@yfarjoun
7
feat: add a web-page to parse an NCBI assembly report
#1066 opened May 19, 2025 by nh13 Member • Draft
4 tasks
feat: add a a read name filtering writer to the API
#1037 opened Feb 28, 2025 by nh13 Member • Draft
@nh13
1
feat: a default base quality may be provided in consensus callers whe… enhancement
#1032 opened Feb 20, 2025 by nh13 Member • Draft
1
@nh13
2
feat: add optical duplicate tagging to GroupReadsByUmi
#1029 opened Feb 16, 2025 by yfarjoun Contributor • Draft
1
@yfarjoun
1
WIP: POC of a tool to re-pick primary alignments.
#1012 opened Sep 23, 2024 by tfenne Member • Draft
1
feat: FastqToBam can extract UMI(s) from the comment in the read name
#989 opened May 20, 2024 by nh13 Member Loading…
@nh13 @clintval
16
Remove VariantContexts from most fgbio tools help wanted
#836 opened Apr 29, 2022 by kstromhaug Loading…
1
Remove VariantContexts and other HTSJDK classes from HapCutToVcf and tests help wanted
#832 opened Apr 25, 2022 by kstromhaug Loading…
3
Remove uses of VariantContextSetBuilder in all unit tests
#819 opened Mar 28, 2022 by kstromhaug • Draft
1
Add scala implementations for some SamRecord methods
#809 opened Mar 10, 2022 by nh13 Member Loading…
@tfenne
47
Very rough draft of parallelizing Sorter.
#792 opened Feb 27, 2022 by tfenne Member • Draft
@tfenne
Command line tool to produce and print pairwise alignments.
#739 opened Nov 11, 2021 by tfenne Member Loading…
@tfenne
6
Add source classes for BED and generic Interval types
#665 opened Feb 28, 2021 by clintval Member Loading…
@tfenne
2
Basic implementation of an adapter for locatable.
#569 opened Mar 5, 2020 by tfenne Member • Draft
@tfenne
7
Adding a tool to left-align indels help wanted
#539 opened Oct 15, 2019 by nh13 Member Loading…
@clintval
18
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