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Pull requests list

Adding some classes to store chain files.
#505 opened Jul 19, 2019 by nh13 • Draft
@nh13
1
Add support for read groups in EstimatePoolingFractions help wanted
#639 opened Dec 12, 2020 by nh13 • Draft
Remove uses of VariantContextSetBuilder in all unit tests
#819 opened Mar 28, 2022 by kstromhaug • Draft
1
WIP: POC of a tool to re-pick primary alignments.
#1012 opened Sep 23, 2024 by tfenne • Draft
1
Very rough draft of parallelizing Sorter.
#792 opened Feb 27, 2022 by tfenne • Draft
@tfenne
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
Add source classes for BED and generic Interval types
#665 opened Feb 28, 2021 by clintval Loading…
@tfenne
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
feat: FastqToBam can extract UMI(s) from the comment in the read name
#989 opened May 20, 2024 by nh13 Loading…
@nh13
16
Basic implementation of an adapter for locatable.
#569 opened Mar 5, 2020 by tfenne • Draft
@tfenne
7
feat: add a web-page to parse an NCBI assembly report
#1066 opened May 19, 2025 by nh13 • Draft
4 tasks
feat: add optical duplicate tagging to GroupReadsByUmi
#1029 opened Feb 16, 2025 by yfarjoun • Draft
1
@yfarjoun
1
Log the JVM maximum runtime memory at startup
#1105 opened Oct 15, 2025 by nh13 Loading…
5
feat: add a a read name filtering writer to the API
#1037 opened Feb 28, 2025 by nh13 • Draft
@nh13
1
feat: update to scala 2.13.17 and dependencies
#1111 opened Nov 19, 2025 by nh13 • Draft
Adding a tool to left-align indels help wanted
#539 opened Oct 15, 2019 by nh13 Loading…
@clintval
18
Support variable length umis
#563 opened Jan 21, 2020 by nh13 Loading…
@nh13
8
feat: improve vanilla consenus caller determinism
#1119 opened Nov 30, 2025 by nh13 Loading…
@tfenne @clintval
2
feat: use an epsilon (2.2204460492503131E-16) when comparing log like…
#1117 opened Nov 30, 2025 by nh13 Loading…
@tfenne @clintval
2
fix: typos in the consensus caller
#1118 opened Nov 30, 2025 by nh13 Loading…
@tfenne @clintval
2
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