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Pull requests: fulcrumgenomics/fgbio

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Pull requests list

Log the JVM maximum runtime memory at startup
#1105 opened Oct 15, 2025 by nh13 Loading…
5
Support cell barcodes in ReadStructure JavaScript validator
#1104 opened Oct 3, 2025 by clintval Loading…
@nh13 @tfenne
1
Support cell barcodes in ReadStructure and FastqToBam
#1103 opened Oct 3, 2025 by clintval Loading…
4 tasks
@tfenne
8
Personal tool to split up large intervals in an interval list.
#1100 opened Sep 29, 2025 by tfenne Loading…
@yfarjoun
7
Merge changes for CODEC consensus calling into main
#1088 opened Aug 4, 2025 by tfenne Loading…
1
@tfenne
41
feat: add a web-page to parse an NCBI assembly report
#1066 opened May 19, 2025 by nh13 • Draft
4 tasks
Often ignore hard clipping when fetching unclipped ends
#1065 opened May 8, 2025 by clintval Loading…
1
@nh13 @tfenne
5
feat: add a cached version of Aligner
#1060 opened Apr 25, 2025 by nh13 Loading…
@tfenne
8
feat: add a a read name filtering writer to the API
#1037 opened Feb 28, 2025 by nh13 • Draft
@nh13
1
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: add optical duplicate tagging to GroupReadsByUmi
#1029 opened Feb 16, 2025 by yfarjoun • Draft
1
@yfarjoun
1
WIP: POC of a tool to re-pick primary alignments.
#1012 opened Sep 23, 2024 by tfenne • Draft
1
feat: FastqToBam can extract UMI(s) from the comment in the read name
#989 opened May 20, 2024 by nh13 Loading…
@nh13
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 Loading…
@nh13
42
Very rough draft of parallelizing Sorter.
#792 opened Feb 27, 2022 by tfenne • Draft
@tfenne
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 help wanted
#639 opened Dec 12, 2020 by nh13 • Draft
Basic implementation of an adapter for locatable.
#569 opened Mar 5, 2020 by tfenne • Draft
@tfenne
7
Support variable length umis
#563 opened Jan 21, 2020 by nh13 Loading…
@nh13
8
Adding a tool to left-align indels help wanted
#539 opened Oct 15, 2019 by nh13 Loading…
@clintval
18
Adding some classes to store chain files.
#505 opened Jul 19, 2019 by nh13 • Draft
@nh13
1
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