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Pull requests: fulcrumgenomics/fgbio

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Pull requests list

Feature/validate and parse vcf
#636 opened Dec 8, 2020 by nh13 • Draft
Add support for read groups in EstimatePoolingFractions
#639 opened Dec 12, 2020 by nh13 • Draft
ErrorRateByReadPosition can ignore intervals
#783 opened Feb 21, 2022 by nh13 • Draft
Very rough draft of parallelizing Sorter.
#792 opened Feb 27, 2022 by tfenne • Draft
Yf coverage unifier
#891 opened Dec 11, 2022 by yfarjoun Loading…
Adding some classes to store chain files.
#505 opened Jul 19, 2019 by nh13 • Draft
1
Adding a tool to validate VCFs
#610 opened Aug 24, 2020 by nh13 • Draft
5
[feature] Add a tool to get percentage of bases falling in each interval by name.
#627 opened Sep 2, 2020 by jacarey • Draft
34
Add caching to DemuxFastqs
#764 opened Jan 27, 2022 by nh13 • Draft
2
Add a github action for generating tool and metrics docs
#811 opened Mar 10, 2022 by nh13 • Draft
1
Remove uses of VariantContextSetBuilder in all unit tests
#819 opened Mar 28, 2022 by kstromhaug • Draft
1
Remove VariantContexts and other HTSJDK classes from HapCutToVcf and tests
#832 opened Apr 25, 2022 by kstromhaug Loading…
3
Remove VariantContexts from most fgbio tools
#836 opened Apr 29, 2022 by kstromhaug Loading…
1
[feat] Add an option to sort by sequence role in CollectAlternateContigNames needs review
#868 opened Jul 31, 2022 by nh13 Loading…
1
Add an option to skip the mate cigar in EstimateRnaSeqInsertSize needs review
#871 opened Aug 16, 2022 by nh13 Loading…
4
GroupReadsByUmi may fail when marking duplicates including secondary/supplementary reads
#964 opened Jan 30, 2024 by nh13 • Draft
20
Add DownsampleVcf tool
#974 opened Mar 29, 2024 by TedBrookings Loading…
28
feat: FastqToBam can extract UMI(s) from the comment in the read name
#989 opened May 20, 2024 by nh13 Loading…
8
Added some tests to the longestDinuc to cover more edge cases
#1007 opened Aug 21, 2024 by yfarjoun Loading…
2
WIP: POC of a tool to re-pick primary alignments.
#1012 opened Sep 23, 2024 by tfenne • Draft
1
Adding in options to DemuxFastqs for asynchronous reading and writing
#345 opened Dec 23, 2017 by nh13 Loading…
@sstadick
27
Allow fgbio tools to access meta information about themselves.
#427 opened Aug 20, 2018 by nh13 Loading…
@tfenne
11
Adding a tool to left-align indels help wanted
#539 opened Oct 15, 2019 by nh13 Loading…
@tfenne
10
Support variable length umis
#563 opened Jan 21, 2020 by nh13 Loading…
@tfenne
8
Basic implementation of an adapter for locatable.
#569 opened Mar 5, 2020 by tfenne • Draft
7
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