Skip to content

Pull requests: AdamaJava/adamajava

New pull request New
Clear current search query, filters, and sorts
2 Open 299 Closed
2 Open 299 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

Upgrade HTSJDK to 5.0.0 in qpicard and related modules, with downstream API compatibility fixes
#406 by Copilot AI was merged May 14, 2026 Loading…
6 tasks done
@holmeso
16
perf(qsignature): updates to the comparison component to speed up the process for multiple inputs
#405 by holmeso Contributor was merged May 12, 2026 Loading…
79
perf(qannotate nanno): better use of threading to speed up nanno
#404 by holmeso Contributor was merged Apr 30, 2026 Loading…
Fix non-deterministic field ordering in AnnotationSourceTSV annotation extraction
#403 by Copilot AI was merged Mar 3, 2026 Loading…
9 of 13 tasks
@holmeso
2
fix(nanno): preserve user-requested field order in AnnotationSourceTSV
#402 by Copilot AI was merged Mar 3, 2026 Loading…
9 of 14 tasks
@holmeso
5
fix(nanno): guard against mismatched array lengths in extractFieldsFromRecord
#401 by Copilot AI was merged Feb 27, 2026 Loading…
7 of 9 tasks
@holmeso
feat(nanno): if snpeff deems a variant to be in multiple genes report them all
#400 by holmeso Contributor was merged Mar 17, 2026 Loading…
11
feat(qannotate): allow the homCutoff option to be used in IndelConfidenceMode
#397 by holmeso Contributor was merged Oct 1, 2025 Loading…
feat(qsignature): add blocklist option that takes a BED file and ignores positions contained therein
#396 by holmeso Contributor was merged Sep 3, 2025 Loading…
1
fix(qsnp): OOM caused by large number of failed filter reads at same location
#395 by holmeso Contributor was merged Aug 5, 2025 Loading…
1 task done
2
Analyze and document qsnp OOM fix for failed filter reads at same genomic location
#394 by Copilot AI was closed Aug 5, 2025 • Draft
@holmeso
style(q3indel): updates suggested and implemented by IDEA
#393 by holmeso Contributor was merged May 26, 2025 Loading…
style(qsignature): updates based on IDEA suggestions
#392 by holmeso Contributor was merged May 26, 2025 Loading…
fix(nanno): default comparator for ChrPosition incorrectly sorting contig names
#391 by holmeso Contributor was merged May 22, 2025 Loading…
1 task done
fix(nanno): deal with contig names that include numbers and letters
#390 by holmeso Contributor was merged May 15, 2025 Loading…
1 task done
3
perf(qbamfilter): minor speedups
#389 by holmeso Contributor was merged Mar 20, 2025 Loading…
6 tasks done
Qsnp track unfiltered cs
#388 by holmeso Contributor was merged Mar 19, 2025 Loading…
8 tasks done
1
fix(qannotate): MIUN was not being applied appropriately to SNPs
#387 by holmeso Contributor was merged Feb 11, 2025 Loading…
8 tasks done
1
Qcoverage fix
#386 by newellf Contributor was merged Nov 29, 2024 Loading…
8 tasks done
1
fix(qsv): fixing issue where references didn't match
#385 by newellf Contributor was merged Nov 26, 2024 Loading…
8 tasks done
1
perf(qpicard - cram): fork htsjdk to include performance enhancements for CRAM file reading
#384 by holmeso Contributor was merged Oct 31, 2024 Loading…
5 tasks done
refactor(qcoverage): minor java21 refactoring based on IDEA suggestions
#383 by newellf Contributor was merged Oct 23, 2024 Loading…
7 tasks done
1
Holmeso patch 1
#382 by holmeso Contributor was merged Oct 17, 2024 Loading…
Update qmotif_1_2.md
#381 by holmeso Contributor was merged Oct 15, 2024 Loading…
Update qmotif_1_2.md
#380 by holmeso Contributor was merged Oct 14, 2024 Loading…
ProTip! Add no:assignee to see everything that’s not assigned.