Skip to content

Pull requests: samtools/htsjdk

New pull request New
44 Open 1,090 Closed
44 Open 1,090 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

Fix SamLocusIterator so that read position is not incorrectly offset …
#1758 opened Mar 24, 2026 by tfenne Loading…
7
fix: catch UnsatisfiedLinkError when loading snappy native library
#1753 opened Jan 13, 2026 by nh13 Loading…
support for VCF4.5 just like (vcf4.4) . Changed optimistic_vcf_4_4 to optimistic_vcf_4_x
#1751 opened Dec 18, 2025 by lindenb Loading…
5 tasks done
touching readme to force a test run
#1746 opened May 15, 2025 by lbergelson • Draft
feat: Add sanity check to indexed FASTA file
#1745 opened May 9, 2025 by yfarjoun Loading…
5 tasks
22
Support for GTF files: GtfCodec and GtfWriter
#1744 opened Apr 15, 2025 by lindenb Loading…
5 tasks done
Wire up CRAM 3.1 codecs for writing and a naive write profile. cram
#1739 opened Mar 24, 2025 by cmnbroad Loading…
Ignore version validation for BCF in VCFHeaderReader because we only need the header
#1707 opened Mar 25, 2024 by lindenb Loading…
5 tasks done
Update for to use Java 21
#1698 opened Dec 18, 2023 by lbergelson • Draft
VCF_CSI_index_implementation
#1684 opened Sep 19, 2023 by gokalpcelik Loading…
5 tasks
1
proposal for a package htsjdk.tribble.gtf
#1662 opened Mar 16, 2023 by lindenb Loading…
5 tasks done
Removed 'backed' last cache hit hard references; it seems that that i…
#1645 opened Jan 11, 2023 by vruano Loading…
1 of 3 tasks
1
7
Test case helper and fix EOF detection
#1641 opened Dec 2, 2022 by lbergelson • Draft
1
Make AbstractVCFCodec thread-safe, allowing for multi-threaded VariantContext genotype decoding
#1636 opened Nov 16, 2022 by rcoleb Loading…
3 of 5 tasks
1
3
Refactoring VariantContextComparator
#1629 opened Oct 28, 2022 by lbergelson Loading…
@cmnbroad
4
Require sequence dictionary MD5s when writing CRAM.
#1612 opened Jun 1, 2022 by cmnbroad • Draft
2
9
Add support for re-serializing (sharding and reassembling) CRAM containers.
#1609 opened May 3, 2022 by cmnbroad Loading…
1
8
Implementation of a SAMRecord comparator that matches samtools' queryname sort order.
#1600 opened Mar 30, 2022 by tfenne • Draft
9
VCF 4.3 writing. vcf VCFHeader Refactor Issues fixed by the header/line refactoring branch
#1596 opened Mar 1, 2022 by cmnbroad • Draft
1
VCFHeader and VCFHeaderLine rewrite/refactoring vcf VCFHeader Refactor Issues fixed by the header/line refactoring branch
#1581 opened Nov 9, 2021 by cmnbroad Loading…
100
handle utf-8 encoding
#1569 opened Sep 27, 2021 by yash-puligundla • Draft
10
convert Runtime exceptions in the CRAM code into CRAMExceptions (also…
#1557 opened Jul 25, 2021 by yfarjoun Loading…
new class: VCFReaderFactory a factory for VCFReader
#1551 opened Apr 23, 2021 by lindenb Loading…
4 of 5 tasks
2
WIP BCF 2.2 vcf VCFHeader Refactor Issues fixed by the header/line refactoring branch
#1550 opened Apr 22, 2021 by andersleung • Draft
5 tasks
3
Add VCF 4.3 writing
#1548 opened Apr 15, 2021 by andersleung • Draft
5 tasks done
78
ProTip! Mix and match filters to narrow down what you’re looking for.