Skip to content

Pull requests: samtools/htsjdk

New pull request New
48 Open 1,071 Closed
48 Open 1,071 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
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Pull requests list

Carrot setup
#1721 opened Oct 8, 2024 by lbergelson • Draft
4
Implementation of CRAM 3.1 codecs. cram
#1714 opened Sep 4, 2024 by cmnbroad • Draft
Support reference bundles.
#1713 opened Aug 6, 2024 by cmnbroad Loading…
9
SamUtils PairOrientation is confusingly ambiguous about paired reads needing to map to the same contig
#1709 opened May 15, 2024 by yfarjoun Loading…
5 tasks done
@tfenne
2
Ignore version validation for BCF in VCFHeaderReader because we only need the header
#1707 opened Mar 25, 2024 by lindenb Loading…
5 tasks done
Add FQZComp Codec (Update CRAM Codecs to CRAM 3.1) cram
#1704 opened Feb 7, 2024 by yash-puligundla Loading…
Minor updates to MemoryMappedFileBuffer
#1700 opened Jan 23, 2024 by lbergelson Loading…
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
Add Name Tokenization Codec (Update CRAM Codecs to CRAM 3.1) cram
#1663 opened Mar 21, 2023 by yash-puligundla Loading…
57
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
Add Range codec (Update CRAM Codecs to CRAM 3.1) cram
#1644 opened Jan 10, 2023 by yash-puligundla • Draft
33
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
Add RANS Nx16 codec (Update CRAM Codecs to CRAM 3.1) cram
#1618 opened Aug 26, 2022 by yash-puligundla Loading…
@cmnbroad
210
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
Change queryname sort to match samtools
#1601 opened Mar 30, 2022 by nh13 Loading…
1
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…
ProTip! Updated in the last three days: updated:>2024-11-14.