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Pull requests: samtools/htsjdk

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Pull requests list

A few targeted optimizations to the BAM decoding path that yield 6-7% improvement in performance
#1764 opened Mar 31, 2026 by tfenne Loading…
1
Full CRAM 3.1 support & performance tuning of CRAM read/write cram Large 🐋
#1763 opened Mar 30, 2026 by tfenne • Draft
4 of 5 tasks
@tfenne
3
Changed SAMRecord.toString() to emit the SAM format string with all fields
#1762 opened Mar 30, 2026 by tfenne Loading…
3 of 5 tasks
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…
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