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Pull requests: samtools/htsjdk

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Pull requests list

Wire up CRAM 3.1 codecs for writing and a trivial write profile. cram
#1739 opened Mar 24, 2025 by cmnbroad Loading…
Wire up CRAM 3.1 codecs for reading. cram
#1736 opened Jan 22, 2025 by cmnbroad Loading…
Support reference bundles.
#1713 opened Aug 6, 2024 by cmnbroad Loading…
9
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
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…
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
Correct NM tag calculation
#1536 opened Feb 8, 2021 by michaelgatzen Loading…
1
6
convert Runtime exceptions in the CRAM code into CRAMExceptions (also…
#1526 opened Dec 23, 2020 by yfarjoun Loading…
5 tasks
4
Introduce local disk cache for references
#1523 opened Dec 21, 2020 by jkaczynski1 Loading…
4 of 5 tasks
17
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