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Pull requests: samtools/htsjdk

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Pull requests list

support for VCF4.5 just like (vcf4.4) . Changed optimistic_vcf_4_4 to optimistic_vcf_4_x feature vcf
#1751 opened Dec 18, 2025 by lindenb Contributor Loading…
5 tasks done
Support for GTF files: GtfCodec and GtfWriter feature tribble
#1744 opened Apr 15, 2025 by lindenb Contributor Loading…
5 tasks done
2
Ignore version validation for BCF in VCFHeaderReader because we only need the header bcf feature
#1707 opened Mar 25, 2024 by lindenb Contributor Loading…
5 tasks done
VCF_CSI_index_implementation feature vcf
#1684 opened Sep 19, 2023 by gokalpcelik Loading…
5 tasks
1
Removed 'backed' last cache hit hard references; it seems that that i… bug cram
#1645 opened Jan 11, 2023 by vruano Contributor Loading…
1 of 3 tasks
1
7
Test case helper and fix EOF detection bug
#1641 opened Dec 2, 2022 by lbergelson Member • Draft
1
Make AbstractVCFCodec thread-safe, allowing for multi-threaded VariantContext genotype decoding bug vcf
#1636 opened Nov 16, 2022 by rcoleb Loading…
3 of 5 tasks
1
3
Refactoring VariantContextComparator chore vcf
#1629 opened Oct 28, 2022 by lbergelson Member Loading…
@cmnbroad
4
Require sequence dictionary MD5s when writing CRAM. cram feature
#1612 opened Jun 1, 2022 by cmnbroad Contributor • Draft
2
9
Add support for re-serializing (sharding and reassembling) CRAM containers. cram feature
#1609 opened May 3, 2022 by cmnbroad Contributor Loading…
1
8
VCF 4.3 writing. feature vcf
#1596 opened Mar 1, 2022 by cmnbroad Contributor • Draft
1
VCFHeader and VCFHeaderLine rewrite/refactoring feature vcf
#1581 opened Nov 9, 2021 by cmnbroad Contributor Loading…
100
handle utf-8 encoding bug sam
#1569 opened Sep 27, 2021 by yash-puligundla Contributor • Draft
10
WIP BCF 2.2 bcf feature vcf
#1550 opened Apr 22, 2021 by andersleung Contributor • Draft
5 tasks
3
Correct NM tag calculation bam bug cram sam
#1536 opened Feb 8, 2021 by michaelgatzen Contributor Loading…
1
6
Introduce local disk cache for references cram feature
#1523 opened Dec 21, 2020 by jkaczynski1 Loading…
4 of 5 tasks
18
Some improvements on CigarOperator enum. bam chore cram sam
#1448 opened Jan 1, 2020 by vruano Contributor Loading…
5 tasks
@lbergelson
22
Proposal: handling UCSC 2bit sequences as ReferenceFile feature Waiting for revisions This PR has received comments from reviewers and is waiting for the Author to respond
#1417 opened Aug 31, 2019 by lindenb Contributor Loading…
7
Allow partially spanned alleles. bcf feature vcf Waiting for revisions This PR has received comments from reviewers and is waiting for the Author to respond
#1413 opened Aug 26, 2019 by tfenne Member Loading…
@tfenne
12
Add support for the TP (topology) tag in the sequence dictionary bam cram feature sam Waiting for revisions This PR has received comments from reviewers and is waiting for the Author to respond
#1363 opened May 2, 2019 by nh13 Member Loading…
@nh13
19
Adding tests revealing 0-length interval nonsense chore
#1320 opened Mar 8, 2019 by lbergelson Member • Draft
4
Async BAM performance improvements bam feature Waiting for revisions This PR has received comments from reviewers and is waiting for the Author to respond
#1249 opened Jan 2, 2019 by d-cameron Contributor Loading…
@lbergelson
58
Disallow tabix indices for non-BGZIP inputs bug tribble Waiting for revisions This PR has received comments from reviewers and is waiting for the Author to respond
#1101 opened Mar 20, 2018 by lbergelson Member Loading…
@lbergelson
12
Tribble writing support feature tribble
#822 opened Mar 10, 2017 by magicDGS Member Loading…
4 of 5 tasks
@jonn-smith
26
Added validation warning if the mapped length of the read is greater than the predicted insert size for FR pairs on the same chromosome. bam cram feature sam Waiting for Review This PR is waiting for a reviewer to respond
#816 opened Mar 3, 2017 by tfenne Member Loading…
3 of 5 tasks
@tfenne @yfarjoun
18
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