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Pull requests: samtools/htsjdk

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Pull requests list

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
Add Name Tokenization Codec (Update CRAM Codecs to CRAM 3.1)
#1663 opened Mar 21, 2023 by yash-puligundla Loading…
56
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)
#1644 opened Jan 10, 2023 by yash-puligundla • Draft
27
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)
#1618 opened Aug 26, 2022 by yash-puligundla Loading…
@cmnbroad
208
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.
#1596 opened Mar 1, 2022 by cmnbroad • Draft
1
VCFHeader and VCFHeaderLine rewrite/refactoring
#1581 opened Nov 9, 2021 by cmnbroad Loading…
24
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
#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
Allow multiple VCFSimpleHeaderLine of same type
#1531 opened Jan 28, 2021 by mjhipp Loading…
5 tasks done
2
11
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
ProTip! Updated in the last three days: updated:>2023-12-20.