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Pull requests: samtools/hts-specs

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Pull requests list

Add a LICENSE.md file for the various CRAM test files.
#768 opened Apr 22, 2024 by jkbonfield • Draft
1
Add SAM recommendation of MAPQ=0 for unmapped reads
sam
#753 opened Jan 29, 2024 by jkbonfield Loading…
1
@jmarshall
3
Recommend 1bp SEQ with QUAL="*" as quality-unavailable.
sam
#752 opened Jan 29, 2024 by jkbonfield Loading…
@jmarshall
1
Adding AEAD support as new encryption method
crypt4gh
#736 opened Jul 22, 2023 by silverdaz Loading…
5
Revert defn of CRAM container size to be sum of block sizes (PR#731)
cram
#731 opened Jun 27, 2023 by jkbonfield Loading…
1
4
Allow for UTF-8 field values in header regular expression
sam
#726 opened May 12, 2023 by jmarshall Loading…
1
@jkbonfield
7
Document the ambiguity of 1-base long seq with QUAL *
sam
#724 opened May 2, 2023 by jkbonfield Loading…
1
@jmarshall
1
Add an MN:i tag (number of SEQ bases at time of modification tag update).
sam sam-tags
#714 opened Mar 29, 2023 by jkbonfield Loading…
1
@jmarshall
8
Fix typos (refget) refget
#700 opened Feb 2, 2023 by jkbonfield Loading…
SAM: add a sentence on case-insensitivity of RG PL (PR #684)
sam
#684 opened Nov 9, 2022 by jkbonfield Loading…
1
@jmarshall
7
Remove "top strand" phrase from MM tag description. sam sam-tags
#668 opened Aug 31, 2022 by jkbonfield Loading…
1
@jmarshall
1
Define optional HTTP 426 response for requests for index files htsget
#665 opened Aug 3, 2022 by jmarshall Loading…
Clarify MI for identifying source molecule strand sam sam-tags
#633 opened Mar 2, 2022 by nh13 Loading…
@jmarshall
15
Clarification of empty vector representation vcf
#617 opened Dec 16, 2021 by pd3 Loading…
@d-cameron
3
Phred scale clarifications sam vcf
#579 opened Jun 16, 2021 by jkbonfield Loading…
1
19
strawman attempt at adding array of booleans vcf
#537 opened Dec 17, 2020 by yfarjoun Loading…
2 tasks
2
document convention for "QC squeezing" in population VCF vcf
#527 opened Sep 7, 2020 by mlin Loading…
1
Cramv4 cram
#502 opened May 28, 2020 by jkbonfield Loading…
2
htsget: add samples query parameter, principally to select subset of VCF columns htsget
#430 opened Jul 10, 2019 by mlin Loading…
5
Sample ID and filter update vcf
#414 opened May 30, 2019 by yfarjoun Loading… VCF v4.4
8
New section describing familial PEDIGREE headers vcf
#413 opened May 29, 2019 by jmarshall Loading…
13
[DRAFT] Cache control for re-using previously-downloaded headers htsget
#325 opened Jul 12, 2018 by jmarshall • Draft
3
Add splitting BAM index to spec sam
#321 opened Jun 5, 2018 by tomwhite Loading…
44
Clarify Number=G tags in INFO as discussed in #272 vcf
#309 opened May 4, 2018 by pd3 Loading…
1
SAM/VCF Strict draft sam vcf
#283 opened Feb 5, 2018 by d-cameron Loading…
72
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