samtools hts-specs issues

samtools / hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

http://samtools.github.io/hts-specs/

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issues

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fix discrepancy of empty bed files

#775 kloetzl opened 5 days ago
5
VCF format: correct representation of complex indels and MNPs

#774 marc-sturm closed 5 days ago
5
Add ID subfield to VCF v4.3 test file's structured header

#773 jmarshall opened 2 weeks ago
0
vcf: Invalid unstructured header line in VCF 4.3 example `complexfile_passed_000.vcf`

#772 zaeleus opened 1 month ago
2
refget: v2 spec for Range header errors does not align with typical usage

#771 davidlougheed opened 1 month ago
0
VCFv4.5 RC2

#770 d-cameron closed 3 weeks ago
4
VCF4.4 SVLEN requirement across different variant representations

#769 tcezard opened 2 months ago
1
Add a LICENSE.md file for the various test files.

#768 jkbonfield opened 2 months ago
1
VCF Draft 4.5 and Modified Bases

#767 cjw85 opened 2 months ago
29
Questions about third-party use of test data

#766 athos opened 2 months ago
6
CSI file is BGZF compressed but this is not mentioned in the CSV1 spec

#765 bguo068 opened 2 months ago
2
Fix a typo, it should be CN, not CICN

#763 pd3 closed 2 months ago
0
bcf: First phasing indicators not set in genotype (GT) value examples

#762 zaeleus closed 2 months ago
0
Fix minor typos in the CRAM tag type lists (PR #761)

#761 jkbonfield closed 3 months ago
1
vcf: Handling structured header records with missing IDs in VCF 4.1/4.2

#760 zaeleus closed 3 weeks ago
1
SA tag CIGAR format

#759 jo-mc closed 3 months ago
0
VCF 4.5 Future of VCF scaling improvements

#758 d-cameron closed 2 months ago
29
cram: Inconsistent descriptions of auxiliary tag types

#757 athos closed 3 months ago
1
Is there a semantic difference between GT=./. and GT=0/0 + GQ=0 ?

#756 yfarjoun closed 3 weeks ago
15
How to retrieve the primary alignment for secondary and supplementary reads

#755 nh13 opened 5 months ago
8
Document CRAM FP is delta-encoded

#754 jkbonfield closed 4 months ago
3
Add SAM recommendation of MAPQ=0 for unmapped reads

#753 jkbonfield opened 5 months ago
6
Recommend 1bp SEQ with QUAL="*" as quality-unavailable.

#752 jkbonfield opened 5 months ago
1
Trivial removal of duplicate tag in SAM test data

#751 jkbonfield closed 4 months ago
0
SVCLAIM: VCF4.4 and backward compatibility with VCF4.3

#750 tcezard closed 5 months ago
1
cram: interpretation of "unmapped" flag in a pseudocode seems incorrect

#749 athos opened 5 months ago
1
is `*` better than `\*`?

#748 zhitian-wu closed 7 months ago
1
CRAM: Need to improve feature positions description

#747 daviesrob closed 4 months ago
1
FAIRsharing Record Query - BED format

#746 allysonlister opened 7 months ago
0
Local Alleles (PR #434) applied to VCFv4.4

#745 jmarshall closed 6 months ago
4
test/vcf: Duplicate contig header record ID

#744 zaeleus closed 2 months ago
0
Add CIGAR =/X entry to version history appendix

#743 jmarshall closed 7 months ago
3
test/sam: Duplicate aux field tags

#742 zaeleus closed 4 months ago
0
Modified base single letter codes update

#741 marcus1487 closed 4 months ago
7
CRAM 3.1 test data

#740 jkbonfield closed 3 months ago
0
primary, secondary, and supplementary alignments with optional MM tags

#739 RichardCorbett closed 9 months ago
5
VCF: "Genotype fields" vs "FORMAT" and per-sample

#738 jkbonfield closed 2 months ago
1
What does `.` mean for an `A`, `R`, or `G` indexed field?

#737 danking opened 11 months ago
6
Adding AEAD support as new encryption method

#736 silverdaz opened 11 months ago
5
Consider 64-bit values in BCF, BAM and CRAM

#735 jkbonfield opened 11 months ago
2
register bgzip in IANA media types?

#734 vidboda closed 10 months ago
5
Circular chromosomes in the VCF header

#733 nh13 opened 12 months ago
1
sam-tags: `MM` field value pattern does not allow ambiguity codes

#732 zaeleus opened 1 year ago
3
Revert defn of CRAM container size to be sum of block sizes (PR#731)

#731 jkbonfield opened 1 year ago
4
VCF test case filenames should be more meaningful

#730 d-cameron opened 1 year ago
1
Resolve #707: remove remaining *ADJ references

#729 d-cameron closed 10 months ago
2
Can ML Tags be zero length arrays?

#728 gileshall closed 11 months ago
5
sam: Consider recommending using 0 for mapping quality when record is unmapped

#727 zaeleus opened 1 year ago
3
Allow for UTF-8 field values in header regular expression

#726 jmarshall opened 1 year ago
7
sam: Consider more conventional format versioning

#725 zaeleus opened 1 year ago
6