Comments (2)
jkbonfield
commented on June 26, 2024
1
While I agree adding this would be beneficial, it's the least problematic bit about the spec!
It certainly would be good if the original authors could add more about it. One thing that confused me lots is the "Auxiliary data", which changes format depending on the thing being indexed. (IIRC it's tabix data for VCF and some BAI-related format for BCF). I assume it's meant to be generic, but it also makes it largely unparseable without custom knowledge.
Ping @lh3 @pd3: is there any more information on CSI somewhere else? It looks like it arrived with this commit and subsequent commits. This appears to be where the original minimal spec documentation came from too.
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zaeleus
commented on June 26, 2024
1
See also #70, a long-standing issue noting this:
It is clear from examination of .csi files that they are stored as BGZF (why?), although this is not mentioned and is at odds with the current behaviour of BAI.
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Related Issues (20)
- VCF: "Genotype fields" vs "FORMAT" and per-sample HOT 1
- primary, secondary, and supplementary alignments with optional MM tags HOT 5
- Modified base single letter codes update HOT 7
- test/sam: Duplicate aux field tags
- test/vcf: Duplicate contig header record ID
- FAIRsharing Record Query - BED format
- CRAM: Need to improve feature positions description HOT 1
- is `*` better than `\*`? HOT 1
- cram: interpretation of "unmapped" flag in a pseudocode seems incorrect HOT 1
- SVCLAIM: VCF4.4 and backward compatibility with VCF4.3 HOT 1
- How to retrieve the primary alignment for secondary and supplementary reads HOT 8
- Is there a semantic difference between GT=./. and GT=0/0 + GQ=0 ? HOT 15
- cram: Inconsistent descriptions of auxiliary tag types HOT 1
- SA tag CIGAR format
- vcf: Handling structured header records with missing IDs in VCF 4.1/4.2 HOT 1
- bcf: First phasing indicators not set in genotype (GT) value examples
- Questions about third-party use of test data HOT 6
- VCF Draft 4.5 and Modified Bases HOT 27
- VCF4.4 SVLEN requirement across different variant representations HOT 1
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