hts-specs
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samtools
Specifications of SAM/BAM and related high-throughput sequencing file formats
We may wish to add a mechanism for specifying the requested `format` as a (comma-separated?) list in preference order. E.g., if the client can accept both BAM and CRAM it...
I am currently implementing a stand-alone BCF implementation and am having some trouble with the IDX fields. These are specified quite poorly if I may say so. This is what...
# A suite of @d-cameron's PRs * [x] https://github.com/samtools/hts-specs/pull/465 Improved Structural Variant Support * [x] https://github.com/samtools/hts-specs/pull/468 Allow multiple SVs per record (housekeeping changes to ensure all SV fields allow for...
For reads, htsget historically allows only BAM and CRAM formats to be selected. I think this was originally for MVP purposes, as there was no sensible reason to ask for...
Is there a document or good summary of the different types / conventions for VCF? For example, VCF, sites-only VCF, gVCF, pVCF, spVCF. EG: - A gVCF (Genomic VCF) contains...
When the FILTER column in a VCF ".", is that a PASS variant or not or something else? Motivation: I was using `pysam`'s `VariantRecord` and noticed that when the VCF...
As noted on PR #521, the specification does not fully describe how to use an index to check whether a particular read intersects with a query interval. In particular, >...
Originally reported by @jmarshall [here](https://github.com/samtools/hts-specs/pull/456#pullrequestreview-658934972) --- Two remaining minor issues that we might wish to address as followups (but that should not delay this PR today): * Rob's comment about...
If the htsget response contains a Bearer token for a URL this token may only have a limited validity. In case of the EGA that validity period is one hour....
As briefly discussed in https://github.com/samtools/hts-specs/pull/385, there seems to be a need to specify which VCF fields to include in the htsget spec, since only BAM fields are mentioned under the...
