hts-specs
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samtools
Specifications of SAM/BAM and related high-throughput sequencing file formats
Currently there is the nice @hts-specs-bot that uploads pdf samples from PRs but the artifacts appear to 404 and then it is hard to review (trying to follow MM/MP/ML thread...
Originally raised by @julesjacobsen as part of [discussions](https://github.com/samtools/hts-specs/pull/465/files#r370675441) in #465 --- Has there been any further discussion about this? I'd like to propose a slight shift in the way things...
These fields use a lot of common semantics and variation types, which should be unified specification-wide as much as possible. See also #469.
Raised as [part of discussions](https://github.com/samtools/hts-specs/pull/465/files#r371978302) in #465 @cwhelan > Is `` a valid first-level symbolic alt (which I think this language implies) according to this PR, or do breakend alts...
Comments extracted from discussions ([1](https://github.com/samtools/hts-specs/pull/465/files#r370681229), [2](https://github.com/samtools/hts-specs/pull/465/files#r370650146)) in #465 @cwhelan > I might add that there's also the option to use `` for a duplication if you know it exists but...
As discussed during GA4GH Connect 2021 calls: @d-cameron > Just checked VCFv4.3: MD5 isn't even formally defined as a ##contig header field. We should add both ga4gh & md5 into...
E.g. page 16 in https://samtools.github.io/hts-specs/VCFv4.3.pdf, as this significantly impairs readability. As one option, just extract all examples into a separate document to avoid cluttering the specification.
Created from @cwhelan comments on https://github.com/samtools/hts-specs/pull/465 --- I think that this section could use a little clarification or a preamble stating what the valid use cases for using symbolic alleles...
In implementing VCF 4.3 writing support for htsjdk, I came across some areas where I feel the spec is ambiguous as to whether percent encoding and decoding should be supported....
Currently the htsget protocol allows reads to be returned by ID, with field values optionally included in the output. It would be helpful if the reads could also be filtered...
