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Mechanism for requesting reads from more than one ID at once #594

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jmarshall opened this issue Sep 1, 2021 · 2 comments
Open

Mechanism for requesting reads from more than one ID at once #594

jmarshall opened this issue Sep 1, 2021 · 2 comments
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htsget

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@jmarshall
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We may wish to add a mechanism to request reads from more than one ID at a time (e.g. for a trio). (Compare PR #430 which proposes a ?samples=S1,S2 query parameter for selecting within a multi-sample VCF file.)

[This issue was previously listed as a “possible future enhancement” within the htsget specification text itself.]
jmarshall added a commit that referenced this issue Sep 1, 2021
@jmarshall
Move enhancement suggestions to GitHub issues
df96264 
Remove enhancement and suggestion sections as they have been created
as issues on the hts-specs repository instead:

- #594 Request reads from more than one ID at a time
- #595 Allow clients to provide a suggested data block size to the server
- #596 Add a way to request reads in GA4GH binary format
- #597 `format` should probably be specified as a (comma separated?) list
@lbergelson
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A solution for something like this really has to nail down how the headers / sequence dictionary compatibility works. There are a lot of subtle chaotic things that can happen if it doesn't.

@jmarshall
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The direct analogue to the VCF ?samples=S1,S2 proposal would be the same query parameter selecting a subset of @RG read groups from within a file, in which case the reference sequence compatibility is assured.

[Anyway, in case it is not clear, this issue is a record of an old potential enhancement suggestion, not a new serious proposal for anything!]

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@jmarshall @lbergelson