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VCF search interface implementation (/variants endpoint) #7

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brainstorm opened this issue Apr 9, 2021 · 0 comments · Fixed by #37
Closed

VCF search interface implementation (/variants endpoint) #7

brainstorm opened this issue Apr 9, 2021 · 0 comments · Fixed by #37
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gsoc Possible qualifying task for GSoC

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brainstorm commented Apr 9, 2021

As per the htsget spec implement the variants endpoint:

GET /variants/<id>

This entails understanding the current BAM (/reads) structure and following suit with how the code is currently structured. In particular, your implementation would have to be living in:

 htsget-mvp/htsget-search/src/htsget/bcf.rs

For information on how a bcf file looks inside (most importantly, its uncompressed counterpart, vcf), please refer to the appropriate PDF under hts-specs. That being said, Noodles has a fairly clean and straightforward module that describes that format idiomatically in Rust.

EDIT: Since the bcf crate for Noodles is currently in the works on the bcf branch, it'd be reasonable to implement vcf.gz business logic instead, plus this format is more commonly found in the wild than bcf, actually.

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