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Assign SNPs on chromosome 0 #13

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apriha opened this issue Jun 14, 2019 · 2 comments
Open

Assign SNPs on chromosome 0 #13

apriha opened this issue Jun 14, 2019 · 2 comments
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enhancement New feature or request

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@apriha
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apriha commented Jun 14, 2019

Some newer Family Tree DNA famfinder files seem to have SNPs assigned to chromosome 0. Similar to SNPs._assign_par_snps, use the RefSNP API to assign each of these SNPs to a chromosome and update the SNP's position to be consistent with the assembly.
apriha added a commit that referenced this issue Nov 2, 2019
@apriha
Don't drop chromosome 0 SNPs; see #13
97940b4
@apriha apriha mentioned this issue Nov 28, 2019
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@willgdjones
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I have noticed that for AncestryDNA files, the _assign_par_snps step can take a substantial amount of time (> 1 minute), because of repeated API requests. I have currently bypassed this issue by setting assign_par_snps=False. Is there a way we can speed this up with the VCF_endpoint like you suggest in #19.

@apriha
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apriha commented Dec 1, 2019

Yeah, I agree that having a resource like discussed in #19 to lookup SNPs would help here as well and would reduce repeated API calls. I'll start looking into this as part of #42.

@apriha apriha added the enhancement New feature or request label Dec 20, 2019
willgdjones pushed a commit that referenced this issue Jul 18, 2020
@afaulconbridge
Merge pull request #13 from sanogenetics/feature/circleci-for-sano
7b14db5 
Support both CircleCI and Travis CI
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@willgdjones @apriha