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parse multiple alleles into distinct Variant records#29

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iskandr merged 1 commit intomasterfrom
parse_multiple_alt_alleles
Mar 4, 2015
Merged

parse multiple alleles into distinct Variant records#29
iskandr merged 1 commit intomasterfrom
parse_multiple_alt_alleles

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@iskandr
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@iskandr iskandr commented Mar 3, 2015

Fixes #22.

Also fixes bug from the last PEP8 PR which removed reverse_complement from string_helpers.

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Comment thread varcode/vcf.py
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I suppose this has always been the case for varcode, but this just made me think about it: we're throwing away the genotype information. Even for a regular non-multiallelic variant, I don't think I have a way to see if it was called a het or hom. Would it make sense to retain that in the variant? Or we could potentially address that in a later PR.

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Yep, currently we're only attaching the INFO dict to variants and not the sample info. What do you think is the right way to handle e.g. genotypes? Should we make a nested sample_name -> key -> value dictionary of dictionaries? That seems messy but I'm not sure what else to do. In any case, that should definitely be a separate PR.

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LGTM

iskandr added a commit that referenced this pull request Mar 4, 2015
parse multiple alleles into distinct Variant records
@iskandr iskandr merged commit c4ba884 into master Mar 4, 2015
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handle multiallelic variants

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