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Loader does not support single number AD fields #6

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naegelyd opened this issue Aug 13, 2014 · 0 comments
Open

Loader does not support single number AD fields #6

naegelyd opened this issue Aug 13, 2014 · 0 comments

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@naegelyd
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We assume that the AD info field will be a variable length number of values as can be seen here where we check the length and truthiness of AD. Unfortunately, if someone tried to load a VCF with this format:

##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">

the loader will crash because ad will be an integer and len(ad) will throw an error. We need to handle the case where ad is just a single number and cannot always assume that people are loading VCFs with this format for AD:

##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">

Originally reported as chop-dbhi/varify#310

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