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Support VCF lines with positions at 0 #1959

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fnothaft opened this Issue Mar 21, 2018 · 0 comments

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@fnothaft
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fnothaft commented Mar 21, 2018

According to the VCF spec, these are admissible:

2. POS - position: The reference position, with the 1st base having position 1. Positions are sorted numerically,
in increasing order, within each reference sequence CHROM. It is permitted to have multiple records with the
same POS. Telomeres are indicated by using positions 0 or N+1, where N is the length of the corresponding
chromosome or contig. (Integer, Required)

We allow these in our schema and converter, but we create an invalid reference position for them.

@fnothaft fnothaft added the bug label Mar 21, 2018

@fnothaft fnothaft added this to the 0.24.0 milestone Mar 21, 2018

@fnothaft fnothaft self-assigned this Mar 21, 2018

fnothaft added a commit to fnothaft/adam that referenced this issue Mar 22, 2018

heuermh added a commit that referenced this issue Mar 22, 2018

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