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kevlar-dev / kevlar

Reference-free variant discovery in large eukaryotic genomes
https://kevlar.readthedocs.io
MIT License
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Check size of reference window in simlike #311

Closed standage closed 5 years ago

standage commented 5 years ago

Currently the simlike module checks for short windows spanning the alternate allele, and discards the problematic ones. However, this check isn't performed for the windows spanning the reference allele.

https://github.com/dib-lab/kevlar/blob/76a82fc029b2c271c61593ab4fd7fc58acaf2062/kevlar/simlike.py#L212

The big question is "why is this happening?" but at the very least the code should gracefully handle any windows smaller than k-size.

standage commented 5 years ago

Closed by #313.