evogytis / fluB

Investigating the (co)evolution of reassorting influenza B lineages.
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LD calculator doesn't ignore gapped columns. #26

Closed evogytis closed 10 years ago

evogytis commented 10 years ago

There's a minor bug where the script will calculate LD after "cleaning up" haplotypes. That has an effect that when there's a clade-wide gap in the alignment it will only use haplotypes that do not have a gap, which leads to inflated LD for NA.