Fix filtering of COGs in annotation pipeline. #108
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Filtering of COGs in the annotation pipeline was actually picking the hits with lowest target sequence id, i.e. random ones, instead of the best ones. We now instead pick the hits with lowest E-value and highest sequence identity.
Function was raising an error when to_return was not defined. That bug was introduced recently when ensuring that all columns were present in the returned DataFrame.
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Filtering of COGs in the annotation pipeline was actually picking the hits with lowest target sequence id, i.e. random ones, instead of the best ones. We now instead pick the hits with lowest E-value and highest sequence identity.
We also fix a small bug that was introduced with #99 and we fix some conda environment issues.
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