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PoonLab / Poplars

Open-source implementations of popular tools from Los Alamos National Laboratory HIV Database
GNU Affero General Public License v3.0
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hypermut: no indication of reference sequence #28

Closed ArtPoon closed 5 years ago

ArtPoon commented 5 years ago

Help text does not explain that a reference sequence is needed to evaluate substitutions. Are we arbitrarily using first sequence in input FASTA? Ideally the script should generate a consensus sequence as the reference.

kwade4 commented 5 years ago

Yes, currently hypermut.py and the LANL's hypermut designate the first sequence as the reference sequence. I will update the help text and add an option for generating the consensus sequence.