immcantation / presto

pRESTO is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq). pRESTO is a bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
https://presto.readthedocs.io
GNU Affero General Public License v3.0
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Should --scanrev be default for AssemblePairs? #67

Open ssnn-airr opened 5 years ago

ssnn-airr commented 5 years ago

Original report by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).


Should we replace --scanrev with --skiprev in AssemblePairs and make the reverse scan process default? Because it is usually best to specify --scanrev. We originally made it non-default for the sake of backward compatibility.