If a file is passed to the --genome parameter or referenced from an entry in the --genome_list, then use it as a genome. The parameter should be of the form FILE:CHROMOSOME.
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Context
This would make it easier to use YAVSAP on more exotic viruses that might not have GenBank entries, or to flesh out less complete GenBank records.
Summary
Allow using FASTA files as reference genomes.
Added Features
AdditionalChanged parametersIf a file is passed to the
--genomeparameter or referenced from an entry in the--genome_list, then use it as a genome. The parameter should be of the formFILE:CHROMOSOME.More Info
Context
This would make it easier to use YAVSAP on more exotic viruses that might not have GenBank entries, or to flesh out less complete GenBank records.