Add disambiguate tool to QC portion of the weave pipeline #33
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skchronicles
approved these changes
Jan 12, 2024
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Partially addresses #25
This pull request implements disambiguate when a command line user identifies a valid host genome using the --host[-t] and pathogen genome by the --pathogen[-p] flags. If does not use a valid fasta, or gzipped fasta, genome an error will be raised.
Currently this implementation of disambiguate only uses
bwa memfor alignment. This will need to change in the future including a method of detecting whether a cohort is DNA [bwa mem or support bowtie2] or RNA [STAR-aligner].