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 mem for 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].
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].