R/outformat2num.R

In HajkD/metablastr: Perform Massive Local BLAST Searches

# helper function to map human readable output format to numeric specification
# used as input by the BLAST command line tool
outformat2num <- function(out.format) {
    if (is_outformat(out.format)) {
        return(switch(
            out.format,
            pair = 0,
            qa.ident = 1,
            qa.nonident = 2,
            fq.ident = 3,
            fq.nonident = 4,
            xml = 5,
            tab = 6,
            tab.comment = 7,
            ASN.1.text = 8,
            ASN.1.binary = 9,
            csv = 10,
            ASN.1 = 11,
            json.seq.aln = 12,
            json.blast.multi = 13,
            xml2.blast.multi = 14,
            json.blast.single = 15,
            xml2.blast.single = 16,
            SAM = 17,
            report = 18
        ))
        
    }
}