func (cmd *cmdCr) runOne(gPiChan genomePiChan) {
// Obtain codon table for identifying four-fold degenerate sites.
codonTable := taxonomy.GeneticCodes()[cmd.codonTableID]
// Profiling genome using reference sequence and protein feature data.
ref := gPiChan.genome
fnaFile := filepath.Join(cmd.genomeDir, ref+".fna")
gffFile := filepath.Join(cmd.genomeDir, ref+".gff")
gffs := readGff(gffFile)
genome := readGenome(fnaFile)
profile := profiling.ProfileGenome(genome, gffs, codonTable)
posType := convertPosType(cmd.pos)
piChunckChan := cmd.split(gPiChan.piChan)
covsChan := cmd.calc(piChunckChan, profile, posType, cmd.maxl)
covMVs, xMVs, yMVs := cmd.collect(covsChan)
cmd.write(ref, covMVs, xMVs, yMVs)
}
// Run is the main function.
func (cmd *cmdCt) Run() {
// The input of pileup can be from standard input,
// or from a file.
var f *os.File
if cmd.pileupFile == "" {
f = os.Stdin
} else {
f = openFile(cmd.pileupFile)
}
defer f.Close()
// Prepare genome position profile.
genome := readGenome(cmd.fastaFile)
gffs := readGff(cmd.gffFile)
codonTable := taxonomy.GeneticCodes()[cmd.codonTableID]
profile := profiling.ProfileGenome(genome, gffs, codonTable)
if cmd.regionEnd <= 0 {
cmd.regionEnd = len(profile)
}
// Convert pos from int to byte.
posType := convertPosType(cmd.pos)
// Read SNP from pileup input.
snpChan := readPileup(f, cmd.regionStart, cmd.regionEnd, cmd.pileupFormat)
// Apply filters.
filteredSNPChan := cmd.filterSNP(snpChan, profile, posType)
// Split SNPs into different chuncks.
snpChanChan := cmd.splitChuncks(filteredSNPChan)
// For each chunck, do the calculation.
covsChan := cmd.doCalculation(snpChanChan)
// Collect results from each chunck.
csMeanVars, crMeanVars, ctMeanVars := cmd.collect(covsChan, cmd.maxl)
// And finally, write results into the output file.
cmd.write(csMeanVars, crMeanVars, ctMeanVars, cmd.outFile)
}