def setCommand(self):
self.outputFile = os.path.splitext(self.contigs)[0] + ".sam"
self.addArg("bowtie -p " + Configuration.instance.getGlobalOption("maxThreads"))
self.addArg("--sam")
if FastqUtils.determineQuality(self.mergedFiles[0]) == 64:
self.addArg("--phred64-quals")
self.addArg(self.bowtieIndex)
self.addArg(",".join(self.mergedFiles))
self.addArg(self.outputFile)
def setCommand(self):
self.outputFile = self.outputDir + "jump_reads_orig.fastb"
self.addArg("PrepareAllPathsInputs.pl")
self.addArg("DATA_DIR=" + self.outputDir)
self.addArg("IN_GROUPS_CSV=" + self.groupsCsv)
self.addArg("IN_LIBS_CSV=" + self.libsCsv)
if FastqUtils.determineQuality(self.forward) == 64:
self.addArg("PHRED_64=True")
self.addArg("PLOIDY=2")
self.addArg("OVERWRITE=1")
