def getVcfSortCmd(vcfPaths, outPath, isDiploid) :
cmd = "\"%s\" -E \"%s\" -u " % (sys.executable,self.params.mantaSortVcf)
cmd += " ".join(quoteStringList(vcfPaths))
# apply the ploidy filter to diploid variants
if isDiploid:
tempVcf = self.paths.getTempDiploidPath()
cmd += " > \"%s\"" % (tempVcf)
cmd += " && \"%s\" -E \"%s\" \"%s\"" % (sys.executable, self.params.mantaPloidyFilter, tempVcf)
cmd += " | \"%s\" -c > \"%s\"" % (self.params.bgzipBin, outPath)
if isDiploid:
cmd += " && " + " ".join(getRmCmd()) + " \"%s\"" % (self.paths.getTempDiploidPath())
return cmd
def getVcfSortCmd(vcfListFile, outPath, isDiploid):
cmd = "\"%s\" -E \"%s\" -u " % (sys.executable,
self.params.mantaSortVcf)
cmd += "-f \"%s\"" % (vcfListFile)
# apply the ploidy filter to diploid variants
if isDiploid:
tempVcf = self.paths.getTempDiploidPath()
cmd += " > \"%s\"" % (tempVcf)
cmd += " && \"%s\" -E \"%s\" \"%s\"" % (
sys.executable, self.params.mantaPloidyFilter, tempVcf)
cmd += " | \"%s\" -c > \"%s\"" % (self.params.bgzipBin, outPath)
if isDiploid:
cmd += " && " + " ".join(
getRmCmd()) + " \"%s\"" % (self.paths.getTempDiploidPath())
return cmd
def getVcfSortCmd(vcfListFile, outPath, isDiploid, isCandidate) :
cmd = "\"%s\" \"%s\" " % (sys.executable, self.params.mantaSortVcf)
cmd += "-f \"%s\"" % (vcfListFile)
# Boolean variable isCandidate is set "True" for candidateSV.vcf
# If it is True, commandline argument "-a" is passed on to sortBam.py to print out all vcf records
if isCandidate:
cmd += " -a"
# apply the ploidy filter to diploid variants
if isDiploid:
tempVcf = self.paths.getTempDiploidPath()
cmd += " > \"%s\"" % (tempVcf)
cmd += " && \"%s\" \"%s\" \"%s\"" % (sys.executable, self.params.mantaPloidyFilter, tempVcf)
cmd += " | \"%s\" -c > \"%s\"" % (self.params.bgzipBin, outPath)
if isDiploid:
cmd += " && " + " ".join(getRmCmd()) + " \"%s\"" % (self.paths.getTempDiploidPath())
return cmd
def getVcfSortCmd(vcfListFile, outPath, isDiploid, isCandidate):
cmd = "\"%s\" \"%s\" " % (sys.executable, self.params.mantaSortVcf)
cmd += "-f \"%s\"" % (vcfListFile)
# Boolean variable isCandidate is set "True" for candidateSV.vcf
# If it is True, commandline argument "-a" is passed on to sortBam.py to print out all vcf records
if isCandidate:
cmd += " -a"
# apply the ploidy filter to diploid variants
if isDiploid:
tempVcf = self.paths.getTempDiploidPath()
cmd += " > \"%s\"" % (tempVcf)
cmd += " && \"%s\" \"%s\" \"%s\"" % (
sys.executable, self.params.mantaPloidyFilter, tempVcf)
cmd += " | \"%s\" -c > \"%s\"" % (self.params.bgzipBin, outPath)
if isDiploid:
cmd += " && " + " ".join(
getRmCmd()) + " \"%s\"" % (self.paths.getTempDiploidPath())
return cmd