def concatIndexBgzipFile(self, taskPrefix, dependencies, inputList, output,
label, fileType):
"""
Internal helper function
@param inputList files to be concatenated (in order), already bgzipped
@param output output filename
@param label used for error task id
@param fileType provided to tabix
"""
assert (len(inputList) > 0)
if len(inputList) > 1:
catCmd = [self.params.bgcatBin, "-o", output]
catCmd.extend(inputList)
else:
catCmd = getMvCmd() + [inputList[0], output]
indexCmd = [self.params.tabixBin, "-p", fileType, output]
catTask = self.addTask(preJoin(taskPrefix,
label + "_concat_" + fileType),
catCmd,
dependencies=dependencies,
isForceLocal=True)
return self.addTask(preJoin(taskPrefix, label + "_index_" + fileType),
indexCmd,
dependencies=catTask,
isForceLocal=True)
def getHeaderFixCmd(fileName) :
tmpName=fileName+".reheader.tmp"
cmd = "\"%s\" \"%s\"" % (sys.executable, self.params.vcfCmdlineSwapper)
cmd += ' "' + " ".join(self.params.configCommandLine) + '"'
cmd += " < \"%s\" > \"%s\"" % (fileName,tmpName)
cmd += " && " + " ".join(getMvCmd()) + " \"%s\" \"%s\"" % (tmpName, fileName)
return cmd
def getHeaderFixCmd(fileName):
tmpName = fileName + ".reheader.tmp"
cmd = "\"%s\" \"%s\"" % (sys.executable,
self.params.vcfCmdlineSwapper)
cmd += ' "' + " ".join(self.params.configCommandLine) + '"'
cmd += " < \"%s\" > \"%s\"" % (fileName, tmpName)
cmd += " && " + " ".join(
getMvCmd()) + " \"%s\" \"%s\"" % (tmpName, fileName)
return cmd