def catRealignedBam(label, segmentList) :
output = self.paths.getRealignedBamPath(label)
bamCatCmd = bamListCatCmd(self.params.samtoolsBin, segmentList, output)
bamCatTaskLabel = preJoin(taskPrefix, "realignedBamCat_" + label)
finishTasks.add(self.addTask(bamCatTaskLabel, bamCatCmd, dependencies=completeSegmentsTask))
def catRealignedBam(sampleIndex) :
segmentList = segFiles.sample[sampleIndex].bamRealign
output = self.paths.getRealignedBamPath(sampleIndex)
bamCatCmd = bamListCatCmd(self.params.samtoolsBin, segmentList, output)
bamCatTaskLabel = preJoin(taskPrefix, "realignedBamCat_" + self.paths.sampleLabel(sampleIndex))
finishTasks.add(self.addTask(bamCatTaskLabel, bamCatCmd, dependencies=completeSegmentsTask))
def finishBam(tmpList, output, label):
cmd = bamListCatCmd(self.params.samtoolsBin, tmpList, output)
finishTasks.add(
self.addTask(preJoin(taskPrefix, label + "_finalizeBAM"),
cmd,
dependencies=completeSegmentsTask))