def strelkaGermlineGetDepthFromAlignments(self,taskPrefix="getChromDepth",dependencies=None):
if len(self.params.bamList) == 0 :
return set()
bamList = self.params.bamList
outputPath=self.paths.getChromDepth()
return getDepthFromAlignments(self, bamList, outputPath, taskPrefix, dependencies)
def strelkaGermlineRunDepthFromAlignments(self,taskPrefix="getChromDepth",dependencies=None):
bamList=[]
if len(self.params.bamList) :
bamList.append(self.params.bamList[0])
else :
return set()
outputPath=self.paths.getChromDepth()
return getDepthFromAlignments(self, bamList, outputPath, taskPrefix, dependencies)
def mantaGetDepthFromAlignments(self,taskPrefix="getChromDepth",dependencies=None):
bamList=[]
if len(self.params.normalBamList) :
bamList = self.params.normalBamList
elif len(self.params.tumorBamList) :
bamList = self.params.tumorBamList
else :
return set()
outputPath=self.paths.getChromDepth()
return getDepthFromAlignments(self, bamList, outputPath, taskPrefix, dependencies)
def strelkaSomaticGetDepthFromAlignments(self,taskPrefix="getChromDepth",dependencies=None):
bamList=[]
if len(self.params.normalBamList) :
bamList.append(self.params.normalBamList[0])
elif len(self.params.tumorBamList) :
bamList.append(self.params.tumorBamList[0])
else :
return set()
outputPath=self.paths.getChromDepth()
return getDepthFromAlignments(self, bamList, outputPath, taskPrefix, dependencies)
def strelkaGermlineGetDepthFromAlignments(self,
taskPrefix="getChromDepth",
dependencies=None):
if len(self.params.bamList) == 0:
return set()
bamList = self.params.bamList
outputPath = self.paths.getChromDepth()
if os.path.exists(outputPath):
print("strelkaGermlineGetDepthFromAlignments: FILE EXISTS: " +
outputPath)
return set()
else:
print("strelkaGermlineGetDepthFromAlignments: FILE NOT FOUND: " +
outputPath)
return getDepthFromAlignments(self, bamList, outputPath, taskPrefix,
dependencies)
