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)