def alignmentArray(self, orientation="native"): """ Direct access to the raw, encoded aligment array, which is a packed representation of the aligned read and reference. """ alnDs = self._alignmentGroup["AlnArray"] alnArray = arrayFromDataset(alnDs, self.Offset_begin, self.Offset_end) if self.RCRefStrand and (orientation == "genomic"): return alnArray[::-1] else: return alnArray
def pulseFeature(self, featureName, aligned=True, orientation="native"): """ Access a pulse feature by name. """ pulseDataset = self._alignmentGroup[featureName] pulseArray = arrayFromDataset(pulseDataset, self.Offset_begin, self.Offset_end) if self.RCRefStrand and orientation == "genomic": alignedPulseArray = pulseArray[::-1] else: alignedPulseArray = pulseArray if aligned: return alignedPulseArray else: return ungappedPulseArray(alignedPulseArray)