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)
