def get_closest_forward_read(self, read):
closest_forward_read = None
if read.query_name.split('_')[-1] == '1':
positions = sorted(list(self.forward_reads_mate2_positions[read.reference_name].keys()))
closest_pos = misc.takeClosestSmaller(positions, read.reference_end-self.context_width)
if closest_pos is not None:
closest_forward_read = self.forward_reads_mate2_positions[read.reference_name][closest_pos]
else:
positions = sorted(list(self.forward_reads_mate1_positions[read.reference_name].keys()))
closest_pos = misc.takeClosestSmaller(positions, read.reference_end-self.context_width)
if closest_pos is not None:
closest_forward_read = self.forward_reads_mate1_positions[read.reference_name][closest_pos]
return closest_forward_read
def has_nearby_3p_mate(self, pos, positions):
closest_3p = misc.takeClosestSmaller(positions, pos)
if closest_3p is None:
return False
if pos - closest_3p <= self.min_distance_to_mate:
return True
else:
return False