INNER CODE UNIT · Python

alignment_length

MariaNattestad/assemblytics · assemblytics/dot_prep.py:78

				alignment_length = abs(int(fields[3])-int(fields[2]))
				ref = fields[6]

				# for index:
				unique_references_by_query[query_name].add(ref)
				queries_by_reference[ref].add(query_name)

				# for ordering:
				ref_position_scores.append(ref_chrom_offsets[ref] + (ref_start+ref_stop)/2)

				# for orientation:
				if query_stop < query_start:
					sum_reverse += alignment_length
				else:
					sum_forward += alignment_length

		# orientation:
		flip = sum_reverse > sum_forward

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