INNER CODE UNIT · Python

alignment_length

MariaNattestad/assemblytics · assemblytics/index.py:76

                alignment_length = abs(int(fields[3])-int(fields[2]))
                ref = fields[6]
                
                # for index:
                references_by_query[query_name].add(ref)
                queries_by_reference[ref].add(query_name)
                # amount_of_reference[ref] += alignment_length 

                # 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_by_query[query_name] = sum_reverse > sum_forward

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