149ee8f29baba035db43cf0133e0cb944526eb61,anvio/contigops.py,Auxiliary,run_SCVs,#Auxiliary#Any#,197

Before Change

                    gene_overlap_start += read.reference_start
                    gene_overlap_stop += read.reference_start - 1
                    start_index = np.where(read[:, 0] == gene_overlap_start)[0][0]
                    stop_index = np.where(read[:, 0] == gene_overlap_stop)[0][0]
                    segment_that_overlaps_gene = read[start_index:stop_index+1]

                if gene_id not in gene_calls:
                    // We make an on-the-fly gene call dict. See the NOTE in

After Change

                    gene_overlap_start, gene_overlap_stop = next(utils.get_constant_value_blocks(gene_id_per_nt_in_read, gene_id))
                    gene_overlap_start += read.reference_start
                    gene_overlap_stop += read.reference_start - 1
                    start_index = next(utils.find_value_index(read[:, 0], gene_overlap_start))
                    stop_index = next(utils.find_value_index(read[:, 0], gene_overlap_stop))
                    segment_that_overlaps_gene = read[start_index:stop_index+1]

                if gene_id not in gene_calls:

Instances