diff --git a/scripts/importer/data_importer/raw_data_importer.py b/scripts/importer/data_importer/raw_data_importer.py index a7521bf48..4f9bccec2 100644 --- a/scripts/importer/data_importer/raw_data_importer.py +++ b/scripts/importer/data_importer/raw_data_importer.py @@ -223,13 +223,13 @@ def _parse_manta(self): if self.settings.add_reversed_mates: # If the vcf only contains one line per breakend, add the reversed version to the database here. reversed = dict(data) - # TODO Note: in general, ref and alt cannot be assumed to be the same in the reversed direction, + # Note: in general, ref and alt cannot be assumed to be the same in the reversed direction, # but our data (so far) only contains N, so we just keep them as is for now. reversed.update({'mate_chrom': data['chrom'], 'chrom': data['mate_chrom'], 'mate_start': data['pos'], 'pos': data['mate_start'], 'chrom_id': data['mate_id'], 'mate_id': data['chrom_id']}) reversed['variant_id'] = '{}-{}-{}-{}'.format(reversed['chrom'], reversed['pos'], reversed['ref'], alt) - # TODO should the `counter` be increased here? + counter += 1 # increase the counter; reversed BNDs are usually kept at their own vcf row batch += [reversed] counter += 1 # count variants (one per vcf row)