Merge 91fed50 into c5ab8db

NBISweden · May 22, 2019 · e58bb6b · e58bb6b
2 parents c5ab8db + 91fed50
commit e58bb6b
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Showing 2 changed files with 6 additions and 7 deletions.
diff --git a/scripts/importer/data_importer/raw_data_importer.py b/scripts/importer/data_importer/raw_data_importer.py
@@ -216,13 +216,12 @@ def _parse_manta(self):
                     if data['mate_chrom'].startswith('GL') or data['mate_chrom'].startswith('MT'):
                         continue
                     if 'MATEID' in info:
-                        data['mate_id'] = info['MATEID']
+                        data['mate_id'] = info.get('MATEID', '')
                     data['variant_id'] = '{}-{}-{}-{}'.format(data['chrom'], data['pos'], data['ref'], alt)
+                    data['allele_count'] = data.get('allele_count', 0)
+                    data['allele_num'] = data.get('allele_num', 0)
 
                     batch += [data]
-                    if self.settings.count_calls:
-                        self.get_callcount(data)  # count calls (one per reference)
-                        self.counter['beaconvariants'] += 1  # count variants (one per alternate)
 
                 counter += 1  # count variants (one per vcf row)
 
@@ -491,7 +490,7 @@ def start_import(self):
         if self.settings.add_mates:
             self._parse_manta()
             if self.settings.count_calls:
-                self._create_beacon_counts()
+                logging.warning('Do not know how to count calls in the manta file. Skipping this...')
         elif self.settings.variant_file:
             self._insert_variants()
             if self.settings.count_calls:

diff --git a/sql/beacon_schema.sql b/sql/beacon_schema.sql
@@ -91,7 +91,7 @@ CREATE OR REPLACE VIEW beacon.beacon_mate_table AS
                           d.short_name,
                           av.dataset_version) AS datasetId,
            substr(dm.chrom, 1, 2) AS chromosome,
-           dm.pos - 1 AS "chromosomeStart",
+           dm.pos - 1 AS chromosomeStart,
            dm.chrom_id as chromosomePos,
            dm.mate_chrom as mate,
            dm.mate_start as mateStart,
@@ -101,7 +101,7 @@ CREATE OR REPLACE VIEW beacon.beacon_mate_table AS
            dm.allele_count as alleleCount,
            dm.allele_num as callCount,
            dm.allele_freq as frequency,
-           dm.mate_start as "end",
+           dm.mate_start - 1 as "end",
            'BND' as variantType
      FROM data.mate AS dm
       JOIN beacon.available_datasets as av