feature-improveclinical: bug fixed at CosmicIndexer - update was needed on columns numbers
@@ -55,10 +55,10 @@ public class CosmicIndexer extends ClinicalIndexer {
// COSMIC v78 GRCh38 includes one more column at position 27 (1-based) "Resistance Mutation" which is not
// provided in the GRCh37 file
if (assembly.equalsIgnoreCase("grch37")) {
- this.mutationSomaticStatusColumn = 28;
- this.pubmedPMIDColumn = 29;
- this.sampleSourceColumn = 31;
- this.tumourOriginColumn = 32;
+ this.mutationSomaticStatusColumn = 29;
+ this.pubmedPMIDColumn = 30;
+ this.sampleSourceColumn = 32;
+ this.tumourOriginColumn = 33;
} else {
this.mutationSomaticStatusColumn = 29;
this.pubmedPMIDColumn = 30;
