This PR corrects the isDuplicateRecord() check in CVRMutationDataReader, CVRNonSignedoutMutationDataReader, and GMLMutationDataReader. Duplicate records were not being caught by this check because the map being used to check for duplicates was not being populated. The addRecordToMap() function now adds to the mutationMap and the duplicate check functions correctly.
This PR also adds the remove-duplicate-maf-variants.py script provided by the curation team. Functionality of script described here. It is now called in the update-az-mskimpact.sh script
isDuplicateRecord()check inCVRMutationDataReader,CVRNonSignedoutMutationDataReader, andGMLMutationDataReader. Duplicate records were not being caught by this check because the map being used to check for duplicates was not being populated. TheaddRecordToMap()function now adds to themutationMapand the duplicate check functions correctly.remove-duplicate-maf-variants.pyscript provided by the curation team. Functionality of script described here. It is now called in theupdate-az-mskimpact.shscript