code: def checkConsistency(self):
          
          for referenceName, (dataUrl, indexFile) in self._chromFileMap.items():
              varFile = pysam.VariantFile(dataUrl, index_filename=indexFile)
              try:
                  for chrom in varFile.index:
                      chrom, _, _ = self.sanitizeVariantFileFetch(chrom)
                      if not isEmptyIter(varFile.fetch(chrom)):
                          self._checkMetadata(varFile)
                          self._checkCallSetIds(varFile)
              finally:
                  varFile.close()
docs: Perform consistency check on the variant set