@ Override public double similarity ( VariantCall call1 , VariantCall call2 ) { int minNumberOfGenotypes = Math . min ( call1 . getGenotypeCount ( ) , call2 . getGenotypeCount ( ) ) ; int numberOfSharedAlleles = 0 ; for ( int i = 0 ; i < minNumberOfGenotypes ; ++ i ) { if ( call1 . getGenotype ( i ) == call2 . getGenotype ( i ) ) { ++ numberOfSharedAlleles ; } } int maxNumberOfGenotypes = Math . max ( call1 . getGenotypeCount ( ) , call2 . getGenotypeCount ( ) ) ; return ( double ) numberOfSharedAlleles / maxNumberOfGenotypes ; }
scores when the number of alleles is different than 2 and when the genotypes are unphased .