16cc2b864e3098e96eaff5727a5583775e392442,public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java,TransmissionDisequilibriumTest,calculateTDT,#VariantContext#Set#,64

Before Change


        final double nAAGivenABandAB = calculateNChildren(vc, triosToTest, REF, HET, HET);
        final double nBBGivenABandAB = calculateNChildren(vc, triosToTest, HOM, HET, HET);
        final double nAAGivenAAandAB = calculateNChildren(vc, triosToTest, REF, REF, HET);
        final double nABGivenAAandAB = calculateNChildren(vc, triosToTest, HET, REF, HET);

        final double numer = (nABGivenABandBB - nBBGivenABandBB) + 2.0 * (nAAGivenABandAB - nBBGivenABandAB) + (nAAGivenAAandAB - nABGivenAAandAB);
        final double denom = (nABGivenABandBB + nBBGivenABandBB) + 4.0 * (nAAGivenABandAB + nBBGivenABandAB) + (nAAGivenAAandAB + nABGivenAAandAB);

After Change


    private double calculateTDT( final VariantContext vc, final Set<Sample> triosToTest ) {

        final double nABGivenABandBB = calculateNChildren(vc, triosToTest, HET, HET, HOM) + calculateNChildren(vc, triosToTest, HET, HOM, HET);
        final double nBBGivenABandBB = calculateNChildren(vc, triosToTest, HOM, HET, HOM) + calculateNChildren(vc, triosToTest, HOM, HOM, HET);
        final double nAAGivenABandAB = calculateNChildren(vc, triosToTest, REF, HET, HET);
        final double nBBGivenABandAB = calculateNChildren(vc, triosToTest, HOM, HET, HET);
        final double nAAGivenAAandAB = calculateNChildren(vc, triosToTest, REF, REF, HET) + calculateNChildren(vc, triosToTest, REF, HET, REF);
        final double nABGivenAAandAB = calculateNChildren(vc, triosToTest, HET, REF, HET) + calculateNChildren(vc, triosToTest, HET, HET, REF);

        final double numer = (nABGivenABandBB - nBBGivenABandBB) + 2.0 * (nAAGivenABandAB - nBBGivenABandAB) + (nAAGivenAAandAB - nABGivenAAandAB);
        final double denom = (nABGivenABandBB + nBBGivenABandBB) + 4.0 * (nAAGivenABandAB + nBBGivenABandAB) + (nAAGivenAAandAB + nABGivenAAandAB);