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Add a conversion from the deprecated PL ordering to the new one. We need this for the DiploidSNPGenotypeLikelihoods which still use the old ordering. My intention is for this to be a temporary patch, but changing the ordering in DiploidSNPGenotypeLikelihoods is not appriopriate for committing to stable as it will break all of the external tools (e.g. MuTec) that are built on top of the class. We will have to talk to e.g. Kristian to see how disruptive this will be. Added unit tests to the GL conversions and indexing.

This commit is contained in:
Eric Banks 2012-03-16 11:14:37 -04:00
parent 41068b6985
commit dce6b91f7d
4 changed files with 25 additions and 6 deletions
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1
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java
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@ -64,7 +64,6 @@ public enum DiploidGenotype {
return r != base2;
else
return base2 == r;
//return MathUtils.countOccurrences(r, this.toString()) == 1;
}
public boolean isHom() {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
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@ -176,7 +176,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
final double[] likelihoods = sampleData.GL.getLikelihoods();
final int PLindexOfBestGL = MathUtils.maxElementIndex(likelihoods);
if ( PLindexOfBestGL != PLindexOfRef ) {
GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(3, PLindexOfBestGL);
GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePairUsingDeprecatedOrdering(PLindexOfBestGL);
if ( alleles.alleleIndex1 != baseIndexOfRef )
likelihoodSums[alleles.alleleIndex1] += likelihoods[PLindexOfBestGL] - likelihoods[PLindexOfRef];
// don't double-count it

23
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
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@ -272,6 +272,29 @@ public class GenotypeLikelihoods {
return PLIndexToAlleleIndex[PLindex];
}
// An index conversion from the deprecated PL ordering to the new VCF-based ordering for up to 3 alternate alleles
protected static int[] PLindexConversion = new int[]{0, 1, 3, 6, 2, 4, 7, 5, 8, 9};
/**
* get the allele index pair for the given PL using the deprecated PL ordering:
* AA,AB,AC,AD,BB,BC,BD,CC,CD,DD instead of AA,AB,BB,AC,BC,CC,AD,BD,CD,DD.
* Although it's painful to keep this conversion around, our DiploidSNPGenotypeLikelihoods class uses the deprecated
* ordering and I know with certainty that external users have built code on top of it; changing it now would
* cause a whole lot of heartache for our collaborators, so for now at least there's a standard conversion method.
* This method assumes at most 3 alternate alleles.
* TODO -- address this issue at the source by updating DiploidSNPGenotypeLikelihoods.
*
* @param PLindex the PL index
* @return the allele index pair
*/
public static GenotypeLikelihoodsAllelePair getAllelePairUsingDeprecatedOrdering(final int PLindex) {
// make sure that we've cached enough data
if ( PLindex >= PLIndexToAlleleIndex.length )
calculatePLcache(PLindex);
return PLIndexToAlleleIndex[PLindexConversion[PLindex]];
}
/**
* get the PL indexes (AA, AB, BB) for the given allele pair; assumes allele1Index <= allele2Index.
*

5
public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java
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@ -137,13 +137,10 @@ public class GenotypeLikelihoodsUnitTest {
@Test
public void testCalculatePLindex(){
// AA,AB,BB,AC,BC,CC,AD,BD,CD,DD called in the order of AA,AB,AC,AD,BB,BC,BD,CC,CD,DD
int[] indexes = new int[]{0, 1, 3, 6, 2, 4, 7, 5, 8, 9};
int counter = 0;
for ( int i = 0; i <= 3; i++ ) {
for ( int j = i; j <= 3; j++ ) {
Assert.assertEquals(GenotypeLikelihoods.calculatePLindex(i, j), indexes[counter++], "PL index of alleles " + i + "," + j + " was not calculated correctly");
Assert.assertEquals(GenotypeLikelihoods.calculatePLindex(i, j), GenotypeLikelihoods.PLindexConversion[counter++], "PL index of alleles " + i + "," + j + " was not calculated correctly");
}
}
}