diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java index ae7c2f5c1..26c777296 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java @@ -317,11 +317,11 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel { } } - public int linearExactMultiAllelic(GenotypesContext GLs, - int numAlternateAlleles, - double[] log10AlleleFrequencyPriors, - double[] log10AlleleFrequencyPosteriors, - boolean preserveData) { + static public int linearExactMultiAllelic(GenotypesContext GLs, + int numAlternateAlleles, + double[] log10AlleleFrequencyPriors, + double[] log10AlleleFrequencyPosteriors, + boolean preserveData) { final ArrayList genotypeLikelihoods = getGLs(GLs); final int numSamples = genotypeLikelihoods.size()-1; @@ -350,8 +350,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel { maxLog10L = Math.max(maxLog10L, log10LofKs); } - // TODO -- finish me - + // TODO -- why do we need to return anything here? return 0; } @@ -471,7 +470,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel { log10ConformationLikelihoods[0] = MathUtils.log10Cache[2*j-totalK] + MathUtils.log10Cache[2*j-totalK-1] + set.log10Likelihoods[j-1] + gl[HOM_REF_INDEX]; // deal with the other possible conformations now - if ( totalK < 2*j ) { + if ( totalK <= 2*j ) { // skip impossible conformations int conformationIndex = 1; for ( Map.Entry mapping : set.ACsetIndexToPLIndex.entrySet() ) log10ConformationLikelihoods[conformationIndex++] = diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 34e1ad30e..11e086db8 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -29,7 +29,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot1() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1, - Arrays.asList("286f0de92e4ce57986ba861390c6019d")); + Arrays.asList("b70732a2f63f8409b61e41fa53eaae3e")); executeTest("test MultiSample Pilot1", spec); }