Make error informative for non-diploid family likelihoods

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriors.java

@@ -185,6 +185,8 @@ import java.util.*;
  *   -o output.withPosteriors.vcf
  * </pre>
  *
+ * <h3>Caveat</h3>
+ * <p>If applying family priors, only diploid family genotypes are supported</p>
  */
 @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} )
 public class CalculateGenotypePosteriors extends RodWalker<Integer,Integer> {

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/FamilyLikelihoodsUtils.java

@@ -51,6 +51,7 @@
 
 package org.broadinstitute.gatk.tools.walkers.variantutils;
 
+import htsjdk.variant.vcf.VCFConstants;
 import org.apache.log4j.Logger;
 import org.broadinstitute.gatk.engine.samples.Sample;
 import org.broadinstitute.gatk.utils.MathUtils;
@@ -263,7 +264,7 @@ public class FamilyLikelihoodsUtils {
             updateFamilyGenotypes(vc, mother, father, child, trioGenotypes);
 
             //replace uses sample names to match genotypes, so order doesn't matter
-            if (trioGenotypes.size() > 0) {
+            if (!trioGenotypes.isEmpty()) {
                 genotypesContext.replace(trioGenotypes.get(0));
                 genotypesContext.replace(trioGenotypes.get(1));
                 genotypesContext.replace(trioGenotypes.get(2));
@@ -440,7 +441,7 @@ public class FamilyLikelihoodsUtils {
 
         //In case of null, unavailable or no call, all likelihoods are log10(1/3)
         else if(genotype == null || !hasCalledGT(genotype.getType()) || genotype.getLikelihoods() == null){
-            likelihoods = new double[3];
+            likelihoods = new double[NUM_CALLED_GENOTYPETYPES];
             likelihoods[0] = LOG10_OF_ONE_THIRD;
             likelihoods[1] = LOG10_OF_ONE_THIRD;
             likelihoods[2] = LOG10_OF_ONE_THIRD;
@@ -450,6 +451,13 @@ public class FamilyLikelihoodsUtils {
         else
             likelihoods = GeneralUtils.normalizeFromLog10(genotype.getLikelihoods().getAsVector(),true,true);
 
+        if (likelihoods.length != NUM_CALLED_GENOTYPETYPES) {
+            final String key = genotype.hasExtendedAttribute(GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY) ?
+                    GATKVCFConstants.PHRED_SCALED_POSTERIORS_KEY : VCFConstants.GENOTYPE_PL_KEY;
+            throw new UserException(genotype + " has " + likelihoods.length + " " + key + " values, should be " + NUM_CALLED_GENOTYPETYPES +
+                    " since only the diploid case is supported when applying family priors.");
+        }
+
         likelihoodsMap.put(GenotypeType.HOM_REF,likelihoods[genotypeTypeToValue(GenotypeType.HOM_REF)]);
         likelihoodsMap.put(GenotypeType.HET,likelihoods[genotypeTypeToValue(GenotypeType.HET)]);
         likelihoodsMap.put(GenotypeType.HOM_VAR, likelihoods[genotypeTypeToValue(GenotypeType.HOM_VAR)]);

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java

@@ -52,6 +52,7 @@
 package org.broadinstitute.gatk.tools.walkers.variantutils;
 
 import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.testng.annotations.Test;
 
 import java.util.Arrays;
@@ -61,6 +62,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
     private static String CEUtrioFamilyFile = privateTestDir + "CEUtrio.ped";
     private static String CEUtrioTest = privateTestDir + "CEUtrioTest.vcf";
     private static String CEUtrioPopPriorsTest = privateTestDir + "CEUtrioPopPriorsTest.vcf";
+    private static String CEUtrioMixedPloidyTest = privateTestDir + "CEUtrioMixedPloidy.vcf";
     private static String threeMemberNonTrioFamilyFile = privateTestDir + "threeMemberNonTrio.ped";
     private static String getThreeMemberNonTrioTest = privateTestDir + "threeMemberNonTrioTest.vcf";
 
@@ -135,5 +137,16 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest {
         executeTest("testFamilyPriors", spec);
     }
 
-
+    @Test(enabled = true)
+    public void testFamilyPriorsMixedPloidy() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T CalculateGenotypePosteriors --no_cmdline_in_header " +
+                        " -o %s" +
+                        " -R " + b37KGReference +
+                        " -ped " + CEUtrioFamilyFile +
+                        " -V " + CEUtrioMixedPloidyTest,
+                1,
+                UserException.class);
+        executeTest("testFamilyPriorsMixedPloidy", spec);
+    }
 }