More allele trimming for VariantAnnotator

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java

@@ -344,6 +344,17 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         executeTest("Testing InbreedingCoeff annotation with PED file", spec);
     }
 
+    @Test(enabled = true)
+    public void testAlleleTrimming() {
+        final String MD5 = "5f4b8dcbd4ec3b773486945e5b38e7f3";
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + privateTestDir + "alleleTrim.vcf.gz" +
+                        " -L 1:26608870-26608875 -no_cmdline_in_header --resource:exac " + privateTestDir +  "exacAlleleTrim.vcf.gz  -E exac.AC_Adj" +
+                        "  -o %s", 1,
+                Arrays.asList(MD5));
+        executeTest("Testing allele trimming annotation", spec);
+    }
+
     @Test
     public void testStrandBiasBySample() throws IOException {
         // pipeline 1: create variant via HalotypeCaller with no default annotations

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java

@@ -41,6 +41,7 @@ import org.broadinstitute.gatk.utils.commandline.RodBinding;
 import org.broadinstitute.gatk.utils.exceptions.UserException;
 import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 
 import java.util.*;
 
@@ -318,12 +319,10 @@ public class VariantAnnotatorEngine {
                 final boolean isMultiAllelic = expressionVC.getNAlleles() > 2;
                 final boolean useRefAndAltAlleles = VCFHeaderLineCount.R == hInfo.getCountType();
                 final boolean useAltAlleles = VCFHeaderLineCount.A == hInfo.getCountType();
+                List<Allele> usedExpressionAlleles = null;
 
                 // Multiallelic and count of A or R
                 if ( isMultiAllelic && (useAltAlleles || useRefAndAltAlleles) ){
-                    // get the alleles common to the expression and variant
-                    final List<Allele> usedExpressionAlleles = useRefAndAltAlleles ? expressionVC.getAlleles() : expressionVC.getAlternateAlleles();
-                    final List<Allele> commonAlleles = ListUtils.intersection(usedExpressionAlleles, vc.getAlleles());
 
                     // remove brackets and spaces from expression attribute
                     final String cleanedExpression = expressionVC.getAttribute(expression.fieldName).toString().replaceAll("[\\[\\]\\s]", "");
@@ -332,18 +331,58 @@ public class VariantAnnotatorEngine {
                     final Map<String, String> mapAlleleToExpressionValue = new HashMap<String, String>();
 
                     // get comma separated expression values
-                    final String [] expressionValues = cleanedExpression.split(",");
+                    ArrayList<String> expressionValuesList = new ArrayList<String>(Arrays.asList(cleanedExpression.split(",")));
+
+                    if ( vc.isSNP() && expressionVC.isMixed() ){
+                        final VariantContextBuilder builder = new VariantContextBuilder(expressionVC);
+                        List<Allele> sameLengthAlleles = new ArrayList<Allele>();
+
+                        // get alt alleles that are the same length as the ref allele
+                        Iterator<String> expressionValuesIterator = expressionValuesList.iterator();
+                        for ( Allele allele : expressionVC.getAlleles() ){
+                            if ( allele.isNonReference() ){
+                                if ( !expressionValuesIterator.hasNext() ){
+                                    logger.warn("Cannot annotate expression " + expression.fullName + " at " + loc + " for expression allele): " + allele);
+                                    break;
+                                }
+                                expressionValuesIterator.next();
+                                if ( allele.length() == expressionVC.getReference().length() ) {
+                                    sameLengthAlleles.add(allele);
+                                }
+                                else {
+                                    // remove unused expression values
+                                    expressionValuesIterator.remove();
+                                }
+                            } else {
+                                if ( useRefAndAltAlleles )
+                                    expressionValuesIterator.remove();
+                            }
+                        }
+
+                        if (!sameLengthAlleles.isEmpty()) {
+                            sameLengthAlleles.add(0, expressionVC.getReference());
+                            VariantContext variantContext = builder.alleles(sameLengthAlleles).make();
+                            // extract the SNPs
+                            VariantContext variantContextTrimmed = GATKVariantContextUtils.trimAlleles(variantContext, true, true);
+                            usedExpressionAlleles = useRefAndAltAlleles ? variantContextTrimmed.getAlleles() : variantContextTrimmed.getAlternateAlleles();
+                        }
+                    } else {
+                        // get the alleles common to the expression and variant
+                        usedExpressionAlleles = useRefAndAltAlleles ? expressionVC.getAlleles() : expressionVC.getAlternateAlleles();
+                    }
+
+                    final List<Allele> commonAlleles = ListUtils.intersection(usedExpressionAlleles, vc.getAlleles());
 
                     // the number of expression values must be the same as the number of alleles
-                    if ( expressionValues.length != usedExpressionAlleles.size() ) {
+                    if ( expressionValuesList.size() != usedExpressionAlleles.size() ) {
                         logger.warn("Cannot annotate expression " + expression.fullName + " at " + loc + " for variant allele(s): " + vc.getAlleles() + ", " +
-                                expressionValues.length + " expression values is not equal to " + usedExpressionAlleles.size() + " expression alleles");
+                                expressionValuesList.size() + " expression values is not equal to " + usedExpressionAlleles.size() + " expression alleles");
                         continue;
                     }
 
                     // map the used expression alleles to it's value
-                    for (int i = 0; i != expressionValues.length; i++)
+                    for (int i = 0; i != expressionValuesList.size(); i++)
-                        mapAlleleToExpressionValue.put(usedExpressionAlleles.get(i).getBaseString(), expressionValues[i]);
+                        mapAlleleToExpressionValue.put(usedExpressionAlleles.get(i).getBaseString(), expressionValuesList.get(i));
 
                     // add the variants expression values to the annotation
                     final List<String> annotationValues = new ArrayList<String>();