fixed edge cases where SomaticValidator counts reads ending inside th…

…e reference allele as alts
broadinstitute · Oct 18, 2018 · 1858eb3 · 1858eb3
1 parent 6d25f29
commit 1858eb3
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Showing 3 changed files with 9 additions and 4 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/GATKProtectedVariantContextUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/GATKProtectedVariantContextUtils.java
@@ -16,6 +16,7 @@
 import org.broadinstitute.hellbender.utils.read.GATKRead;
 
 import java.lang.reflect.Array;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Objects;
 import java.util.OptionalInt;
@@ -435,7 +436,10 @@ public static Allele chooseAlleleForRead(final PileupElement pileupElement, fina
         Utils.nonNull(altAlleles);
         ParamUtils.isPositiveOrZero(minBaseQualityCutoff, "Minimum base quality must be positive or zero.");
 
-        final boolean isRef = referenceAllele.basesMatch(getBasesForAlleleInRead(pileupElement, referenceAllele))
+        final byte[] basesForAlleleInRead = getBasesForAlleleInRead(pileupElement, referenceAllele);
+        final byte[] refBasesTruncatedToRead = ArrayUtils.subarray(referenceAllele.getBases(), 0, basesForAlleleInRead.length);
+
+        final boolean isRef = Arrays.equals(basesForAlleleInRead, refBasesTruncatedToRead)
                 && !pileupElement.isBeforeDeletionStart() && !pileupElement.isBeforeInsertion();
 
         Allele pileupAllele = null;

diff --git a/...ers/validation/basicshortmutpileup/ValidateBasicSomaticShortMutationsIntegrationTest.java b/...ers/validation/basicshortmutpileup/ValidateBasicSomaticShortMutationsIntegrationTest.java
@@ -144,12 +144,12 @@ public void testIndelCase() {
         // INS2: 20	3076299	.	A	AAGAAGCATGC
 
         assertValidationResult(variantValidationResults, new SimpleInterval("20", 1330646, 1330646),
-                "CCTTGGCTTATTCCA", "C", 7, 21, 10,
+                "CCTTGGCTTATTCCA", "C", 7, 22, 10,
                 26, 0);
 
         // TODO: This next one actually has an incorrect gtNumAltReadsInValidationNormal, since the validator thinks of this as AT<insT>.  There are supporting reads in the validation normal for A<insT>T.  See https://github.com/broadinstitute/gatk/issues/5061
         assertValidationResult(variantValidationResults, new SimpleInterval("20", 3076247, 3076247),
-                "AT", "ATT", 4, 33, 4,
+                "AT", "ATT", 4, 35, 4,
                 25,0);
         assertValidationResult(variantValidationResults, new SimpleInterval("20", 3076299, 3076299),
                 "A", "AAGAAGCATGC", 9, 41, 12,

diff --git a/...st/java/org/broadinstitute/hellbender/utils/GATKProtectedVariantContextUtilsUnitTest.java b/...st/java/org/broadinstitute/hellbender/utils/GATKProtectedVariantContextUtilsUnitTest.java
@@ -224,7 +224,8 @@ public Object[][] createTestDeletions() {
                 {0, "ATT", "A", true},
                 {0, "ATT", "A", false},
                 {10, "ATT", "A", true},
-                {10, "ATT", "A", false}
+                {10, "ATT", "A", false},
+                {LENGTH_OF_ARTIFICIAL_READ - 1, "AT", "A", false}
         };
     }