Mutect2 warns but does not fail when three or more reads have the same name

src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/SomaticGenotypingEngine.java

@@ -90,7 +90,7 @@ public CalledHaplotypes callMutations(
         if (MTAC.likelihoodArgs.phredScaledGlobalReadMismappingRate > 0) {
             logReadLikelihoods.normalizeLikelihoods(NaturalLogUtils.qualToLogErrorProb(MTAC.likelihoodArgs.phredScaledGlobalReadMismappingRate));
         }
-        final AlleleLikelihoods<Fragment, Haplotype> logFragmentLikelihoods = logReadLikelihoods.groupEvidence(MTAC.independentMates ? read -> read : GATKRead::getName, Fragment::create);
+        final AlleleLikelihoods<Fragment, Haplotype> logFragmentLikelihoods = logReadLikelihoods.groupEvidence(MTAC.independentMates ? read -> read : GATKRead::getName, Fragment::createAndAvoidFailure);
 
         for( final int loc : startPosKeySet ) {
             final List<VariantContext> eventsAtThisLoc = AssemblyBasedCallerUtils.getVariantContextsFromActiveHaplotypes(loc, haplotypes, false);

src/main/java/org/broadinstitute/hellbender/utils/read/Fragment.java

@@ -3,12 +3,15 @@
 import htsjdk.samtools.util.Locatable;
 import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.apache.commons.lang3.tuple.Pair;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.Utils;
 
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
+import java.util.stream.Collectors;
 
 /**
  * All available evidence coming from a single biological fragment.  Either one read or a read pair.
@@ -19,6 +22,9 @@ public class Fragment implements Locatable {
 
     private final List<GATKRead> reads;
 
+    private static final Logger logger = LogManager.getLogger(Fragment.class);
+
+
 
     public Fragment(final GATKRead read) {
         reads = Collections.singletonList(read);
@@ -38,6 +44,21 @@ public static Fragment create(final List<GATKRead> reads) {
         return reads.size() == 1 ? new Fragment(reads.get(0)) : new Fragment(ImmutablePair.of(reads.get(0), reads.get(1)));
     }
 
+    public static Fragment createAndAvoidFailure(final List<GATKRead> reads) {
+        if (reads.size() <= 2) {
+            return create(reads);
+        } else {
+            final List<GATKRead> nonSupplementaryReads = reads.stream()
+                    .filter(read -> !(read.isDuplicate() || read.isSecondaryAlignment() || read.isSupplementaryAlignment()))
+                    .collect(Collectors.toList());
+            if (nonSupplementaryReads.size() > 2) {
+                logger.warn("More than two reads with the same name found.  Using two reads randomly to combine as a fragment.");
+                return create(nonSupplementaryReads.subList(0,2));
+            }
+            return create(nonSupplementaryReads);
+        }
+    }
+
     public List<GATKRead> getReads() {
         return reads;
     }

src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java

@@ -464,8 +464,7 @@ public void testBamWithRepeatedReads() {
         final File bam = new File(toolsTestDir + "mutect/repeated_reads.bam");
         final File outputVcf = createTempFile("output", ".vcf");
 
-        runMutect2(bam, outputVcf, "20:10018000-10020000", b37Reference, Optional.empty(),
-                args -> args.addBooleanArgument(M2ArgumentCollection.INDEPENDENT_MATES_LONG_NAME, true));
+        runMutect2(bam, outputVcf, "20:10018000-10020000", b37Reference, Optional.empty());
     }
 
     // basic test on a small chunk of NA12878 mitochondria.  This is not a validation, but rather a sanity check