Modified Fragment creation for mutect2 to not fail in the special cas…

…e that a Fragment is only supported by supplementary and/or secondary and/or duplicate reads

Fixes #6310

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

@@ -11,6 +11,7 @@
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
+import java.util.Optional;
 import java.util.stream.Collectors;
 
 /**
@@ -55,6 +56,11 @@ public static Fragment createAndAvoidFailure(final List<GATKRead> reads) {
                 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));
             }
+            //If there are no nonsupplementary reads, try supplementary/secondary/duplicate reads instead
+            else if(nonSupplementaryReads.isEmpty())
+            {
+                return create(reads.subList(0,1));
+            }
             return create(nonSupplementaryReads);
         }
     }

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

@@ -467,6 +467,16 @@ public void testBamWithRepeatedReads() {
         runMutect2(bam, outputVcf, "20:10018000-10020000", b37Reference, Optional.empty());
     }
 
+    // In the rare case that a particular fragment is only supported by supplementary reads, that should not
+    // result in an exception.  This test ensures that Mutect2 does not fail to finish in that case.
+    @Test
+    public void testBamWithOnlySupplementaryReads() {
+        final File bam = new File(toolsTestDir + "mutect/only_supplementary_reads.bam");
+        final File outputVcf = createTempFile("output", ".vcf");
+
+        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
     // that M2 makes obvious calls, doesn't trip up on the beginning of the circular chromosome, and can handle high depth
     @Test