Fix NPE in VariantEval when run with no intervals/reference

* Fixes an NPE that happened when using certain evaluators with VariantEval and not specifying a reference or intervals * Fixes #6212
broadinstitute · Dec 9, 2019 · 396636e · 396636e
1 parent d9fd22f
commit 396636e
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Showing 2 changed files with 23 additions and 2 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEval.java
@@ -29,6 +29,7 @@
 import org.broadinstitute.hellbender.utils.SimpleInterval;
 import org.broadinstitute.hellbender.utils.Utils;
 import org.broadinstitute.hellbender.utils.io.IOUtils;
+import org.broadinstitute.hellbender.utils.logging.OneShotLogger;
 import org.broadinstitute.hellbender.utils.samples.PedigreeValidationType;
 import org.broadinstitute.hellbender.utils.samples.SampleDB;
 import org.broadinstitute.hellbender.utils.samples.SampleDBBuilder;
@@ -235,7 +236,7 @@ public class VariantEval extends MultiVariantWalker {
     /**
      * File containing tribble-readable features for the IntervalStratificiation
      */
-    @Argument(fullName="strat-intervals", shortName="strat-intervals", doc="File containing tribble-readable features for the IntervalStratificiation", optional=true)
+    @Argument(fullName="strat-intervals", shortName="strat-intervals", doc="File containing tribble-readable features for the IntervalStratification", optional=true)
     public FeatureInput<Feature> intervalsFile = null;
 
     /**
@@ -304,6 +305,8 @@ protected void initializeDrivingVariants() {
     // maintain the mapping of FeatureInput to name used in output file
     Map<FeatureInput<VariantContext>, String> inputToNameMap = new HashMap<>();
 
+    private final OneShotLogger territoryUnknownWarningLogger = new OneShotLogger(logger);
+
     /**
      * Initialize the stratifications, evaluations, evaluation contexts, and reporting object
      */
@@ -819,7 +822,13 @@ public SampleDB getSampleDB() {
     }
 
     public long getnProcessedLoci() {
-        return getTraversalIntervals().stream().mapToLong(SimpleInterval::size).sum();
+        if(getTraversalIntervals() == null) {
+            territoryUnknownWarningLogger.warn("No reference or intervals were provided so it is not clear how much genomic " +
+                    "territory the input covered. Values that rely on the size of the input territory will not be correct.");
+            return 0;
+        } else {
+            return getTraversalIntervals().stream().mapToLong(SimpleInterval::size).sum();
+        }
     }
 
     public FeatureInput<Feature> getKnownCNVsFile() {

diff --git a/...a/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEvalIntegrationTest.java b/...a/org/broadinstitute/hellbender/tools/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -666,4 +666,16 @@ public void testOutputFileCreation() throws IOException {
                 new File(getToolTestDataDir() + "expected/" + "testPrintMissingComp" + ".expected.txt"));
     }
 
+    @Test
+    public void testCountWithNoReferenceOrIntervals() {
+        //Test for https://github.com/broadinstitute/gatk/issues/6212 just make sure we don't crash.
+        final String vcf = getTestFilePath("/CEU.trio.callsForVE.vcf");
+        final ArgumentsBuilder args = new ArgumentsBuilder();
+                args.addOutput( createTempFile("out",".stuff"))
+                        .addArgument("eval", vcf)
+                        .addArgument("EV", "CountVariants");
+
+        runCommandLine(args);
+    }
+
 }