Fixed a bug where invalid feature file intervals weren't being checke…

…d for validity against the sequence dictionary (#7295)

* Fixed a bug where invalid feature file intervals weren't being checked for validity against the sequence dictionary

Resolves #7289

src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/VariantSummary.java

@@ -167,9 +167,10 @@ private boolean overlapsKnownCNV(VariantContext cnv, VariantEvalContext context)
         if ( knownCNVs != null ) {
             List<Feature> overlaps = context.queryFeaturesIncludingOverlapping(knownCNVs, new SimpleInterval(cnv.getContig(), cnv.getStart(), cnv.getEnd()));
             GenomeLocParser parser = new GenomeLocParser(context.getSequenceDictionaryForDrivingVariants());
-            GenomeLoc loc1 = parser.createGenomeLoc(cnv);
+            // NOTE: by using this overload we are explicitly allowing variants that don't correctly overlap the reference intervals
+            GenomeLoc loc1 = parser.createGenomeLoc(cnv, false);
             for (Feature vc : overlaps) {
-                GenomeLoc loc2 = parser.createGenomeLoc(vc);
+                GenomeLoc loc2 = parser.createGenomeLoc(vc, false);
                 final double overlapP = loc1.reciprocialOverlapFraction(loc2);
                 if ( overlapP > MIN_CNV_OVERLAP )
                     return true;

src/main/java/org/broadinstitute/hellbender/utils/GenomeLocParser.java

@@ -393,7 +393,15 @@ public GenomeLoc createGenomeLoc( final GATKRead read ) {
      * @return
      */
     public GenomeLoc createGenomeLoc(final Feature feature) {
-        return createGenomeLoc(feature.getContig(), feature.getStart(), feature.getEnd());
+        return createGenomeLoc(feature.getContig(), feature.getStart(), feature.getEnd(), true);
+    }
+
+    /**
+     * Creates a GenomeLoc from a Tribble feature
+     * @return
+     */
+    public GenomeLoc createGenomeLoc(final Feature feature, final boolean mustBeOnReference) {
+        return createGenomeLoc(feature.getContig(), feature.getStart(), feature.getEnd(), mustBeOnReference);
     }
 
     /**
@@ -405,7 +413,7 @@ public GenomeLoc createGenomeLoc(final Feature feature) {
      */
     public GenomeLoc createGenomeLoc(final Locatable locatable) {
         Utils.nonNull(locatable, "the input locatable cannot be null");
-        return createGenomeLoc(locatable.getContig(), locatable.getStart(), locatable.getEnd());
+        return createGenomeLoc(locatable.getContig(), locatable.getStart(), locatable.getEnd(), false);
     }
 
     /**

src/main/java/org/broadinstitute/hellbender/utils/IntervalUtils.java

@@ -357,7 +357,7 @@ public static List<GenomeLoc> featureFileToIntervals( final GenomeLocParser pars
             final List<GenomeLoc> featureIntervals = new ArrayList<>();
 
             for ( final Feature feature : dataSource ) {
-                featureIntervals.add(parser.createGenomeLoc(feature));
+                featureIntervals.add(parser.createGenomeLoc(feature, true));
             }
             return featureIntervals;
         }

src/test/java/org/broadinstitute/hellbender/utils/IntervalUtilsUnitTest.java

@@ -608,6 +608,29 @@ public void testUseAllHG38ContigsInIntervalQuery() {
         );
     }
 
+    @Test(expectedExceptions = UserException.MalformedGenomeLoc.class)
+    public void testReasonableErrorWithInvalidBedFile() throws IOException {
+        File outOfBoundsBedFile = new File(INTERVAL_TEST_DATA + "bad_hg19_interval_span.bed"); // this bed file has a bogus interval the extends past the end chr1 and should throw an exception
+        // this should throw a user exception because of the invalid interval
+        IntervalUtils.parseIntervalArguments(hg19GenomeLocParser, outOfBoundsBedFile.getAbsolutePath());
+    }
+
+    @Test(expectedExceptions = UserException.MalformedGenomeLoc.class)
+    public void testReasonableErrorWithInvalidListFile() throws IOException {
+        File outOfBoundListFile = new File(INTERVAL_TEST_DATA + "bad_hg19_example_intervals.list"); // this list file has a bogus interval the extends past the end chr1 and should throw an exception
+        // this should throw a user exception because of the invalid interval
+        IntervalUtils.parseIntervalArguments(hg19GenomeLocParser, outOfBoundListFile.getAbsolutePath());
+    }
+
+    //NOTE the .interval_list style argument input gets handled differently from the other -L inputs but we still get a reasonable exception in this case
+    @Test(expectedExceptions = UserException.MalformedFile.class)
+    public void testReasonableErrorWithInvalidPicardListFile() throws IOException {
+        File outOfBoundsIntervalListFile = new File(INTERVAL_TEST_DATA + "bad_hg19.interval_list"); // this list file has a bogus interval the extends past the end chr1 and should throw an exception
+        // this should throw a user exception because of the invalid interval
+        IntervalUtils.parseIntervalArguments(hg19GenomeLocParser, outOfBoundsIntervalListFile.getAbsolutePath());
+    }
+
+
     @Test
     public void testResolveAmbiguousIntervalQueryUsingBEDFormat() throws IOException {
         // For the rare case where an interval query is ambiguous, make sure it can be resolved by using a bed file.