Added further integration tests for rod-based intervals that deal with more complex cases. Good call by Mark to test the empty VCF example because we were failing on it; fixed.

public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -385,7 +385,7 @@ public class GenomeAnalysisEngine {
         // this was very likely unintentional, the user should be informed of this. Note that this is different
         // from the case where intervals == null, which indicates either that there were no interval arguments,
         // or that -L all was specified.
-        if ( intervals != null && intervals.isEmpty() ) {
+        if ( intervals != null && intervals.isEmpty() && argCollection.excludeIntervals != null ) {
             throw new ArgumentException("The given combination of -L and -XL options results in an empty set. " +
                                         "No intervals to process.");
         }

public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java

@@ -109,20 +109,6 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
         };
     }
 
-    @Test(expectedExceptions=UserException.class, dataProvider="invalidIntervalTestData")
-    public void testInvalidBedIntervalHandling(GenomeAnalysisEngine testEngine, GenomeLocParser genomeLocParser,
-                                               String contig, int intervalStart, int intervalEnd ) throws Exception {
-        // We need to adjust intervalStart, since BED intervals are 0-based. We don't need to adjust intervalEnd,
-        // since the ending point is an open interval.
-        File bedFile = createTempFile("testInvalidBedIntervalHandling", ".bed",
-                                      String.format("%s %d %d", contig, intervalStart -1, intervalEnd));
-
-        List<IntervalBinding<Feature>> intervalArgs = new ArrayList<IntervalBinding<Feature>>(1);
-        intervalArgs.add(new IntervalBinding<Feature>(bedFile.getAbsolutePath()));
-
-        testEngine.loadIntervals(intervalArgs, IntervalSetRule.UNION);
-    }
-
     @Test(expectedExceptions=UserException.class, dataProvider="invalidIntervalTestData")
     public void testInvalidPicardIntervalHandling(GenomeAnalysisEngine testEngine, GenomeLocParser genomeLocParser,
                                                   String contig, int intervalStart, int intervalEnd ) throws Exception {
@@ -154,6 +140,11 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
         testEngine.loadIntervals(intervalArgs, IntervalSetRule.UNION);
     }
 
+
+
+
+
+
     private File createTempFile( String tempFilePrefix, String tempFileExtension, String... lines ) throws Exception {
         File tempFile = File.createTempFile(tempFilePrefix, tempFileExtension);
         tempFile.deleteOnExit();

public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java

@@ -25,6 +25,8 @@
 package org.broadinstitute.sting.utils.interval;
 
 import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.sting.commandline.ArgumentException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.testng.annotations.Test;
 
 import java.io.File;
@@ -161,4 +163,79 @@ public class IntervalIntegrationTest extends WalkerTest {
                         Arrays.asList(md5));
         executeTest("testMixedIntervalMerging", spec);
     }
+
+    @Test(enabled = true)
+    public void testComplexVCF() {
+        String md5 = "166d77ac1b46a1ec38aa35ab7e628ab5";
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T CountLoci" +
+                        " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
+                        " -R " + hg18Reference +
+                        " -o %s" +
+                        " -L " + validationDataLocation + "intervalTest.3.vcf",
+                        1, // just one output file
+                        Arrays.asList(md5));
+        executeTest("testComplexVCF", spec);
+    }
+
+    @Test(enabled = true)
+    public void testMergingWithComplexVCF() {
+        String md5 = "6d7fce9fee471194aa8b5b6e47267f03";
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T CountLoci" +
+                        " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
+                        " -R " + hg18Reference +
+                        " -o %s" +
+                        " -L " + validationDataLocation + "intervalTest.1.vcf" +
+                        " -XL " + validationDataLocation + "intervalTest.3.vcf",
+                        1, // just one output file
+                        Arrays.asList(md5));
+        executeTest("testMergingWithComplexVCF", spec);
+    }
+
+    @Test(enabled = true, expectedExceptions = RuntimeException.class)
+    public void testEmptyVCFError() {
+        String md5 = "";
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T CountLoci" +
+                        " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
+                        " -R " + hg18Reference +
+                        " -o %s" +
+                        " -L " + validationDataLocation + "intervalTest.empty.vcf",
+                        1, // just one output file
+                        Arrays.asList(md5));
+        executeTest("testEmptyVCFError", spec);
+    }
+
+    @Test(enabled = true)
+    public void testEmptyVCFNoError() {
+        String md5 = "";
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T CountLoci" +
+                        " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
+                        " -R " + hg18Reference +
+                        " -o %s" +
+                        " -U ALLOW_EMPTY_INTERVAL_LIST" +
+                        " -L " + validationDataLocation + "intervalTest.empty.vcf",
+                        1, // just one output file
+                        Arrays.asList(md5));
+        executeTest("testEmptyVCFNoError", spec);
+    }
+
+    @Test(enabled = true, expectedExceptions = RuntimeException.class)
+    public void testIncludeExcludeIsTheSame() {
+        String md5 = "";
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T CountLoci" +
+                        " -I " + validationDataLocation + "OV-0930.normal.chunk.bam" +
+                        " -R " + hg18Reference +
+                        " -o %s" +
+                        " -L " + validationDataLocation + "intervalTest.1.vcf" +
+                        " -XL " + validationDataLocation + "intervalTest.1.vcf",
+                        1, // just one output file
+                        Arrays.asList(md5));
+        executeTest("testIncludeExcludeIsTheSame", spec);
+    }
+
+
 }