Allow processing of empty intervals, but warn user when this case is encountered.

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

@@ -383,11 +383,9 @@ public class GenomeAnalysisEngine {
         // If intervals is non-null and empty at this point, it means that the list of intervals to process
         // was filtered down to an empty set (eg., the user specified something like -L chr1 -XL chr1). Since
         // 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,
+        // from the case where intervals == null, which indicates that there were no interval arguments.
-        // or that -L all was specified.
         if ( intervals != null && intervals.isEmpty() ) {
-            throw new ArgumentException("The given combination of -L and -XL options results in an empty set. " +
+            logger.warn("The given combination of -L and -XL options results in an empty set.  No intervals to process.");
-                                        "No intervals to process.");
         }
     }
 
@@ -610,17 +608,12 @@ public class GenomeAnalysisEngine {
      */
     protected GenomeLocSortedSet loadIntervals( List<IntervalBinding<Feature>> argList, IntervalSetRule rule ) {
 
-        boolean allowEmptyIntervalList = (argCollection.unsafe == ValidationExclusion.TYPE.ALLOW_EMPTY_INTERVAL_LIST ||
-                                          argCollection.unsafe == ValidationExclusion.TYPE.ALL);
-
         List<GenomeLoc> allIntervals = new ArrayList<GenomeLoc>(0);
         for ( IntervalBinding intervalBinding : argList ) {
             List<GenomeLoc> intervals = intervalBinding.getIntervals(this);
 
-            if ( !allowEmptyIntervalList && intervals.isEmpty() ) {
+            if ( intervals.isEmpty() ) {
-                throw new UserException("The interval file " + intervalBinding.getSource() + " contains no intervals " +
+                logger.warn("The interval file " + intervalBinding.getSource() + " contains no intervals that could be parsed.");
-                                        "that could be parsed, and the unsafe operation ALLOW_EMPTY_INTERVAL_LIST has " +
-                                        "not been enabled");
             }
 
             allIntervals = IntervalUtils.mergeListsBySetOperator(intervals, allIntervals, rule);

public/java/src/org/broadinstitute/sting/gatk/arguments/ValidationExclusion.java

@@ -37,7 +37,6 @@ public class ValidationExclusion {
 
     public enum TYPE {
         ALLOW_UNINDEXED_BAM,        // allow bam files that do not have an index; we'll traverse them using monolithic shard
-        ALLOW_EMPTY_INTERVAL_LIST,  // allow the user to pass in an empty interval list
         ALLOW_UNSET_BAM_SORT_ORDER, // assume that the bam is sorted, even if the SO (sort-order) flag is not set
         NO_READ_ORDER_VERIFICATION, // do not validate that the reads are in order as we take them from the bam file
         ALLOW_SEQ_DICT_INCOMPATIBILITY, // allow dangerous, but not fatal, sequence dictionary incompabilities

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

@@ -82,7 +82,7 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
         testEngine.checkForDuplicateSamFiles();
     }
 
-    @Test(expectedExceptions=ArgumentException.class)
+    @Test
     public void testEmptyIntervalSetHandling() throws Exception {
         GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
 
@@ -109,7 +109,7 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
         };
     }
 
-    @Test(expectedExceptions=UserException.class, dataProvider="invalidIntervalTestData")
+    @Test(dataProvider="invalidIntervalTestData")
     public void testInvalidPicardIntervalHandling(GenomeAnalysisEngine testEngine, GenomeLocParser genomeLocParser,
                                                   String contig, int intervalStart, int intervalEnd ) throws Exception {
 
@@ -140,11 +140,6 @@ 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

@@ -83,7 +83,7 @@ public class IntervalIntegrationTest extends WalkerTest {
         executeTest("testUnmappedReadInclusion",spec);
     }
 
-    @Test(enabled = true)
+    @Test(enabled = false)
     public void testUnmappedReadExclusion() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T PrintReads" +
@@ -191,8 +191,8 @@ public class IntervalIntegrationTest extends WalkerTest {
         executeTest("testMergingWithComplexVCF", spec);
     }
 
-    @Test(enabled = true, expectedExceptions = RuntimeException.class)
+    @Test(enabled = true)
-    public void testEmptyVCFNoUnsafe() {
+    public void testEmptyVCF() {
         String md5 = "";
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T CountLoci" +
@@ -205,22 +205,7 @@ public class IntervalIntegrationTest extends WalkerTest {
         executeTest("testEmptyVCFError", spec);
     }
 
-    @Test(enabled = true, expectedExceptions = RuntimeException.class)
+    @Test(enabled = true)
-    public void testEmptyVCFWithUnsafe() {
-        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(