Merge pull request #1452 from broadinstitute/pf_excludeIntervalPadding

addresses issue #1280 now interval padding works for exclude intervals

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java

@@ -88,6 +88,18 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         executeTest("testDiscordanceNoSampleSpecified--" + testFile, spec);
     }
 
+    @Test
+    public void testExcludeIntervalsPadding(){
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T SelectVariants -R " + hg19Reference + " -L 1:1715011-1734970 -XL 1:1725305 -ip 200 --variant "
+                        + b37hapmapGenotypes + " -o %s --no_cmdline_in_header",
+                1,
+                Arrays.asList("2e31c0be0d639d7110e639a11c03f4ca")
+        );
+
+        executeTest("testExcludeIntervalsPadding--", spec);
+    }
+
     @Test
     public void testRepeatedLineSelection() {
         String testfile = privateTestDir + "test.dup.vcf";

public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/interval/IntervalUtils.java

@@ -658,7 +658,7 @@ public class IntervalUtils {
 
         GenomeLocSortedSet excludeSortedSet = null;
         if (excludeIntervals != null && excludeIntervals.size() > 0) {
-            excludeSortedSet = loadIntervals(excludeIntervals, IntervalSetRule.UNION, intervalMergingRule, 0, genomeLocParser);
+            excludeSortedSet = loadIntervals(excludeIntervals, IntervalSetRule.UNION, intervalMergingRule, intervalPadding, genomeLocParser);
         }
         return new Pair<GenomeLocSortedSet, GenomeLocSortedSet>(includeSortedSet, excludeSortedSet);
     }