From a5acb0b7a6763659a73881f6c7d1527082126e5e Mon Sep 17 00:00:00 2001
From: droazen <droazen@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 4 Apr 2011 18:41:55 +0000
Subject: [PATCH] Fix for bug GSA-314: Detect -XL and -L incompatibility. An
 ArgumentException is now thrown if the combination of -L and -XL intervals
 specified on the command line results in an empty interval set after set
 subtraction.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5571 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/GenomeAnalysisEngine.java       | 18 ++++++++++++++++++
 .../gatk/GenomeAnalysisEngineUnitTest.java     | 17 +++++++++++++++--
 2 files changed, 33 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 239b9ad1a..9523ae50b 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -118,6 +118,14 @@ public class GenomeAnalysisEngine {
      */
     private GenomeLocSortedSet intervals = null;
 
+    /**
+     * Explicitly assign the interval set to use for this traversal (for unit testing purposes)
+     * @param intervals set of intervals to use for this traversal
+     */
+    public void setIntervals( GenomeLocSortedSet intervals ) {
+        this.intervals = intervals;
+    }
+
     /**
      * Collection of inputs used by the engine.
      */
@@ -395,6 +403,16 @@ public class GenomeAnalysisEngine {
             if(intervals != null && getIntervals().contains(GenomeLoc.UNMAPPED))
                 throw new ArgumentException("Interval list specifies unmapped region.  Only read walkers may include the unmapped region.");
         }
+
+        // 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,
+        // 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. " +
+                                        "No intervals to process.");
+        }
     }
 
     /**
diff --git a/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java b/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
index 30bf2db07..7242f88ec 100644
--- a/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
@@ -24,12 +24,13 @@
 
 package org.broadinstitute.sting.gatk;
 
-import org.testng.annotations.Test;
-
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.commandline.ArgumentException;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
 import org.broadinstitute.sting.commandline.Tags;
+import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+
+import org.testng.annotations.Test;
 
 import java.io.File;
 import java.util.ArrayList;
@@ -66,4 +67,16 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
         testEngine.setSAMFileIDs(samFiles);
         testEngine.checkForDuplicateSamFiles();
     }
+
+    @Test(expectedExceptions=ArgumentException.class)
+    public void testEmptyIntervalSetHandling() throws Exception {
+        GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
+
+        WalkerManager walkerManager = new WalkerManager();
+        testEngine.setWalker(walkerManager.createByName("PrintReadsWalker"));
+
+        testEngine.setIntervals(new GenomeLocSortedSet(null));
+
+        testEngine.validateSuppliedIntervals();
+    }
 }