add unit tests

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java

@@ -259,27 +259,24 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
         out.close();
     }
 
-    private int getPositionInTarget(final GenomeLoc interval, final List<GenomeLoc> hits) {
+    protected static int getPositionInTarget(final GenomeLoc interval, final List<GenomeLoc> targets) {
-        if (hits.size() > 0) {
+        if (targets.size() > 0) {
-            final GenomeLoc hit = hits.get(0);
+            final GenomeLoc target = targets.get(0);
 
             // interval is larger on both ends than the target -- return the maximum distance to either side as a negative number. (min of 2 negative numbers)
-            if (interval.getStart() < hit.getStart() && interval.getStop() > hit.getStop())
+            if (interval.getStart() < target.getStart() && interval.getStop() > target.getStop())
-                return Math.min(interval.getStart() - hit.getStart(),
+                return Math.min(target.getStart() - interval.getStart(), target.getStop() - interval.getStop());
-                                interval.getStop() - hit.getStop());
 
             // interval is a left overlap -- return a negative number representing the distance between the two starts
-            else if (interval.getStart() < hit.getStart())
+            else if (interval.getStart() < target.getStart())
-                return hit.getStart() - interval.getStart();
+                return interval.getStart() - target.getStart();
 
             // interval is a right overlap -- return a negative number representing the distance between the two stops
-            else if (interval.getStop() > hit.getStop())
+            else if (interval.getStop() > target.getStop())
-                return hit.getStop() - interval.getStop();
+                return target.getStop() - interval.getStop();
 
             // interval is fully contained -- return the smallest distance to the edge of the target (left or right) as a positive number
-            else
+            return Math.min(interval.getStart() - target.getStart(), target.getStop() - interval.getStop());
-                return Math.min(Math.abs(hit.getStart() - interval.getStart()),
-                                Math.abs(hit.getStop() - interval.getStop()));
         }
         // if there is no overlapping interval, return int min value.
         return Integer.MIN_VALUE;

protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java

@@ -46,6 +46,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.diagnostics.missing;
 
+import it.unimi.dsi.fastutil.objects.ObjectArrayList;
+import java.util.List;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.UnvalidatingGenomeLoc;
@@ -57,7 +59,6 @@ import org.testng.annotations.Test;
  * User: carneiro
  * Date: 9/20/13
  * Time: 3:59 PM
- * To change this template use File | Settings | File Templates.
  */
 public class QualifyMissingIntervalsUnitTest extends BaseTest {
     @Test(enabled = true)
@@ -92,4 +93,39 @@ public class QualifyMissingIntervalsUnitTest extends BaseTest {
         for (Metrics m : array)
             Assert.assertEquals(tool.interpret(m, smallInterval), QualifyMissingIntervals.Interpretation.SMALL_INTERVAL.toString());
     }
+
+    @Test(enabled = true)
+    void testGetPositionInTarget () {
+        final UnvalidatingGenomeLoc target = new UnvalidatingGenomeLoc("a", 0, 30, 50);
+        final List<GenomeLoc> targets = new ObjectArrayList<>(1);
+        targets.add(target);
+
+        // left overlap
+        UnvalidatingGenomeLoc interval = new UnvalidatingGenomeLoc("a", 0, 10, 50);
+        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), -20);
+
+        // right overlap
+        interval = new UnvalidatingGenomeLoc("a", 0, 40, 60);
+        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), -10);
+
+        // interval > target with short right tail
+        interval = new UnvalidatingGenomeLoc("a", 0, 10, 60);
+        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), -10);
+
+        // interval > target with short left tail
+        interval = new UnvalidatingGenomeLoc("a", 0, 10, 80);
+        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), -30);
+
+        // interval < target with short right tail
+        interval = new UnvalidatingGenomeLoc("a", 0, 32, 40);
+        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), 2);
+
+        // interval < target with short left tail
+        interval = new UnvalidatingGenomeLoc("a", 0, 40, 42);
+        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), 8);
+
+        // no overlap
+        interval = new UnvalidatingGenomeLoc("a", 0, 40, 42);
+        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, new ObjectArrayList<GenomeLoc>()), Integer.MIN_VALUE);
+    }
 }