Fix bug in IntervalList.getUniqueIntervals that caused missing interv…

…al names (#1265)

* Fixes a bug in IntervalList.getUniqueIntervals() where two intervals with identical coordinates didn't correctly keep both interval names in the merged interval.  This was because the intervals were being stored in a Set and Interval doesn't examine name in it's equals() method.  Now both names will be correctly concatenated.

src/main/java/htsjdk/samtools/util/IntervalList.java

@@ -273,7 +273,7 @@ public static List<Interval> getUniqueIntervals(final IntervalList list, final b
         }
 
         final List<Interval> unique = new ArrayList<>();
-        final TreeSet<Interval> toBeMerged = new TreeSet<>();
+        final List<Interval> toBeMerged = new ArrayList<>();
         Interval current = null;
 
         for (final Interval next : intervals) {
@@ -383,11 +383,12 @@ private static List<Interval> breakIntervalAtBandMultiples(final Interval interv
     /**
      * Merges a sorted collection of intervals and optionally concatenates unique names or takes the first name.
      */
-    static Interval merge(final SortedSet<Interval> intervals, final boolean concatenateNames) {
-        final String chrom = intervals.first().getContig();
-        int start = intervals.first().getStart();
-        int end = intervals.last().getEnd();
-        final boolean neg = intervals.first().isNegativeStrand();
+    static Interval merge(final Iterable<Interval> intervals, final boolean concatenateNames) {
+        final Interval first = intervals.iterator().next();
+        final String chrom = first.getContig();
+        int start = first.getStart();
+        int end = start;
+        final boolean neg = first.isNegativeStrand();
         final LinkedHashSet<String> names = new LinkedHashSet<>();
         final String name;
 

src/test/java/htsjdk/samtools/util/IntervalListTest.java

@@ -238,6 +238,21 @@ public void testUnionIntervalLists(final List<IntervalList> lists, final Interva
                 CollectionUtil.makeCollection(list.iterator()));
     }
 
+
+    @Test
+    public void testUnionSamePosition() {
+        final IntervalList iList= new IntervalList(fileHeader);
+
+        final List<Interval> intervals = Arrays.asList(
+                new Interval("1", 2, 100, true, "test1"),
+                new Interval("1", 2, 100, true, "test2")
+        );
+        iList.addall(intervals);
+        final List<Interval> uniqued = iList.uniqued().getIntervals();
+        Assert.assertEquals(uniqued.size(),1);
+        Assert.assertEquals(uniqued.get(0).getName(),"test1|test2");
+    }
+
     @DataProvider(name = "invertData")
     public Object[][] invertData() {
         final IntervalList invert1 = new IntervalList(fileHeader);