Merged bug fix from Stable into Unstable

public/java/src/net/sf/samtools/GATKBAMFileSpan.java

@@ -143,10 +143,14 @@ public class GATKBAMFileSpan extends BAMFileSpan {
         List<GATKChunk> mergedUnion = new ArrayList<GATKChunk>();
         GATKChunk currentChunk = unmergedUnion.remove();
         while(!unmergedUnion.isEmpty()) {
-            // Find the end of this range of chunks.
-            while(!unmergedUnion.isEmpty() && currentChunk.getChunkEnd() >= unmergedUnion.peek().getChunkStart()) {
+
+            // While the current chunk can be merged with the next chunk:
+            while( ! unmergedUnion.isEmpty() &&
+                   (currentChunk.overlaps(unmergedUnion.peek()) || currentChunk.isAdjacentTo(unmergedUnion.peek())) ) {
+
+                // Merge the current chunk with the next chunk:
                 GATKChunk nextChunk = unmergedUnion.remove();
-                currentChunk = new GATKChunk(currentChunk.getChunkStart(),nextChunk.getChunkEnd());
+                currentChunk = currentChunk.merge(nextChunk);
             }
             // Add the accumulated range.
             mergedUnion.add(currentChunk);

public/java/src/net/sf/samtools/GATKChunk.java

@@ -100,4 +100,16 @@ public class GATKChunk extends Chunk {
         final int offsetSpan = (int)((getChunkEnd()&0xFFFF)-(getChunkStart()&0xFFFF));
         return chunkSpan + offsetSpan;
     }
+
+    /**
+     * Merges two chunks together. The caller is responsible for testing whether the
+     * chunks overlap/are adjacent before calling this method!
+     *
+     * @param other the chunk to merge with this chunk
+     * @return a new chunk representing the union of the two chunks (provided the chunks were
+     *         overlapping/adjacent)
+     */
+    public GATKChunk merge ( GATKChunk other ) {
+        return new GATKChunk(Math.min(getChunkStart(), other.getChunkStart()), Math.max(getChunkEnd(), other.getChunkEnd()));
+    }
 }

public/java/test/net/sf/samtools/GATKBAMFileSpanUnitTest.java

@@ -50,7 +50,10 @@ public class GATKBAMFileSpanUnitTest {
     }
 
     @Test
-    public void testUnionOfOverlappingFileSpans() {
+    public void testUnionOfContiguousFileSpans() {
+        // Region 1 ends at position adjacent to Region 2 start:
+        // |---1----|---2----|
+
         GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,1<<16));
         GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|65535));
         GATKBAMFileSpan union = regionOne.union(regionTwo);
@@ -58,6 +61,71 @@ public class GATKBAMFileSpanUnitTest {
         Assert.assertEquals(union.getGATKChunks().get(0),new GATKChunk(0,(1<<16)|65535));
     }
 
+    @Test
+    public void testUnionOfFileSpansFirstRegionEndsWithinSecondRegion() {
+        // Region 1 ends within Region 2:
+        //        |---2----|
+        // |---1----|
+
+        GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,(1<<16)|32767));
+        GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|65535));
+        GATKBAMFileSpan union = regionOne.union(regionTwo);
+        Assert.assertEquals(union.getGATKChunks().size(),1,"Elements to be merged were not.");
+        Assert.assertEquals(union.getGATKChunks().get(0),new GATKChunk(0,(1<<16)|65535));
+    }
+
+    @Test
+    public void testUnionOfFileSpansFirstRegionEndsAtSecondRegionEnd() {
+        // Region 1 ends at Region 2 end:
+        //        |---2----|
+        // |---1-----------|
+
+        GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,(1<<16)|65535));
+        GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|65535));
+        GATKBAMFileSpan union = regionOne.union(regionTwo);
+        Assert.assertEquals(union.getGATKChunks().size(),1,"Elements to be merged were not.");
+        Assert.assertEquals(union.getGATKChunks().get(0),new GATKChunk(0,(1<<16)|65535));
+    }
+
+    @Test
+    public void testUnionOfFileSpansFirstRegionEndsAfterSecondRegionEnd() {
+        // Region 1 ends after Region 2 end:
+        //        |---2----|
+        // |---1---------------|
+
+        GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(0,(1<<16)|65535));
+        GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|32767));
+        GATKBAMFileSpan union = regionOne.union(regionTwo);
+        Assert.assertEquals(union.getGATKChunks().size(),1,"Elements to be merged were not.");
+        Assert.assertEquals(union.getGATKChunks().get(0),new GATKChunk(0,(1<<16)|65535));
+    }
+
+    @Test
+    public void testUnionOfFileSpansFirstRegionStartsAtSecondRegionStart() {
+        // Region 1 starts at Region 2 start, but ends before Region 2:
+        // |---2--------|
+        // |---1----|
+
+        GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|32767));
+        GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|65535));
+        GATKBAMFileSpan union = regionOne.union(regionTwo);
+        Assert.assertEquals(union.getGATKChunks().size(),1,"Elements to be merged were not.");
+        Assert.assertEquals(union.getGATKChunks().get(0),new GATKChunk(1<<16,(1<<16)|65535));
+    }
+
+    @Test
+    public void testUnionOfFileSpansFirstRegionEqualToSecondRegion() {
+        // Region 1 and Region 2 represent the same region:
+        // |---2----|
+        // |---1----|
+
+        GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|65535));
+        GATKBAMFileSpan regionTwo = new GATKBAMFileSpan(new GATKChunk(1<<16,(1<<16)|65535));
+        GATKBAMFileSpan union = regionOne.union(regionTwo);
+        Assert.assertEquals(union.getGATKChunks().size(),1,"Elements to be merged were not.");
+        Assert.assertEquals(union.getGATKChunks().get(0),new GATKChunk(1<<16,(1<<16)|65535));
+    }
+
     @Test
     public void testUnionOfStringOfFileSpans() {
         GATKBAMFileSpan regionOne = new GATKBAMFileSpan(new GATKChunk[] { new GATKChunk(0,1<<16), new GATKChunk(2<<16,3<<16) });