Bugfix for BAM index bins

src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java

@@ -107,6 +107,10 @@ public static int getNumIndexLevels() {
      * @return The first bin in this level.
      */
     public static int getFirstBinInLevel(final int levelNumber) {
+        if (levelNumber >= getNumIndexLevels()) {
+            throw new SAMException("Level number is too big (" + levelNumber + ").");
+        }
+
         return GenomicIndexUtil.LEVEL_STARTS[levelNumber];
     }
 
@@ -116,10 +120,15 @@ public static int getFirstBinInLevel(final int levelNumber) {
      * @return The size (number of possible bins) of the given level.
      */
     public int getLevelSize(final int levelNumber) {
-        if(levelNumber == getNumIndexLevels())
-            return GenomicIndexUtil.MAX_BINS+1-GenomicIndexUtil.LEVEL_STARTS[levelNumber];
-        else
-            return GenomicIndexUtil.LEVEL_STARTS[levelNumber+1]-GenomicIndexUtil.LEVEL_STARTS[levelNumber];
+        if (levelNumber >= getNumIndexLevels()) {
+            throw new SAMException("Level number is too big (" + levelNumber + ").");
+        }
+
+        if (levelNumber == getNumIndexLevels()-1) {
+            return GenomicIndexUtil.MAX_BINS - GenomicIndexUtil.LEVEL_STARTS[levelNumber] - 1;
+        } else {
+            return GenomicIndexUtil.LEVEL_STARTS[levelNumber + 1] - GenomicIndexUtil.LEVEL_STARTS[levelNumber];
+        }
     }
 
     /**
@@ -365,30 +374,6 @@ protected int getMaxAddressibleGenomicLocation() {
         return GenomicIndexUtil.BIN_GENOMIC_SPAN;
     }
 
-    /**
-     * Get candidate bins for the specified region
-     * @param startPos 1-based start of target region, inclusive.
-     * @param endPos 1-based end of target region, inclusive.
-     * @return bit set for each bin that may contain SAMRecords in the target region.
-     */
-    protected BitSet regionToBins(final int startPos, final int endPos) {
-        final int maxPos = 0x1FFFFFFF;
-        final int start = (startPos <= 0) ? 0 : (startPos-1) & maxPos;
-        final int end = (endPos <= 0) ? maxPos : (endPos-1) & maxPos;
-        if (start > end) {
-            return null;
-        }
-        int k;
-        final BitSet bitSet = new BitSet(GenomicIndexUtil.MAX_BINS);
-        bitSet.set(0);
-        for (k =    1 + (start>>26); k <=    1 + (end>>26); ++k) bitSet.set(k);
-        for (k =    9 + (start>>23); k <=    9 + (end>>23); ++k) bitSet.set(k);
-        for (k =   73 + (start>>20); k <=   73 + (end>>20); ++k) bitSet.set(k);
-        for (k =  585 + (start>>17); k <=  585 + (end>>17); ++k) bitSet.set(k);
-        for (k = 4681 + (start>>14); k <= 4681 + (end>>14); ++k) bitSet.set(k);
-        return bitSet;
-    }
-
     /**
      * @deprecated Invoke {@link Chunk#optimizeChunkList} directly.
      */

src/test/java/htsjdk/samtools/AbstractBAMFileIndexTest.java

@@ -2,12 +2,16 @@
 
 import htsjdk.HtsjdkTest;
 import htsjdk.samtools.seekablestream.SeekableStream;
+import org.testng.Assert;
 import org.testng.annotations.Test;
 
+import java.io.File;
 import java.io.IOException;
 
 public class AbstractBAMFileIndexTest extends HtsjdkTest {
 
+    private static final AbstractBAMFileIndex afi = new DiskBasedBAMFileIndex(new File("src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai"), null);
+
     /**
      * @see <a href="https://github.com/samtools/htsjdk/issues/73">https://github.com/samtools/htsjdk/issues/73</a>
      */
@@ -60,4 +64,39 @@ public int read() throws IOException {
         buffer.readInteger();
         buffer.readBytes(new byte[10000]);
     }
+
+    @Test
+    public static void testGetNumIndexLevels() {
+        Assert.assertEquals(AbstractBAMFileIndex.getNumIndexLevels(), 6);
+    }
+
+    @Test
+    public static void testGetFirstBinInLevelOK() {
+        Assert.assertEquals(AbstractBAMFileIndex.getFirstBinInLevel(0), 0);
+        Assert.assertEquals(AbstractBAMFileIndex.getFirstBinInLevel(1), 1);
+        Assert.assertEquals(AbstractBAMFileIndex.getFirstBinInLevel(2), 9);
+        Assert.assertEquals(AbstractBAMFileIndex.getFirstBinInLevel(3), 73);
+        Assert.assertEquals(AbstractBAMFileIndex.getFirstBinInLevel(4), 585);
+        Assert.assertEquals(AbstractBAMFileIndex.getFirstBinInLevel(5), 4681);
+    }
+
+    @Test (expectedExceptions = SAMException.class)
+    public static void testGetFirstBinInLevelFail() {
+        AbstractBAMFileIndex.getFirstBinInLevel(6);
+    }
+
+    @Test
+    public static void testGetLevelSizeOK() {
+        Assert.assertEquals(afi.getLevelSize(0), 1);
+        Assert.assertEquals(afi.getLevelSize(1), 8);
+        Assert.assertEquals(afi.getLevelSize(2), 64);
+        Assert.assertEquals(afi.getLevelSize(3), 512);
+        Assert.assertEquals(afi.getLevelSize(4), 4096);
+        Assert.assertEquals(afi.getLevelSize(5), 32768);
+    }
+
+    @Test (expectedExceptions = SAMException.class)
+    public static void testGetLevelSizeFail() {
+        afi.getLevelSize(6);
+    }
 }