fix for unsigned int in CRAM tags, issue #322

samtools · Oct 23, 2015 · 0b259ff · 0b259ff
1 parent 7ae8940
commit 0b259ff
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Showing 4 changed files with 20 additions and 19 deletions.
diff --git a/src/java/htsjdk/samtools/SAMRecord.java b/src/java/htsjdk/samtools/SAMRecord.java
@@ -1203,7 +1203,7 @@ protected void setAttribute(final short tag, final Object value) {
 
     protected void setAttribute(final short tag, final Object value, final boolean isUnsignedArray) {
         if (value != null &&
-                !(value instanceof Byte || value instanceof Short || value instanceof Integer ||
+                !(value instanceof Byte || value instanceof Short || value instanceof Integer || value instanceof Long ||
                         value instanceof String || value instanceof Character || value instanceof Float ||
                         value instanceof byte[] || value instanceof short[] || value instanceof int[] ||
                         value instanceof float[])) {

diff --git a/src/java/htsjdk/samtools/cram/structure/ReadTag.java b/src/java/htsjdk/samtools/cram/structure/ReadTag.java
@@ -21,6 +21,8 @@
 import htsjdk.samtools.SAMFormatException;
 import htsjdk.samtools.SAMRecord.SAMTagAndValue;
 import htsjdk.samtools.SAMTagUtil;
+import htsjdk.samtools.SAMUtils;
+import htsjdk.samtools.SAMValidationError;
 import htsjdk.samtools.TagValueAndUnsignedArrayFlag;
 import htsjdk.samtools.util.StringUtil;
 
@@ -372,12 +374,7 @@ public static Object readSingleValue(final byte tagType,
             case 'A':
                 return (char) byteBuffer.get();
             case 'I':
-                final long val = byteBuffer.getInt() & 0xffffffffL;
-                if (val <= Integer.MAX_VALUE) {
-                    return (int) val;
-                }
-                throw new RuntimeException(
-                        "Tag value is too large to store as signed integer.");
+                return byteBuffer.getInt() & 0xffffffffL;
             case 'i':
                 return byteBuffer.getInt();
             case 's':

diff --git a/src/tests/java/htsjdk/samtools/SAMIntegerTagTest.java b/src/tests/java/htsjdk/samtools/SAMIntegerTagTest.java
@@ -68,22 +68,14 @@ public void testSAM() throws Exception {
         Assert.assertEquals(((Number) rec.getAttribute(INTEGER_TAG)).intValue(), 1);
     }
 
-    @Test(expectedExceptions = SAMException.class)
+    @Test
     public void testUnsignedIntegerBAM() throws Exception {
         SAMRecord rec = createSamRecord();
         final long val = 1l + Integer.MAX_VALUE;
         rec.setAttribute(UNSIGNED_INTEGER_TAG, val);
-        Assert.fail("Exception should have been thrown.");
-    }
-
-    /**
-     * Cannot store unsigned int in SAM text format.
-     */
-    @Test(expectedExceptions = SAMException.class)
-    public void testUnsignedIntegerSAM() throws Exception {
-        final SAMRecord rec = createSamRecord();
-        final long val = 1l + Integer.MAX_VALUE;
-        rec.setAttribute(UNSIGNED_INTEGER_TAG, val);
+        Object roundTripValue = rec.getAttribute(UNSIGNED_INTEGER_TAG);
+        Assert.assertTrue(roundTripValue instanceof Long);
+        Assert.assertEquals(roundTripValue, val);
     }
 
     @Test

diff --git a/src/tests/java/htsjdk/samtools/cram/structure/ReadTagTest.java b/src/tests/java/htsjdk/samtools/cram/structure/ReadTagTest.java
@@ -71,6 +71,18 @@ public void test () {
         Assert.assertEquals((byte[]) value, baValue);
     }
 
+    @Test
+    public void testUnsignedInt() {
+        long intValue = Integer.MAX_VALUE+1L;
+        byte[] data = ReadTag.writeSingleValue((byte) 'I', intValue, false);
+        ByteBuffer byteBuffer = ByteBuffer.wrap(data);
+        byteBuffer.order(ByteOrder.LITTLE_ENDIAN);
+        Object value = ReadTag.readSingleValue((byte) 'I', byteBuffer);
+        Assert.assertTrue(value instanceof Long);
+        long lValue = (Long)value;
+        Assert.assertEquals (lValue & 0xFFFFFFFF, intValue);
+    }
+
     @Test
     public void testParallelReadTag() throws Exception {
         // NOTE: testng 5.5 (circa 2007) doesn't support parallel data providers, but modern versions do.