split populateSlicesAndIndexingParametersTest into 1 and 2 slice vers…

…ions
samtools · Mar 15, 2019 · 63a30b5 · 63a30b5
1 parent 336fe6b
commit 63a30b5
Showing 1 changed file with 66 additions and 13 deletions.
diff --git a/src/test/java/htsjdk/samtools/cram/structure/ContainerTest.java b/src/test/java/htsjdk/samtools/cram/structure/ContainerTest.java
@@ -156,19 +156,70 @@ public void getSpansTest(final List<CramCompressionRecord> records,
 
     // this is part of the deserialization process, and supports index creation
 
+    // single slice
+
     @Test
-    public static void populateSlicesAndIndexingParametersTest() {
+    public static void populateSlicesAndIndexingParametersTest1() {
         // this container starts 100,000 bytes into the CRAM stream
         final int containerStreamByteOffset = 100000;
 
         // this Container consists of:
         // a header of size 1234 bytes
-        // a Slice of size 789 bytes
-        // a Slice of size 5555 bytes
+        // a Slice of size 6262 bytes
 
         final int containerHeaderSize = 1234;
-        final int slice0size = 789;
+        final int sliceSize = 6262;
+
+        final Container container = createContainer1(containerStreamByteOffset, containerHeaderSize, sliceSize);
+
+        assertSliceIndexingParams(container.slices[0], 0, containerStreamByteOffset, sliceSize, containerHeaderSize);
+    }
+
+    // two slices
+
+    @Test
+    public static void populateSlicesAndIndexingParametersTest2() {
+        // this container starts 200,000 bytes into the CRAM stream
+        final int containerStreamByteOffset = 200000;
+
+        // this Container consists of:
+        // a header of size 3234 bytes
+        // a Slice of size 7890 bytes
+        // a Slice of size 5555 bytes
+
+        final int containerHeaderSize = 3234;
+        final int slice0size = 7890;
         final int slice1size = 5555;
+
+        final Container container = createContainer2(containerStreamByteOffset, containerHeaderSize, slice0size, slice1size);
+
+        assertSliceIndexingParams(container.slices[0], 0, containerStreamByteOffset, slice0size, containerHeaderSize);
+        assertSliceIndexingParams(container.slices[1], 1, containerStreamByteOffset, slice1size, containerHeaderSize + slice0size);
+    }
+
+    private static Container createContainer1(final int containerStreamByteOffset,
+                                              final int containerHeaderSize,
+                                              final int slice0size) {
+        final ReferenceContext refContext = new ReferenceContext(0);
+
+        final Container container = new Container(refContext);
+        container.offset = containerStreamByteOffset;
+        container.containerByteSize = slice0size;
+        container.landmarks = new int[]{
+                containerHeaderSize,                // beginning of slice
+        };
+
+        final ArrayList<Slice> slices = new ArrayList<Slice>() {{
+            add(new Slice(refContext));
+        }};
+        container.populateSlicesAndIndexingParameters(slices);
+        return container;
+    }
+
+    private static Container createContainer2(final int containerStreamByteOffset,
+                                              final int containerHeaderSize,
+                                              final int slice0size,
+                                              final int slice1size) {
         final int containerDataSize = slice0size + slice1size;
 
         final ReferenceContext refContext = new ReferenceContext(0);
@@ -186,15 +237,17 @@ public static void populateSlicesAndIndexingParametersTest() {
             add(new Slice(refContext));
         }};
         container.populateSlicesAndIndexingParameters(slices);
+        return container;
+    }
 
-        Assert.assertEquals(container.slices[0].index, 0);
-        Assert.assertEquals(container.slices[0].containerOffset, containerStreamByteOffset);
-        Assert.assertEquals(container.slices[0].size, slice0size);
-        Assert.assertEquals(container.slices[0].offset, containerHeaderSize);
-
-        Assert.assertEquals(container.slices[1].index, 1);
-        Assert.assertEquals(container.slices[1].containerOffset, containerStreamByteOffset);
-        Assert.assertEquals(container.slices[1].size, slice1size);
-        Assert.assertEquals(container.slices[1].offset, containerHeaderSize + slice0size);
+    private static void assertSliceIndexingParams(final Slice slice,
+                                                  final int expectedIndex,
+                                                  final int expectedContainerOffset,
+                                                  final int expectedSize,
+                                                  final int expectedOffset) {
+        Assert.assertEquals(slice.index, expectedIndex);
+        Assert.assertEquals(slice.containerOffset, expectedContainerOffset);
+        Assert.assertEquals(slice.size, expectedSize);
+        Assert.assertEquals(slice.offset, expectedOffset);
     }
 }