Adding support for 0-length B arrays in SAM files to conform to 1.6 spec

src/test/java/htsjdk/samtools/TextTagCodecTest.java

@@ -41,7 +41,6 @@ public void testEmptyAndNonEmptyArrayEncoding(Object array, boolean isSigned, St
                 ? textTagCodec.encode(tagName, array)
                 : textTagCodec.encodeUnsignedArray(tagName, array);
         Assert.assertEquals(encodedTag, expectedTag);
-
     }
 
     @DataProvider

src/test/java/htsjdk/tribble/TestUtils.java

@@ -64,6 +64,4 @@ public static Path getTribbleFileInJimfs(String vcf, String index, FileSystem fi
         }
         return Files.copy(vcfPath, vcfDestination);
     }
-
-
 }

src/test/java/htsjdk/utils/TestNGUtils.java

@@ -44,6 +44,10 @@ public static Iterator<Object[]> getDataProviders(final String packageName) {
     }
 
     /**
+     * Combine two or more Dataproviders by taking the cartesian product of the their test cases.
+     *
+     * Note:  In the case of a an empty provider, the result will be the product of the non-empty providers.
+     * This isdifferent from the traditional definition of the cartesian product.
      * @return the cartesian product of two or more DataProviders than can be used as a new dataprovider
      */
     public static Object[][] cartesianProduct(Object[][]... dataProviders) {

src/test/java/htsjdk/utils/TestNGUtilsTest.java

@@ -6,10 +6,13 @@
 import org.testng.annotations.Test;
 
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
 public class TestNGUtilsTest extends HtsjdkTest {
 
+    public static final Object[] EMPTY_ARRAY = new Object[0];
+
     @DataProvider
     public Object[][] getArraysAndLists() {
         return new Object[][]{
@@ -80,11 +83,19 @@ public Object[][] getDataProviders() {
         return new Object[][]{
                 {new Object[][]{{1, 2}}, new Object[][]{{3}, {4}}, new Object[][]{{1, 2, 3}, {1, 2, 4}}},
                 {new Object[][]{{1}}, new Object[][]{{2}}, new Object[][]{{1, 2}}},
+                {new Object[][]{{1}}, new Object[][]{{2, 3}}, new Object[][]{{1, 2, 3}}},
                 {new Object[][]{{1}, {2}, {3}}, new Object[][]{{'a', 'b'}, {'c', 'd'}},
                         new Object[][]{{1, 'a', 'b'}, {1, 'c', 'd'},
                                 {2, 'a', 'b'}, {2, 'c', 'd'},
                                 {3, 'a', 'b'}, {3, 'c', 'd'}}},
-                {new Object[][]{ new Object[0], new Object[0], new Object[0]}}
+                {new Object[][]{{}}, new Object[][]{{}}, new Object[][]{{}}},
+                {new Object[][]{{}}, new Object[][]{{1}}, new Object[][]{{1}}},
+                {new Object[][]{{}}, new Object[][]{{1, 2}}, new Object[][]{{1, 2}}},
+                {new Object[][]{{1}}, new Object[][]{{}}, new Object[][]{{1}}},
+                {new Object[][]{{}}, new Object[][]{{1}}, new Object[][]{{1}}},
+                {new Object[][]{{EMPTY_ARRAY}}, new Object[][]{{1}}, new Object[][]{{EMPTY_ARRAY, 1}}},
+                {new Object[][]{{1}, {2}, {3}}, new Object[][]{{4}, {5}, {6}},
+                        new Object[][]{{1,4}, {1,5}, {1,6}, {2, 4}, {2, 5}, {2, 6}, {3, 4}, {3, 5}, {3, 6}}}
         };
     }
 
@@ -93,4 +104,48 @@ public void testProduct(Object[][] dataProvider1, Object[][] dataProvider2, Obje
         final Object[][] actual = TestNGUtils.cartesianProduct(dataProvider1, dataProvider2);
         assertNestedArraysEqual(actual, expectedResult);
     }
+
+
+    @DataProvider
+    public Object[][] getDifferingNumbersOfProviders() {
+        final Object[][] p1 = new Object[][]{{1}, {2}};
+        final Object[][] p2 = new Object[][]{{"a", "b"}};
+        final Object[][] p3 = new Object[][]{{}};
+        final Object[][] p4 = new Object[][]{{3}, {4}, {5}};
+
+        final Object[][] expected0 = new Object[][]{{}};
+        final Object[][] expected1 = new Object[][]{{1}, {2}};
+        final Object[][] expected2 = new Object[][]{{1, "a", "b"}, {2, "a", "b"}};
+        final Object[][] expected3 = expected2;
+        final Object[][] expected4 = new Object[][]{
+                {1, "a", "b", 3},
+                {1, "a", "b", 4},
+                {1, "a", "b", 5},
+                {2, "a", "b", 3},
+                {2, "a", "b", 4},
+                {2, "a", "b", 5}
+        };
+
+        return new Object[][]{
+                {Arrays.asList(), expected0},
+                {Collections.singletonList(p1), expected1},
+                {Arrays.asList(p1, p2), expected2},
+                {Arrays.asList(p1, p2, p3), expected3},
+                {Arrays.asList(p1, p2, p3, p4), expected4}
+        };
+    }
+
+    @Test(dataProvider = "getDifferingNumbersOfProviders")
+    public void testCartesianProductOfManyProviders(List<Object[]> providers, Object[][] expected){
+        final Object[][] product = TestNGUtils.cartesianProduct(providers.toArray(new Object[][][]{}));
+        assertNestedArraysEqual(product, expected);
+    }
+
+    @Test
+    public void testSingleProvider() {
+        final Object[][] expected = {{1, 2}};
+        final Object[][] product = TestNGUtils.cartesianProduct(expected);
+        assertNestedArraysEqual(product, expected);
+    }
+
 }