+
+ /**
+ * Tests for the method that converts a series of [start, end] ranges to
+ * single positions, where the mapping is to a reverse strand i.e. start is
+ * greater than end point mapped to
+ */
+ @Test(groups = { "Functional" })
+ public void testFlattenRanges_reverseStrand()
+ {
+ assertEquals("[4, 3, 2, 1]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[] { 4, 1 })));
+ assertEquals(
+ "[4, 3, 2, 1]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[] { 4, 3, 2,
+ 1 })));
+ assertEquals(
+ "[4, 3, 2, 1]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[] { 4, 4, 3,
+ 3, 2, 2, 1, 1 })));
+ assertEquals(
+ "[12, 9, 8, 7, 4, 3, 2, 1]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[] { 12, 12,
+ 9, 7, 4, 1 })));
+ // forwards and backwards anyone?
+ assertEquals(
+ "[4, 5, 6, 3, 2, 1]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[] { 4, 6, 3,
+ 1 })));
+ // backwards and forwards
+ assertEquals(
+ "[3, 2, 1, 4, 5, 6]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[] { 3, 1, 4,
+ 6 })));
+ // trailing unpaired start position is ignored:
+ assertEquals(
+ "[12, 9, 8, 7, 4, 3, 2]",
+ Arrays.toString(MappingUtils.flattenRanges(new int[] { 12, 12,
+ 9, 7, 4, 2, 1 })));
+ }