optimizeIntervals fails to merge abutting intervals

[jean-philippe-martin]

Subject of the issue

QueryInterval.optimizeIntervals does not merge adjacent intervals as I would have expected.

Here is test code to demonstrate the issue:

  @Test
  public void testOptimizeIntervals() throws Exception {
    QueryInterval[] intervals = new QueryInterval[] {
        new QueryInterval(0, 1519, 1520),
        new QueryInterval(0, 1521, 1525)
    };
    QueryInterval[] expected = new QueryInterval[] {
        new QueryInterval(0, 1519, 1525),
    };
    final QueryInterval[] got = QueryInterval.optimizeIntervals(intervals);
    Assert.assertEquals(expected, got);
  }

It fails because got still contains the two initial intervals, even though they touch.

Your environment

I tried using htsjdk 2.10.1, java 8 and Linux.

Steps to reproduce

Compile and run the test code above. Observe it fail.

Expected behaviour

I expect abutting intervals to be merged.

Actual behaviour

Overlapping intervals are merged, but abutting ones are not.

[yfarjoun]

fixed by #979