ReadPosRankSumTest doesn't work for two deletions with one base in between

[davidbenjamin]

When ReadPosRankSumTest.getReadPosition encounters the second of two deletions with two bases in between it hits the following code:

if ( AlignmentUtils.isInsideDeletion(read.getCigar(), offset) ) {
            return OptionalDouble.of(INVALID_ELEMENT_FROM_READ);
}

which returns negative infinity. Those with TCGA access can reproduce the issue by running on the TCGA exome pair ESCA-IG-A3YB-TP-NB at 15:34525804-34525810.

[davidbenjamin]

You can consider this fixed if it passes a simple unit test where you run ReadPosRankSumTest.getReadPosition on a few artificial read of the form <short ref match of 1-5 or so bases>.