ReadPosRankSumTest doesn't work for two deletions with one base in between
open | Created 2018-12-07 | Last updated 2018-12-07| Posted by davidbenjamin | See in Github

Annotations bug

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.

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