PileupBuilder should not report insertions when checking the final mapped base before soft-clipping #956
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I was using the PileupBuilder and ran into an error when attempting to collect an insertion sequence:
The call to
substring
failed becauseinsEnd
was0
.I tracked this down to the
PileupBuilder
making an incorrect check.rec.length
includes soft-clipped bases, so checkingoffset < rec.length - 1
will always be true at a pileup for the last mapped base as long as there is at least 1 soft-clipped base. The second half of the check (rec.refPosAtReadPos(offset + 1)
) will also be true, but for the wrong reason (it's soft-clipped, not an insertion).I shoehorned in a test where it seems appropriate.