PileupBuilder should not report insertions when checking the final mapped base before soft-clipping

[jrm5100]

I was using the PileupBuilder and ran into an error when attempting to collect an insertion sequence:

case entry: InsertionEntry if entry.rec.start < pos  =>
  // Get insertion bases
  val insStart     = entry.rec.readPosAtRefPos(pos, returnLastBaseIfDeleted = true)
  val insEnd       = entry.rec.readPosAtRefPos(pos + 1, returnLastBaseIfDeleted = true)
  val alleleString = entry.rec.basesString.substring(insStart - 1, insEnd - 1)

The call to substring failed because insEnd was 0.

I tracked this down to the PileupBuilder making an incorrect check. rec.length includes soft-clipped bases, so checking offset < 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.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (abb741b) 95.62% compared to head (bc462fb) 95.62%.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #956   +/-   ##
=======================================
  Coverage   95.62%   95.62%           
=======================================
  Files         126      126           
  Lines        7355     7355           
  Branches      512      528   +16     
=======================================
  Hits         7033     7033           
  Misses        322      322           

Flag	Coverage Δ
unittests	95.62% <100.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[clintval]

Took me a bit to walk through the logic using the underlying functions. This does indeed appear to be a bug fix! Thanks for this @jrm5100!