fix: prevent integer overflow and truncation in MergedPileup weighted mean

[nh13]

Summary

• Fix integer overflow in MergedPileup weighted mean calculation where p.total * p.left_pos (Int*Int) can overflow for large genomic positions
• Fix per-term truncation where integer division inside map() truncates each term before summing, producing inaccurate mean positions
• Use Long arithmetic for the intermediate product and perform a single division at the end

Test plan

• Existing tests pass (./mill tools.test)
• Verify with large genomic positions (e.g. chr1 at ~200M) that mean is calculated correctly

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📝 Walkthrough

Walkthrough

This pull request makes two changes: the Tools index documentation version identifier is updated, and the FilterAndMerge calculation logic is modified to perform intermediate multiplication using 64-bit integers before division and casting to Int. The arithmetic change affects both left and right position calculations, replacing direct integer division with a two-step approach that computes the sum as a Long before converting the final result to Int.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title directly and precisely describes the main change: fixing integer overflow and truncation in MergedPileup weighted mean calculation.
Description check	✅ Passed	The description clearly explains the two bugs being fixed, the solution approach, and provides a test plan aligned with the changeset.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch fix/merged-pileup-integer-overflow

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[nh13]

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Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)

src/main/scala/com/fulcrumgenomics/sv/tools/FilterAndMerge.scala (1)

116-116: ⚠️ Potential issue | 🟡 Minor

Math.round(_.toFloat) re-introduces precision loss for large genomic positions.

leftMean / rightMean are already Int after the .toInt at lines 108–109. Converting them to Float (24-bit mantissa, exact only up to 2²³ ≈ 8.4 M) before rounding silently corrupts positions on any chromosome beyond ~8 Mbp — including the chr1 ~200 M case motivating this PR.

🐛 Proposed fix

-      left_mean      = Math.round(leftMean.toFloat),
+      left_mean      = leftMean,
...
-      right_mean     = Math.round(rightMean.toFloat),
+      right_mean     = rightMean,

Also applies to: 121-121

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@src/main/scala/com/fulcrumgenomics/sv/tools/FilterAndMerge.scala` at line
116, The code is converting already-truncated Ints back to Float and rounding
(via Math.round(leftMean.toFloat / rightMean.toFloat)), which re-introduces
precision loss for large genomic positions; update the assignments that set
left_mean and right_mean in FilterAndMerge.scala to use the existing Int values
(leftMean and rightMean) directly (or cast to Long/Int as required by the
surrounding record type) instead of converting to Float and calling Math.round;
apply the same change to the symmetric occurrence for right_mean so the stored
positions remain exact.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Outside diff comments:
In `@src/main/scala/com/fulcrumgenomics/sv/tools/FilterAndMerge.scala`:
- Line 116: The code is converting already-truncated Ints back to Float and
rounding (via Math.round(leftMean.toFloat / rightMean.toFloat)), which
re-introduces precision loss for large genomic positions; update the assignments
that set left_mean and right_mean in FilterAndMerge.scala to use the existing
Int values (leftMean and rightMean) directly (or cast to Long/Int as required by
the surrounding record type) instead of converting to Float and calling
Math.round; apply the same change to the symmetric occurrence for right_mean so
the stored positions remain exact.