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fix: prevent integer overflow and truncation in MergedPileup weighted mean #56

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Merged
nh13 merged 2 commits into from
Mar 2, 2026
Merged

fix: prevent integer overflow and truncation in MergedPileup weighted mean #56

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fix: prevent integer overflow and truncation in MergedPileup weighted…
nh13 Feb 20, 2026
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nh13 Feb 21, 2026
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2 changes: 1 addition & 1 deletion docs/tools/index.md
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Expand Up @@ -4,7 +4,7 @@ title: fgsv tools

# fgsv tools

The following tools are available in fgsv version 0.2.1-77ca3f0.
The following tools are available in fgsv version 0.2.1-21111db.
## Breakpoint and SV Tools

Primary tools for calling and transforming breakpoints and SVs.
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4 changes: 2 additions & 2 deletions src/main/scala/com/fulcrumgenomics/sv/tools/FilterAndMerge.scala
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Expand Up @@ -105,8 +105,8 @@ object MergedPileup {
val readPairs = pileups.sumBy(_.read_pairs)
val counts = NumericCounter(pileups.map(_.total).iterator)
val total = splitReads + readPairs
val leftMean = pileups.iterator.map(p => p.total * p.left_pos / total).sum
val rightMean = pileups.iterator.map(p => p.total * p.right_pos / total).sum
val leftMean = (pileups.iterator.map(p => p.total.toLong * p.left_pos).sum / total).toInt
val rightMean = (pileups.iterator.map(p => p.total.toLong * p.right_pos).sum / total).toInt
val meanCount = counts.mean()

new MergedPileup(
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