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fix: sort aggregated pileup IDs numerically instead of lexicographically #63

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Merged
nh13 merged 2 commits into from
Feb 21, 2026
Merged

fix: sort aggregated pileup IDs numerically instead of lexicographically #63

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77ca3f0
fix: sort aggregated pileup IDs numerically instead of lexicographically
nh13 Feb 20, 2026
2c92edb
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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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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ title: fgsv tools

# fgsv tools

The following tools are available in fgsv version 0.2.1-b54e45d.
The following tools are available in fgsv version 0.2.1-77ca3f0.
## Breakpoint and SV Tools

Primary tools for calling and transforming breakpoints and SVs.
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6 changes: 3 additions & 3 deletions src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala
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Expand Up @@ -294,8 +294,8 @@ case class AggregatedBreakpointPileup(id: String,
right_targets: Option[String] = None
) extends Metric with LazyLogging {

/** Returns the IDs of constituent breakpoints */
def pileupIds(): Seq[String] = id.split("_").toSeq.sorted
/** Returns the IDs of constituent breakpoints, sorted numerically */
def pileupIds(): Seq[String] = id.split("_").toSeq.sortBy(_.toInt)

/** Combines the comma-delimited list of target strings when aggregating the `left_targets` and `right_target` fields. */
private def combineTargetStrings(first: Option[String], second: Option[String]): Option[String] = {
Expand All @@ -317,7 +317,7 @@ case class AggregatedBreakpointPileup(id: String,
assert(pileup.right_strand == right_strand)

AggregatedBreakpointPileup(
id = pileupIds().appended(pileup.id).sorted.mkString("_"),
id = pileupIds().appended(pileup.id).sortBy(_.toInt).mkString("_"),
category = category,
left_contig = left_contig,
left_min_pos = Math.min(left_min_pos, pileup.left_pos),
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8 changes: 4 additions & 4 deletions src/test/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileupTest.scala
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Expand Up @@ -274,7 +274,7 @@ class AggregateSvPileupTest extends UnitSpec {
)

val expAgg1 = AggregatedBreakpointPileup(
id = "112_456_5_7_8_9",
id = "5_7_8_9_112_456",
category = "Inter-contig rearrangement",
left_contig = "chr1",
left_min_pos = 100,
Expand Down Expand Up @@ -363,7 +363,7 @@ class AggregateSvPileupTest extends UnitSpec {
)

val expAgg1 = AggregatedBreakpointPileup(
id = "10_7_8_9",
id = "7_8_9_10",
category = "Inter-contig rearrangement",
left_contig = "chr1",
left_min_pos = 400,
Expand Down Expand Up @@ -426,7 +426,7 @@ class AggregateSvPileupTest extends UnitSpec {
)

val expAgg = AggregatedBreakpointPileup(
id = "10_7_8_9",
id = "7_8_9_10",
category = "Inter-contig rearrangement",
left_contig = "chr1",
left_min_pos = 400,
Expand Down Expand Up @@ -462,7 +462,7 @@ class AggregateSvPileupTest extends UnitSpec {
)

val expAgg = AggregatedBreakpointPileup(
id = "10_7_8_9",
id = "7_8_9_10",
category = "Inter-contig rearrangement",
left_contig = "chr1",
left_min_pos = 400,
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