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

* fix: sort aggregated pileup IDs numerically instead of lexicographically

Compound breakpoint IDs were sorted as strings, causing non-intuitive
ordering (e.g. "112_456_5_7_8_9" instead of "5_7_8_9_112_456").
Change to numeric sorting via sortBy(_.toInt) for consistency.

* Generate docs files

Author: nh13

docs/tools/index.md

@@ -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.

src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala

@@ -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] = {
@@ -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),

src/test/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileupTest.scala

@@ -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,
@@ -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,
@@ -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,
@@ -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,