From 07c651cef649b884f4ec6fcaa3b2f27a50e7ddf8 Mon Sep 17 00:00:00 2001
From: Nils Homer <nilshomer@gmail.com>
Date: Mon, 5 Jun 2023 16:04:49 -0700
Subject: [PATCH] add some tests

---
 .../sv/tools/AggregateSvPileup.scala              |  8 ++++----
 .../sv/tools/AggregateSvPileupTest.scala          | 15 ++++++++-------
 2 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala b/src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala
index 8811887..d2aab31 100644
--- a/src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala
+++ b/src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala
@@ -432,9 +432,9 @@ case class AggregatedBreakpointPileup(id: String,
    */
   def addTargetOverlap(targets: Option[OverlapDetector[BEDFeature]]): AggregatedBreakpointPileup = {
 
-    def annotations(contig: String, minPos: Int , maxPos: Int): (Boolean, Option[String]) = {
+    def annotations(contig: String, minPos: Int , maxPos: Int, defaultTargets: Option[String] = None): (Boolean, Option[String]) = {
       targets match {
-        case None => (false, None)
+        case None => (false, defaultTargets)
         case Some(detector) =>
           val span = new Interval(contig, minPos, maxPos)
           if (detector.overlapsAny(span)) {
@@ -446,8 +446,8 @@ case class AggregatedBreakpointPileup(id: String,
       }
     }
 
-    val (leftOverlaps, leftTargets)   = annotations(left_contig, left_min_pos, left_max_pos)
-    val (rightOverlaps, rightTargets) = annotations(right_contig, right_min_pos, right_max_pos)
+    val (leftOverlaps, leftTargets)   = annotations(left_contig, left_min_pos, left_max_pos, this.left_targets)
+    val (rightOverlaps, rightTargets) = annotations(right_contig, right_min_pos, right_max_pos, this.right_targets)
     this.copy(
       left_overlaps_target  = leftOverlaps,
       right_overlaps_target = rightOverlaps,
diff --git a/src/test/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileupTest.scala b/src/test/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileupTest.scala
index 33f1c31..28c4fa1 100644
--- a/src/test/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileupTest.scala
+++ b/src/test/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileupTest.scala
@@ -117,6 +117,7 @@ class AggregateSvPileupTest extends UnitSpec {
     split_reads  = 1,
     read_pairs   = 1,
     total        = 2,
+    left_targets = Some("1,2,5")
   )
 
   private val pileup_id8_1_500_plus_3_400_plus = BreakpointPileup(
@@ -210,7 +211,7 @@ class AggregateSvPileupTest extends UnitSpec {
 
   private val bed = makeTempFile("targets", ".bed")
   private val bedWriter = new BufferedWriter(new FileWriter(bed.toFile))
-  bedWriter.write("#header\nchr1\t400\t410\nchr3\t401\t402\n")
+  bedWriter.write("#header\nchr1\t400\t410\ttarget-1\nchr3\t401\t402\ttarget-2\n")
   bedWriter.flush()
   bedWriter.close()
 
@@ -288,6 +289,7 @@ class AggregateSvPileupTest extends UnitSpec {
       total          = 12,
       left_pileups   = PositionList(100, 200, 300, 400, 500, 600),
       right_pileups  = PositionList(100, 200, 200, 300, 400, 500),
+      left_targets   = Some("1,2,5")
     )
 
     // pileup_id222_1_100_plus_1_200_plus does not combine due to different chromosome
@@ -380,6 +382,8 @@ class AggregateSvPileupTest extends UnitSpec {
       right_frequency = Some(8d/8),
       left_overlaps_target = true,
       right_overlaps_target = true,
+      left_targets = Some("target-1"),
+      right_targets = Some("target-2"),
     )
 
     val expAgg2 = AggregatedBreakpointPileup(
@@ -405,11 +409,6 @@ class AggregateSvPileupTest extends UnitSpec {
     )
 
     val aggregatedPileups = runEndToEnd(pileups, bam = Some(bam), targets = Some(bed))
-
-    aggregatedPileups.foreach { p =>
-      println(s"Pileup ${p.id} ${p.left_targets.isEmpty} ${p.left_targets.contains("")}")
-    }
-
     aggregatedPileups should contain theSameElementsAs IndexedSeq(expAgg1, expAgg2)
 
   }
@@ -422,7 +421,6 @@ class AggregateSvPileupTest extends UnitSpec {
       pileup_id10_1_525_plus_3_425_plus,
     )
 
-
     val expAgg = AggregatedBreakpointPileup(
       id             = "10_7_8_9",
       category       = "Inter-contig rearrangement",
@@ -441,6 +439,7 @@ class AggregateSvPileupTest extends UnitSpec {
       right_pileups  = PositionList(300, 400, 425, 500),
       left_frequency = Some(8d/16),
       right_frequency = Some(8d/8),
+      left_targets   = Some("1,2,5")
     )
 
     val aggregatedPileups = runEndToEnd(pileups, bam = Some(bam))
@@ -476,6 +475,8 @@ class AggregateSvPileupTest extends UnitSpec {
       right_frequency = None,
       left_overlaps_target = true,
       right_overlaps_target = true,
+      left_targets = Some("target-1"),
+      right_targets = Some("target-2"),
     )
 
     val aggregatedPileups = runEndToEnd(pileups, targets = Some(bed))