chore: increase test coverage

neodisambiguate/test/src/io/cvbio/neodisambiguate/DisambiguateTest.scala

@@ -114,7 +114,7 @@ class DisambiguateTest extends UnitSpec {
     val input  = builder.toTempFile(deleteOnExit = true)
     val prefix = PathUtil.pathTo(dir.toString, more = "insilico")
 
-    val disambiguate = new Disambiguate(input = Seq(input), prefix = prefix)
+    val disambiguate = new Disambiguate(input = Seq(input), prefix = prefix, referenceNames = Seq("hg38"))
     disambiguate.execute()
 
     val source = SamSource(PathUtil.pathTo(Seq(prefix, assembly).mkString(".") + BamExtension))
@@ -154,6 +154,46 @@ class DisambiguateTest extends UnitSpec {
     Io.assertWritableDirectory(PathUtil.pathTo(dir.toString, more = "ambiguous-alignments")) // will raise exception if non-existent.
   }
 
+  it should "write out ambiguous templates to ambiguous-specific BAM files" in {
+    val humanAssembly: String = "hg38"
+    val mouseAssembly: String = "mm10"
+    val dir: DirPath          = Io.makeTempDir("disambiguate")
+    //dir.toFile.deleteOnExit()
+
+    val humanBuilder = new SamBuilder(sort = Some(SamOrder.Queryname))
+    val mouseBuilder = new SamBuilder(sort = Some(SamOrder.Queryname))
+
+    val humanPair = humanBuilder.addPair(name = "pair", attrs = Map(NM.toString -> 2, AS.toString -> 32), start1 = 2, start2 = 101)
+    val mousePair = mouseBuilder.addPair(name = "pair", attrs = Map(NM.toString -> 2, AS.toString -> 32), start1 = 2, start2 = 101)
+
+    humanBuilder.header.getSequenceDictionary.getSequences.forEach { seq: SAMSequenceRecord  => val _ = seq.setAssembly(humanAssembly) }
+    mouseBuilder.header.getSequenceDictionary.getSequences.forEach { seq: SAMSequenceRecord  => val _ = seq.setAssembly(mouseAssembly) }
+
+    val prefix = PathUtil.pathTo(dir.toString, more = "insilico")
+
+    val humanBam = humanBuilder.toTempFile(deleteOnExit = false)
+    val mouseBam = mouseBuilder.toTempFile(deleteOnExit = false)
+
+    val disambiguate = new Disambiguate(input = Seq(mouseBam, humanBam), prefix = prefix)
+    disambiguate.execute()
+
+    val humanSource = SamSource(PathUtil.pathTo(Seq(prefix, humanAssembly).mkString(".") + BamExtension))
+    val mouseSource = SamSource(PathUtil.pathTo(Seq(prefix, mouseAssembly).mkString(".") + BamExtension))
+
+    humanSource.iterator.toSeq shouldBe empty
+    mouseSource.iterator.toSeq shouldBe empty
+
+    val ambiguousAlignments = PathUtil.pathTo(dir.toString, more = "ambiguous-alignments")
+
+    Io.assertWritableDirectory(ambiguousAlignments) // will raise exception if non-existent.
+
+    val ambiguousHumanSource = SamSource(ambiguousAlignments.resolve(PathUtil.replaceExtension(humanBam.getFileName, ".ambiguous" + BamExtension)))
+    val ambiguousMouseSource = SamSource(ambiguousAlignments.resolve(PathUtil.replaceExtension(mouseBam.getFileName, ".ambiguous" + BamExtension)))
+
+    ambiguousHumanSource.map(_.name).toSeq should contain theSameElementsInOrderAs humanPair.map(_.name)
+    ambiguousMouseSource.map(_.name).toSeq should contain theSameElementsInOrderAs mousePair.map(_.name)
+  }
+
   "NeoNeodisambiguate" should "run end-to-end via the CLI entrypoint" in {
     val humanAssembly: String = "hg38"
     val mouseAssembly: String = "mm10"