chore: increase test coverage

clintval · Jul 28, 2024 · 4c19d02 · 4c19d02
1 parent 1b35229
commit 4c19d02
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Showing 3 changed files with 35 additions and 2 deletions.
diff --git a/neodisambiguate/src/io/cvbio/neodisambiguate/Disambiguate.scala b/neodisambiguate/src/io/cvbio/neodisambiguate/Disambiguate.scala
@@ -87,7 +87,7 @@ object Disambiguate {
   }
 
   /** Command line configuration. */
-  private class NeodisambiguateConf(args: Seq[String]) extends ScallopConf(args) {
+  private[neodisambiguate] class NeodisambiguateConf(args: Seq[String]) extends ScallopConf(args) {
     private val packageName: String = Option(this.getClass.getPackage.getImplementationTitle).getOrElse("neodisambiguate")
     private val version: String     = Option(this.getClass.getPackage.getImplementationVersion).getOrElse("UNKNOWN")
     version(s"$packageName $version\n")

diff --git a/neodisambiguate/src/io/cvbio/neodisambiguate/metric/MetricPair.scala b/neodisambiguate/src/io/cvbio/neodisambiguate/metric/MetricPair.scala
@@ -36,7 +36,7 @@ object MetricPair {
 
   /** Build a [[MetricPair]] from a [[Template]]. A function is required to reduce the tag values to one canonical value. */
   def apply[T](template: Template, tag: SAMTag)(fn: (T, T) => T)(implicit cmp: Ordering[T]): MetricPair[T] = {
-    apply(template = template, tag = tag.toString)(fn = fn)
+    apply(template = template, tag = tag.toString)(fn = fn)(cmp = cmp)
   }
 
   /** Build an empty [[MetricPair]]. */

diff --git a/neodisambiguate/test/src/io/cvbio/neodisambiguate/DisambiguateTest.scala b/neodisambiguate/test/src/io/cvbio/neodisambiguate/DisambiguateTest.scala
@@ -9,6 +9,7 @@ import htsjdk.samtools.SAMSequenceRecord
 import htsjdk.samtools.SAMTag.{AS, NM}
 import io.cvbio.neodisambiguate.CommonsDef.BamExtension
 import io.cvbio.neodisambiguate.DisambiguationStrategy.Classic
+import io.cvbio.neodisambiguate.Disambiguate.NeodisambiguateConf
 import io.cvbio.neodisambiguate.testing.{TemplateBuilder, UnitSpec}
 
 class DisambiguateTest extends UnitSpec {
@@ -152,4 +153,36 @@ class DisambiguateTest extends UnitSpec {
 
     Io.assertWritableDirectory(PathUtil.pathTo(dir.toString, more = "ambiguous-alignments")) // will raise exception if non-existent.
   }
+
+  "NeoNeodisambiguate" should "run end-to-end via the CLI entrypoint" 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 _ = humanBuilder.addPair(name = "pair", attrs = Map(NM.toString -> 6, 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 mouseBam = mouseBuilder.toTempFile(deleteOnExit = true)
+    val humanBam = humanBuilder.toTempFile(deleteOnExit = true)
+
+    val conf = new NeodisambiguateConf(args = Seq("--input", mouseBam.toString, humanBam.toString, "--output", prefix.toString))
+    Disambiguate.main(Array.from(conf.args))
+
+    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.map(_.name).toSeq should contain theSameElementsInOrderAs mousePair.map(_.name)
+
+    Io.assertWritableDirectory(PathUtil.pathTo(dir.toString, more = "ambiguous-alignments")) // will raise exception if non-existent.
+  }
 }