Add test for Alignment.revcomped

fulcrumgenomics · Nov 11, 2021 · 8f63f9b · 8f63f9b
1 parent 87b6416
commit 8f63f9b
Showing 1 changed file with 22 additions and 0 deletions.
diff --git a/src/test/scala/com/fulcrumgenomics/alignment/AlignmentTest.scala b/src/test/scala/com/fulcrumgenomics/alignment/AlignmentTest.scala
@@ -280,4 +280,26 @@ class AlignmentTest extends UnitSpec {
     alignment.subByTarget(6, 10).cigar.toString() shouldBe "5D"
     alignment.subByTarget(6, 11).cigar.toString() shouldBe "5D1="
   }
+
+  "Alignment.revcomped" should "reverse complement a simple alignment" in {
+    val in = Alignment("TTTTT", "TTTTT", 1, 1, Cigar("5M"), 5)
+    val rc = in.revcomped
+    rc.query.map(_.toChar).mkString shouldBe "AAAAA"
+    rc.target.map(_.toChar).mkString shouldBe "AAAAA"
+    rc.queryStart shouldBe 1
+    rc.targetStart shouldBe 1
+    rc.cigar.toString shouldBe "5M"
+    rc.score shouldBe 5
+  }
+
+  it should "correctly reverse a non-global alignment" in {
+    val in = Alignment("..GTAACCGGTT".filter(_ != '.'), "ACGTAA.CGGTTCCCCC".filter(_ != '.'), 1, 3, Cigar("5M1I4M"), 10)
+    val rc = in.revcomped
+    rc.query.map(_.toChar).mkString shouldBe "AACCGGTTAC"
+    rc.target.map(_.toChar).mkString shouldBe "GGGGGAACCGTTACGT"
+    rc.queryStart shouldBe 1
+    rc.targetStart shouldBe 6
+    rc.cigar.toString shouldBe "4M1I5M"
+    rc.score shouldBe 10
+  }
 }