review fixups

fulcrumgenomics · Aug 16, 2023 · a789098 · a789098
1 parent 279dfcf
commit a789098
Showing 1 changed file with 14 additions and 2 deletions.
diff --git a/src/test/scala/com/fulcrumgenomics/fastq/TrimFastqTest.scala b/src/test/scala/com/fulcrumgenomics/fastq/TrimFastqTest.scala
@@ -133,10 +133,10 @@ class TrimFastqTest extends UnitSpec {
  r2Map("20x20").length shouldBe 15
  }
 
- it should "trim each FASTQ independently to a FASTQ-specific length" in {
+ it should "trim each FASTQ independently to a FASTQ-specific length and not discard reads" in {
  val (r1, r2) = fqFiles
  val (r1Out, r2Out) = (makeTempFile("r1out.", ".fq"), makeTempFile("r2out.", ".fq"))
- new TrimFastq(input = Seq(r1, r2), output=Seq(r1Out, r2Out), length = Seq(10, 15), exclude = false).execute()
+ new TrimFastq(input = Seq(r1, r2), output = Seq(r1Out, r2Out), length = Seq(10, 15), exclude = false).execute()
  val r1Map = FastqSource(r1Out).map(r => r.name -> r).toMap
  val r2Map = FastqSource(r2Out).map(r => r.name -> r).toMap
  r1Map.size shouldBe 3
@@ -148,4 +148,16 @@ class TrimFastqTest extends UnitSpec {
  r2Map("10x20").length shouldBe 15
  r2Map("20x20").length shouldBe 15
  }
+
+ it should "trim each FASTQ independently to a FASTQ-specific length and discard reads" in {
+ val (r1, r2) = fqFiles
+ val (r1Out, r2Out) = (makeTempFile("r1out.", ".fq"), makeTempFile("r2out.", ".fq"))
+ new TrimFastq(input = Seq(r1, r2), output=Seq(r1Out, r2Out), length = Seq(20, 20), exclude = true).execute()
+ val r1Map = FastqSource(r1Out).map(r => r.name -> r).toMap
+ val r2Map = FastqSource(r2Out).map(r => r.name -> r).toMap
+ r1Map.size shouldBe 1
+ r2Map.size shouldBe r1Map.size
+ r1Map("20x20").length shouldBe 20
+ r2Map("20x20").length shouldBe 20
+ }
 }