Fix FastQC test since we now include the reverse complement of a found...

Fix FastQC test since we now include the reverse complement of a found adapter, the test had to be modified to check the change.

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala

@@ -185,10 +185,9 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
       val fromKnownList: Set[AdapterSequence] = (adapterSet ++ contaminantSet)
         .filter(x => foundAdapterNames.exists(_.startsWith(x.name)))
 
-      val fromKnownListRC: Set[AdapterSequence] = (adapterSet ++ contaminantSet)
-        .filter(x => foundAdapterNames.exists(_.startsWith(x.name))).map {
-          x => AdapterSequence(x.name + "_RC", reverseComplement(x.seq))
-        }
+      val fromKnownListRC: Set[AdapterSequence] = fromKnownList.map {
+        x => AdapterSequence(x.name + "_RC", reverseComplement(x.seq))
+      }
 
       // list all sequences found by FastQC
       val fastQCFoundSequences: Seq[AdapterSequence] = if (sensitiveAdapterSearch) {

public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FastqcV0101Test.scala

@@ -71,10 +71,16 @@ class FastqcV0101Test extends TestNGSuite with Matchers {
     val fqc = new Fastqc(null)
     fqc.output = outputv0101
     fqc.contaminants = Option(resourceFile("fqc_contaminants_v0101.txt"))
+    // found adapters also contain the adapters in reverse complement (done within flexiprep/fastqc only)
     val adapters = fqc.foundAdapters
-    adapters.size shouldBe 1
-    adapters.head.name should ===("TruSeq Adapter, Index 1")
-    // from fqc_contaminants_v0101.txt
-    adapters.head.seq should ===("GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG")
+    // we find 1 adapter which comes with the Reverse Complement counterpart
+    adapters.size shouldBe 2
+
+    adapters.head.name shouldEqual "TruSeq Adapter, Index 1_RC"
+    adapters.head.seq shouldEqual "CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC"
+
+    adapters.last.name shouldEqual "TruSeq Adapter, Index 1"
+    adapters.last.seq shouldEqual "GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG"
+
   }
 }
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