Unit test updates

biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqUnitTest.scala

@@ -96,7 +96,7 @@ class ExtractAlignedFastqUnitTest extends TestNGSuite with Matchers {
   def testSingleBamDefault(name: String, feat: Feature, inAln: File,
                            fastqMap: Map[String, FastqPair], resultMap: Map[String, Boolean]) = {
     require(resultMap.keySet == fastqMap.keySet)
-    val memFunc = makeMembershipFunction(Iterable(feat), inAln)
+    val memFunc = makeMembershipFunction(Iterator(feat), inAln)
     for ((key, (rec1, rec2)) <- fastqMap) {
       withClue(makeClue(name, inAln, key)) {
         memFunc(rec1, rec2) shouldBe resultMap(key)
@@ -104,6 +104,33 @@ class ExtractAlignedFastqUnitTest extends TestNGSuite with Matchers {
     }
   }
 
+  @DataProvider(name = "singleAlnProvider2", parallel = true)
+  def singleAlnProvider2() = {
+    val sFastq2 = makeSingleRecords("r01", "r02", "r04", "r07", "r06", "r08")
+    val sFastq2Default = sFastq2.keys.map(x => (x, false)).toMap
+    val sBam02 = resourceFile("/single02.bam")
+
+    Array(
+      Array("less than minimum MAPQ",
+        makeFeature("chrQ", 830, 890), sBam02, 60, sFastq2, sFastq2Default),
+      Array("greater than minimum MAPQ",
+        makeFeature("chrQ", 830, 890), sBam02, 20, sFastq2, sFastq2Default.updated("r07", true)),
+      Array("equal to minimum MAPQ",
+        makeFeature("chrQ", 260, 320), sBam02, 30, sFastq2, sFastq2Default.updated("r01", true))
+    )
+  }
+
+  @Test(dataProvider = "singleAlnProvider2")
+  def testSingleBamMinMapQ(name: String, feat: Feature, inAln: File, minMapQ: Int,
+                           fastqMap: Map[String, FastqPair], resultMap: Map[String, Boolean]) = {
+    require(resultMap.keySet == fastqMap.keySet)
+    val memFunc = makeMembershipFunction(Iterator(feat), inAln, minMapQ)
+    for ((key, (rec1, rec2)) <- fastqMap) {
+      withClue(makeClue(name, inAln, key)) {
+        memFunc(rec1, rec2) shouldBe resultMap(key)
+      }
+    }
+  }
   @DataProvider(name = "pairAlnProvider1", parallel = true)
   def pairAlnProvider1() = {
     val pFastq1 = makePairRecords(
@@ -135,7 +162,7 @@ class ExtractAlignedFastqUnitTest extends TestNGSuite with Matchers {
   def testPairBamDefault(name: String, feat: Feature, inAln: File,
                          fastqMap: Map[String, FastqPair], resultMap: Map[String, Boolean]) = {
     require(resultMap.keySet == fastqMap.keySet)
-    val memFunc = makeMembershipFunction(Iterable(feat), inAln, commonSuffixLength = 2)
+    val memFunc = makeMembershipFunction(Iterator(feat), inAln, commonSuffixLength = 2)
     for ((key, (rec1, rec2)) <- fastqMap) {
       withClue(makeClue(name, inAln, key)) {
         memFunc(rec1, rec2) shouldBe resultMap(key)