Adding a pre-test check that looks for java files in the test/scala d…

build.gradle

@@ -81,6 +81,11 @@ tasks.withType(Test) { task ->
     task.jvmArgs '-Djava.awt.headless=true'  //this prevents awt from displaying a java icon while the tests are running
 }
 
+task findScalaAndJavaTypes(type: Exec) {
+    description = "Check that Scala files only exist in the scala test dir and that java files do not reside in the scala test dir."
+    commandLine './scripts/checkScalaAndJavaFiles.sh'
+}
+
 test {
     description = "Runs the unit tests other than the SRA tests"
 
@@ -98,7 +103,7 @@ test {
         if (System.env.CI == "false") exclude "sra"
         if (!OperatingSystem.current().isUnix()) exclude "unix"
     }
-}
+} dependsOn findScalaAndJavaTypes
 
 task testSRA(type: Test) {
     description = "Run the SRA tests"

scripts/checkScalaAndJavaFiles.sh

@@ -0,0 +1,17 @@
+#/bin/bash
+
+# Check that Scala files only exist in the scala test dir and
+# that java files do not reside in the scala test dir
+
+if `find src | grep -v '^src/test/scala' | grep -q '\.scala$' ` ; then
+	echo 'Found scala file(s) outside of scala test directory';
+	find src | grep -v '^src/test/scala' | grep '\.scala$'
+	exit 1; 
+fi
+
+if `find src/test/scala | grep -q '\.java$' ` ; then
+        echo 'Found java file(s) in scala test directory';
+	find src/test/scala | grep '\.java$'        
+	exit 1;
+fi
+

src/test/scala/htsjdk/samtools/util/StringUtilTest.scala

@@ -106,7 +106,7 @@ class StringUtilTest extends UnitSpec {
     StringUtil.assertCharactersNotInString("HelloWorld", ' ', '!', '_')
   }
 
-  val textForWrapping =
+  val textForWrapping: String =
     """This is a little bit
       |of text with nice short
       |lines.