Fix most of #196. Only documentation remaining

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala

@@ -71,7 +71,7 @@ object SamplesTsvToJson extends ToolCommand {
         t <- 0 until values.size if !values(t).isEmpty && t != sampleColumn && t != libraryColumn
       ) yield header(t) -> values(t)).toMap
       library match {
-        case Some(lib) => Map("samples" -> Map(sample -> Map("libraries" -> Map(library -> valuesMap))))
+        case Some(lib) => Map("samples" -> Map(sample -> Map("libraries" -> Map(library.get -> valuesMap))))
         case _         => Map("samples" -> Map(sample -> valuesMap))
       }
     }

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

@@ -8,6 +8,7 @@ import org.scalatest.mock.MockitoSugar
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
+
 /**
  * Created by ahbbollen on 28-8-15.
  */
@@ -46,6 +47,32 @@ class SamplesTsvToJsonTest extends TestNGSuite with MockitoSugar with Matchers {
 
   }
 
+  @Test
+  def testJson = {
+    val tsv = new File(resourcePath("/sample.tsv"))
+    val json = stringFromInputs(List(tsv))
+
+    json should equal (
+      """|{
+        |  "samples" : {
+        |    "Sample_ID_1" : {
+        |      "libraries" : {
+        |        "Lib_ID_1" : {
+        |          "bam" : "MyFirst.bam"
+        |        }
+        |      }
+        |    },
+        |    "Sample_ID_2" : {
+        |      "libraries" : {
+        |        "Lib_ID_2" : {
+        |          "bam" : "MySecond.bam"
+        |        }
+        |      }
+        |    }
+        |  }
+        |}""".stripMargin)
+  }
+
 
 
 }