Some extras for VcfWithVcfTest

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

@@ -99,7 +99,7 @@ object VcfWithVcf extends ToolCommand {
               | By default we will return all values found for a given field.
               | With <method> the values will processed after getting it from the secondary VCF file, posible methods are:
               |   - max   : takes maximum of found value, only works for numeric (integer/float) fields
-              |   - min   : takes minemal of found value, only works for numeric (integer/float) fields
+              |   - min   : takes minimum of found value, only works for numeric (integer/float) fields
               |   - unique: takes only unique values """.stripMargin
     opt[Boolean]("match") valueName "<Boolean>" maxOccurs 1 action { (x, c) =>
       c.copy(matchAllele = x)
@@ -124,7 +124,7 @@ object VcfWithVcf extends ToolCommand {
 
     for (x <- commandArgs.fields) {
       if (header.hasInfoLine(x.outputField))
-        throw new IllegalArgumentException("Field '" + x.outputField + "' already exist in input vcf")
+        throw new IllegalArgumentException("Field '" + x.outputField + "' already exists in input vcf")
       if (!secondHeader.hasInfoLine(x.inputField))
         throw new IllegalArgumentException("Field '" + x.inputField + "' does not exist in secondary vcf")
 

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

@@ -48,15 +48,47 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
   }
 
   @Test def testOutputTypeVcfGz() = {
-    val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
+    val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf.gz").getAbsolutePath
     val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ")
     main(arguments)
   }
 
   @Test def testOutputTypeBcf() = {
-    val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
+    val tmpPath = File.createTempFile("VcfWithVcf_", ".bcf").getAbsolutePath
     val arguments = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ")
     main(arguments)
   }
 
+  @Test def testOutputFieldException = {
+    val tmpPath = File.createTempFile("VCFWithVCf", ".vcf").getAbsolutePath
+    val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ:AC")
+    an [IllegalArgumentException] should be thrownBy main(args)
+    val thrown = the [IllegalArgumentException] thrownBy main(args)
+    thrown.getMessage should equal("Field 'AC' already exists in input vcf")
+  }
+
+  @Test def testInputFieldException = {
+    val tmpPath = File.createTempFile("VCFWithVCf", ".vcf").getAbsolutePath
+    val args = Array("-I", unveppedPath, "-s", unveppedPath, "-o", tmpPath, "-f", "CSQ:NEW_CSQ")
+    an [IllegalArgumentException] should be thrownBy main(args)
+    val thrown = the [IllegalArgumentException] thrownBy main(args)
+    thrown.getMessage should equal("Field 'CSQ' does not exist in secondary vcf")
+  }
+
+  @Test def testMinMethodException = {
+    val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
+    val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ:CSQ:min")
+    an [IllegalArgumentException] should be thrownBy main(args)
+    val thrown = the [IllegalArgumentException] thrownBy main(args)
+    thrown.getMessage should equal("Type of field CSQ is not numeric")
+  }
+
+  @Test def testMaxMethodException = {
+    val tmpPath = File.createTempFile("VcfWithVcf_", ".vcf").getAbsolutePath
+    val args = Array("-I", unveppedPath, "-s", veppedPath, "-o", tmpPath, "-f", "CSQ:CSQ:max")
+    an [IllegalArgumentException] should be thrownBy main(args)
+    val thrown = the [IllegalArgumentException] thrownBy main(args)
+    thrown.getMessage should equal("Type of field CSQ is not numeric")
+  }
+
 }