refactor (move test and packages to correct folder)

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala → public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.bcftools
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Output, Input}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 /**
  * Created by ahbbollen on 12-10-15.
@@ -112,8 +112,6 @@ class BcftoolsView(val root: Configurable) extends Bcftools {
   @Argument(doc = "Exclude privates")
   var excludePrivate: Boolean = false
 
-
-
   override def beforeGraph() = {
     super.beforeGraph()
 
@@ -126,21 +124,21 @@ class BcftoolsView(val root: Configurable) extends Bcftools {
 
   def baseCmd = {
     executable + conditional(dropGenotype, "-G") + conditional(headerOnly, "-h") +
-    required("-l", compressionLevel) + required("-O", outputType) +
-    optional("-r", regions) + optional("-R", regionFile) +
-    optional("-t", targets) + optional("-T", targetFile) +
-    conditional(trimAltAlleles, "-a") + conditional(noUpdate, "-I") +
-    repeat("-s", samples) + optional("-S", sampleFile) +
-    optional("-c", minAC) + optional("-C", maxAC) +
-    optional("-e", exclude) + optional("-f", applyFilters) +
-    optional("-g", genotype) + optional("-i", include) +
-    conditional(known, "-k") + optional("-m", minAlleles) +
-    optional("-M", maxAlleles) + conditional(novel, "-n") +
-    conditional(phased, "-p") + conditional(excludePhased, "-P") +
-    optional("-q", minAF) + optional("-Q", maxAF) +
-    conditional(uncalled, "-u") + conditional(excludeUncalled, "-U") +
-    optional("-v", types) + conditional(onlyPrivate, "-x") +
-    conditional(excludePrivate, "-X")
+      required("-l", compressionLevel) + required("-O", outputType) +
+      optional("-r", regions) + optional("-R", regionFile) +
+      optional("-t", targets) + optional("-T", targetFile) +
+      conditional(trimAltAlleles, "-a") + conditional(noUpdate, "-I") +
+      repeat("-s", samples) + optional("-S", sampleFile) +
+      optional("-c", minAC) + optional("-C", maxAC) +
+      optional("-e", exclude) + optional("-f", applyFilters) +
+      optional("-g", genotype) + optional("-i", include) +
+      conditional(known, "-k") + optional("-m", minAlleles) +
+      optional("-M", maxAlleles) + conditional(novel, "-n") +
+      conditional(phased, "-p") + conditional(excludePhased, "-P") +
+      optional("-q", minAF) + optional("-Q", maxAF) +
+      conditional(uncalled, "-u") + conditional(excludeUncalled, "-U") +
+      optional("-v", types) + conditional(onlyPrivate, "-x") +
+      conditional(excludePrivate, "-X")
   }
 
   def cmdPipeInput = {

public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/BcfToolsTest.scala

+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsView
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by ahbbollen on 12-10-15.
+ */
+class BcfToolsTest extends TestNGSuite with MockitoSugar with Matchers {
+
+  @Test
+  def BcfToolsViewTest = {
+    val view = new BcftoolsView(null)
+
+    view.executable = "bcftools"
+
+    val tmpInput = File.createTempFile("bcftoolstest", ".vcf")
+    tmpInput.deleteOnExit()
+    val tmpOutput = File.createTempFile("bcftoolstest", ".vcf.gz")
+    tmpOutput.deleteOnExit()
+    val inputPath = tmpInput.getAbsolutePath
+    val outputPath = tmpOutput.getAbsolutePath
+
+    view.input = tmpInput
+    view.output = tmpOutput
+
+    // view.cmdLine should equal(s"bcftools -o $outputPath $inputPath}")
+  }
+
+}

public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala → public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala

@@ -89,7 +89,7 @@ class ManweTest extends TestNGSuite with Matchers {
     out.deleteOnExit()
 
     manwe.output = out
-    manwe.uri = Some("/uri/1")
+    manwe.uri = "/uri/1"
     manwe.cmd should equal(s"manwe data-sources download /uri/1 -c /usr/local/nonexistent.conf > ${out.getAbsolutePath}")
   }
 
@@ -130,7 +130,7 @@ class ManweTest extends TestNGSuite with Matchers {
     out.deleteOnExit()
 
     manwe.output = out
-    manwe.uri = Some("/uri/1")
+    manwe.uri = "/uri/1"
     manwe.cmd should equal(s"manwe samples activate /uri/1 -c /usr/local/nonexistent.conf > ${out.getAbsolutePath}")
   }
 

public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweActivateAfterAnnotImport.scala

 package nl.lumc.sasc.biopet.pipelines.toucan
 
-import nl.lumc.sasc.biopet.extensions.manwe.{ManweAnnotateVcf, ManweSamplesActivate, ManweSamplesImport}
+import nl.lumc.sasc.biopet.extensions.manwe.{ ManweAnnotateVcf, ManweSamplesActivate, ManweSamplesImport }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 import scala.io.Source
@@ -10,8 +10,8 @@ import scala.io.Source
  * Wrapper for manwe activate after importing and annotating
  */
 class ManweActivateAfterAnnotImport(root: Configurable,
-                                     annotate: ManweAnnotateVcf,
-                                     imported: ManweSamplesImport) extends ManweSamplesActivate(root) {
+                                    annotate: ManweAnnotateVcf,
+                                    imported: ManweSamplesImport) extends ManweSamplesActivate(root) {
 
   override def beforeGraph: Unit = {
     super.beforeGraph

public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweDownloadAfterAnnotate.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.toucan
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.extensions.manwe.{ManweAnnotateVcf, ManweDataSourcesDownload}
+import nl.lumc.sasc.biopet.extensions.manwe.{ ManweAnnotateVcf, ManweDataSourcesDownload }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 import scala.io.Source
@@ -13,7 +13,6 @@ import scala.io.Source
 class ManweDownloadAfterAnnotate(root: Configurable,
                                  annotate: ManweAnnotateVcf) extends ManweDataSourcesDownload(root) {
 
-
   override def beforeGraph: Unit = {
     super.beforeGraph
     require(annotate != null, "Annotate should be defined")
@@ -23,7 +22,6 @@ class ManweDownloadAfterAnnotate(root: Configurable,
   override def beforeCmd: Unit = {
     super.beforeCmd
 
-
     val reader = Source.fromFile(annotate.output)
     this.uri = reader.getLines().toList.head
     reader.close()