Added more tests

protected/biopet-gatk-pipelines/pom.xml

@@ -44,5 +44,17 @@
             <artifactId>Shiva</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <version>6.8</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.scalatest</groupId>
+            <artifactId>scalatest_2.11</artifactId>
+            <version>2.2.1</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 </project>

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingGatk.scala

@@ -13,19 +13,18 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
   qscript =>
   def this() = this(null)
 
-  override def callers = {
+  override def callersList = {
     new HaplotypeCallerGvcf ::
       new HaplotypeCallerAllele ::
       new UnifiedGenotyperAllele ::
       new UnifiedGenotyper ::
       new HaplotypeCaller ::
-      super.callers
+      super.callersList
   }
 
   class HaplotypeCaller extends Variantcaller {
     val name = "haplotypecaller"
     protected val defaultPrio = 1
-    protected val defaultUse = true
 
     def outputFile = new File(outputDir, namePrefix + ".haplotypecaller.vcf.gz")
 
@@ -40,7 +39,6 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
   class UnifiedGenotyper extends Variantcaller {
     val name = "unifiedgenotyper"
     protected val defaultPrio = 20
-    protected val defaultUse = false
 
     def outputFile = new File(outputDir, namePrefix + ".unifiedgenotyper.vcf.gz")
 
@@ -55,7 +53,6 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
   class HaplotypeCallerAllele extends Variantcaller {
     val name = "haplotypecaller_allele"
     protected val defaultPrio = 5
-    protected val defaultUse = false
 
     def outputFile = new File(outputDir, namePrefix + ".haplotypecaller_allele.vcf.gz")
 
@@ -72,7 +69,6 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
   class UnifiedGenotyperAllele extends Variantcaller {
     val name = "unifiedgenotyper_allele"
     protected val defaultPrio = 9
-    protected val defaultUse = false
 
     def outputFile = new File(outputDir, namePrefix + ".unifiedgenotyper_allele.vcf.gz")
 
@@ -89,7 +85,6 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
   class HaplotypeCallerGvcf extends Variantcaller {
     val name = "haplotypecaller_gvcf"
     protected val defaultPrio = 5
-    protected val defaultUse = false
 
     def outputFile = new File(outputDir, namePrefix + ".haplotypecaller_gvcf.vcf.gz")
 

protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala

+package nl.lumc.sasc.biopet.pipelines.gatk
+
+import java.io.File
+
+import com.google.common.io.Files
+import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
+import nl.lumc.sasc.biopet.extensions.gatk.broad.{UnifiedGenotyper, HaplotypeCaller}
+import nl.lumc.sasc.biopet.tools.{VcfStats, MpileupToVcf, VcfFilter}
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.apache.commons.io.FileUtils
+import org.broadinstitute.gatk.queue.QSettings
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.{DataProvider, Test, AfterClass}
+
+import scala.collection.mutable.ListBuffer
+
+/**
+ * Created by pjvan_thof on 3/2/15.
+ */
+class ShivaVariantcallingTest extends TestNGSuite with Matchers {
+  def initPipeline(map: Map[String, Any]): ShivaVariantcallingGatk = {
+    new ShivaVariantcallingGatk() {
+      override def configName = "shivavariantcalling"
+      override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaVariantcallingTest.config))
+      qSettings = new QSettings
+      qSettings.runName = "test"
+    }
+  }
+
+  @DataProvider(name = "shivaVariantcallingOptions")
+  def shivaVariantcallingOptions = {
+    val raw = Array(true, false)
+    val bcftools = Array(true, false)
+    val haplotypeCallerGvcf = Array(true, false)
+    val haplotypeCallerAllele = Array(true, false)
+    val unifiedGenotyperAllele = Array(true, false)
+    val unifiedGenotyper = Array(true, false)
+    val haplotypeCaller = Array(true, false)
+
+    (for (
+      bams <- 0 to 2;
+      raw <- raw;
+      bcftools <- bcftools;
+      haplotypeCallerGvcf <- haplotypeCallerGvcf;
+      haplotypeCallerAllele <- haplotypeCallerAllele;
+      unifiedGenotyperAllele <- unifiedGenotyperAllele;
+      unifiedGenotyper <- unifiedGenotyper;
+      haplotypeCaller <- haplotypeCaller
+    ) yield Array[Any](bams, raw, bcftools, unifiedGenotyper, haplotypeCaller, haplotypeCallerGvcf, haplotypeCallerAllele, unifiedGenotyperAllele)
+    ).toArray
+  }
+
+  @Test(dataProvider = "shivaVariantcallingOptions")
+  def testShivaVariantcalling(bams: Int,
+                              raw: Boolean,
+                              bcftools: Boolean,
+                              unifiedGenotyper: Boolean,
+                              haplotypeCaller: Boolean,
+                              haplotypeCallerGvcf: Boolean,
+                              haplotypeCallerAllele: Boolean,
+                              unifiedGenotyperAllele: Boolean) = {
+    val callers: ListBuffer[String] = ListBuffer()
+    if (raw) callers.append("raw")
+    if (bcftools) callers.append("bcftools")
+    if (unifiedGenotyper) callers.append("unifiedgenotyper")
+    if (haplotypeCallerGvcf) callers.append("haplotypecaller_gvcf")
+    if (haplotypeCallerAllele) callers.append("haplotypecaller_allele")
+    if (unifiedGenotyperAllele) callers.append("unifiedgenotyper_allele")
+    if (haplotypeCaller) callers.append("haplotypecaller")
+    val map = Map("variantcallers"-> callers.toList)
+    val pipeline = initPipeline(map)
+
+    pipeline.inputBams = (for (n <- 1 to bams) yield new File("bam_" + n + ".bam")).toList
+
+    val illegalArgumentException = pipeline.inputBams.isEmpty ||
+      (!raw && !bcftools &&
+        !haplotypeCaller && !unifiedGenotyper &&
+        !haplotypeCallerGvcf && !haplotypeCallerAllele && !unifiedGenotyperAllele)
+
+    if (illegalArgumentException) intercept[IllegalArgumentException] {
+      pipeline.script()
+    }
+
+    if (!illegalArgumentException) {
+      pipeline.script()
+
+      pipeline.functions.count(_.isInstanceOf[CombineVariants]) shouldBe 1 + (if (raw) 1 else 0)
+      //pipeline.functions.count(_.isInstanceOf[Bcftools]) shouldBe (if (bcftools) 1 else 0)
+      //FIXME: Can not check for bcftools because of piping
+      pipeline.functions.count(_.isInstanceOf[MpileupToVcf]) shouldBe (if (raw) bams else 0)
+      pipeline.functions.count(_.isInstanceOf[VcfFilter]) shouldBe (if (raw) bams else 0)
+      pipeline.functions.count(_.isInstanceOf[HaplotypeCaller]) shouldBe (if (haplotypeCaller) 1 else 0) +
+        (if (haplotypeCallerAllele) 1 else 0) + (if (haplotypeCallerGvcf) bams else 0)
+      pipeline.functions.count(_.isInstanceOf[UnifiedGenotyper]) shouldBe (if (unifiedGenotyper) 1 else 0) +
+        (if (unifiedGenotyperAllele) 1 else 0)
+      pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (1 + callers.size)
+    }
+  }
+
+  @AfterClass def removeTempOutputDir() = {
+    FileUtils.deleteDirectory(ShivaVariantcallingTest.outputDir)
+  }
+}
+
+object ShivaVariantcallingTest {
+  val outputDir = Files.createTempDir()
+
+  val config = Map(
+    "name_prefix" -> "test",
+    "output_dir" -> outputDir,
+    "reference" -> "test",
+    "gatk_jar" -> "test",
+    "samtools" -> Map("exe" -> "test"),
+    "bcftools" -> Map("exe" -> "test"),
+    "input_alleles" -> "test"
+  )
+}
\ No newline at end of file

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala

@@ -38,10 +38,11 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
   def finalFile = new File(outputDir, namePrefix + ".final.vcf.gz")
 
   def biopetScript: Unit = {
-    val callers = usedCallers.sortBy(_.prio)
+    val configCallers: Set[String] = config("variantcallers")
+    val callers = callersList.filter(x => configCallers.contains(x.name)).sortBy(_.prio)
 
     require(!inputBams.isEmpty, "No input bams found")
-    require(callers.exists(_.use), "must select atleast 1 variantcaller")
+    require(!callers.isEmpty, "must select atleast 1 variantcaller, possible to use: " + callersList.map(_.name).mkString(", "))
 
     val cv = new CombineVariants(qscript)
     cv.outputFile = finalFile
@@ -69,15 +70,11 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
     addSummaryJobs
   }
 
-  def callers: List[Variantcaller] = List(new RawVcf, new Bcftools)
-
-  def usedCallers: List[Variantcaller] = callers.filter(_.use)
+  protected def callersList: List[Variantcaller] = List(new RawVcf, new Bcftools)
 
   trait Variantcaller {
     val name: String
     def outputDir = new File(qscript.outputDir, name)
-    protected val defaultUse: Boolean
-    lazy val use: Boolean = config("use_" + name, default = defaultUse)
     protected val defaultPrio: Int
     lazy val prio: Int = config("prio_" + name, default = defaultPrio)
     def addJobs()
@@ -87,7 +84,6 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
   class Bcftools extends Variantcaller {
     val name = "bcftools"
     protected val defaultPrio = 8
-    protected val defaultUse = true
 
     def outputFile = new File(outputDir, namePrefix + ".bcftools.vcf.gz")
 
@@ -117,7 +113,6 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
   class RawVcf extends Variantcaller {
     val name = "raw"
     protected val defaultPrio = 999
-    protected val defaultUse = true
 
     def outputFile = new File(outputDir, namePrefix + ".raw.vcf.gz")
 
@@ -154,5 +149,8 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
 
   def summarySettings = Map()
 
-  def summaryFiles: Map[String, File] = usedCallers.map(x => (x.name -> x.outputFile)).toMap + ("final" -> finalFile)
+  def summaryFiles: Map[String, File] = {
+    val callers: Set[String] = config("variantcallers")
+    callersList.filter(x => callers.contains(x.name)).map(x => (x.name -> x.outputFile)).toMap + ("final" -> finalFile)
+  }
 }
\ No newline at end of file

public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala

@@ -13,6 +13,8 @@ import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.{ AfterClass, Test, DataProvider }
 
+import scala.collection.mutable.ListBuffer
+
 /**
  * Created by pjvan_thof on 3/2/15.
  */
@@ -36,17 +38,20 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
       raw <- raw;
       bcftools <- bcftools
     ) yield Array[Any](bams, raw, bcftools)
-    ).toArray
+      ).toArray
   }
 
   @Test(dataProvider = "shivaVariantcallingOptions")
   def testShivaVariantcalling(bams: Int, raw: Boolean, bcftools: Boolean) = {
-    val map = Map("use_raw" -> raw, "use_bcftools" -> bcftools)
+    val callers: ListBuffer[String] = ListBuffer()
+    if (raw) callers.append("raw")
+    if (bcftools) callers.append("bcftools")
+    val map = Map("variantcallers"-> callers.toList)
     val pipeline = initPipeline(map)
 
     pipeline.inputBams = (for (n <- 1 to bams) yield new File("bam_" + n + ".bam")).toList
 
-    val illegalArgumentException = pipeline.inputBams.isEmpty || !raw && !bcftools
+    val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools)
 
     if (illegalArgumentException) intercept[IllegalArgumentException] {
       pipeline.script()
@@ -66,7 +71,6 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
   @AfterClass def removeTempOutputDir() = {
     FileUtils.deleteDirectory(ShivaVariantcallingTest.outputDir)
   }
-
 }
 
 object ShivaVariantcallingTest {