Merge branch 'feature-queue_3.6' into 'develop'

Switch to Queue 3.6

Fixes #335 and biopet/Biopet-FunctionalTests#25

See merge request !420

biopet-core/pom.xml

@@ -56,7 +56,7 @@
         <dependency>
             <groupId>org.broadinstitute.gatk</groupId>
             <artifactId>gatk-queue</artifactId>
-            <version>3.5</version>
+            <version>3.6</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.broadinstitute.gatk</groupId>
@@ -67,7 +67,7 @@
         <dependency>
             <groupId>org.broadinstitute.gatk</groupId>
             <artifactId>gatk-queue-extensions-public</artifactId>
-            <version>3.5</version>
+            <version>3.6</version>
         </dependency>
         <dependency>
             <groupId>org.scalatra.scalate</groupId>

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala

@@ -16,17 +16,16 @@ package nl.lumc.sasc.biopet.extensions.gatk
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
 import nl.lumc.sasc.biopet.utils.VcfUtils
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
-import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, Input }
 
-//TODO: check gathering
-class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with ScatterGatherableFunction */ {
+class BaseRecalibrator(val root: Configurable) extends CommandLineGATK  with ScatterGatherableFunction {
   def analysis_type = "BaseRecalibrator"
-  //TODO: check gathering
-  //scatterClass = classOf[ContigScatterFunction]
-  //setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
+  scatterClass = classOf[ContigScatterFunction]
+  setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
 
   /** A database of known polymorphic sites */
   @Input(fullName = "knownSites", shortName = "knownSites", doc = "A database of known polymorphic sites", required = false, exclusiveOf = "", validation = "")
@@ -38,7 +37,7 @@ class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with S
 
   /** The output recalibration table file to create */
   @Output(fullName = "out", shortName = "o", doc = "The output recalibration table file to create", required = true, exclusiveOf = "", validation = "") //TODO: check gathering
-  //@Gather(classOf[org.broadinstitute.gatk.engine.recalibration.BQSRGatherer])
+  @Gather(classOf[org.broadinstitute.gatk.engine.recalibration.BQSRGatherer])
   var out: File = _
 
   /** One or more covariates to be used in the recalibration. Can be specified multiple times */

biopet-tools/pom.xml

@@ -65,7 +65,7 @@
         <dependency>
             <groupId>com.github.broadinstitute</groupId>
             <artifactId>picard</artifactId>
-            <version>1.141</version>
+            <version>2.4.1</version>
         </dependency>
     </dependencies>
 </project>
\ No newline at end of file

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

@@ -177,10 +177,10 @@ object VcfWithVcf extends ToolCommand {
   def getSecondaryRecords(secondaryReader: VCFFileReader,
                           record: VariantContext, matchAllele: Boolean): List[VariantContext] = {
     if (matchAllele) {
-      secondaryReader.query(record.getContig, record.getStart, record.getEnd).toList.
-        filter(x => record.getAlternateAlleles.exists(x.hasAlternateAllele))
+      secondaryReader.query(record.getContig, record.getStart, record.getEnd).
+        filter(x => record.getAlternateAlleles.exists(x.hasAlternateAllele)).toList
     } else {
-      secondaryReader.query(record.getContig, record.getStart, record.getEnd).toList
+      secondaryReader.query(record.getContig, record.getStart, record.getEnd).toIterable.toList
     }
   }
 

biopet-utils/pom.xml

@@ -66,7 +66,7 @@
         <dependency>
             <groupId>com.github.samtools</groupId>
             <artifactId>htsjdk</artifactId>
-            <version>1.141</version>
+            <version>2.4.1</version>
         </dependency>
         <dependency>
             <groupId>org.scala-lang</groupId>

gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala

@@ -11,8 +11,8 @@ import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
 /**
-  * Created by pjvan_thof on 31-5-16.
-  */
+ * Created by pjvan_thof on 31-5-16.
+ */
 class Impute2VcfTest extends TestNGSuite with Matchers {
   def initPipeline(map: Map[String, Any]): Impute2Vcf = {
     new Impute2Vcf {

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerAllele.scala

@@ -28,7 +28,7 @@ class HaplotypeCallerAllele(val root: Configurable) extends Variantcaller {
   val name = "haplotypecaller_allele"
   protected def defaultPrio = 5
 
-  val alleles: File = config("input_alleles")
+  lazy val alleles: File = config("input_alleles")
 
   def biopetScript() {
     val hc = gatk.HaplotypeCaller(this, inputBams.values.toList, outputFile)

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyperAllele.scala

@@ -27,7 +27,7 @@ class UnifiedGenotyperAllele(val root: Configurable) extends Variantcaller {
   val name = "unifiedgenotyper_allele"
   protected def defaultPrio = 9
 
-  val alleles: File = config("input_alleles")
+  lazy val alleles: File = config("input_alleles")
 
   def biopetScript() {
     val ug = gatk.UnifiedGenotyper(this, inputBams.values.toList, outputFile)