Switch to Queue 3.6

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-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 {