Merge branch 'feature-queue_upgrade_3.5' into 'develop'

Upgrade queue to 3.5

Fixes #244 

See merge request !286

protected/biopet-gatk-extensions/pom.xml

@@ -31,7 +31,7 @@
         <dependency>
             <groupId>org.broadinstitute.gatk</groupId>
             <artifactId>gatk-queue-extensions-distribution</artifactId>
-            <version>3.4</version>
+            <version>3.5</version>
         </dependency>
     </dependencies>
 </project>

public/biopet-core/pom.xml

@@ -57,7 +57,7 @@
         <dependency>
             <groupId>org.broadinstitute.gatk</groupId>
             <artifactId>gatk-queue</artifactId>
-            <version>3.4</version>
+            <version>3.5</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.broadinstitute.gatk</groupId>
@@ -68,7 +68,7 @@
         <dependency>
             <groupId>org.broadinstitute.gatk</groupId>
             <artifactId>gatk-queue-extensions-public</artifactId>
-            <version>3.4</version>
+            <version>3.5</version>
         </dependency>
         <dependency>
             <groupId>org.scalatra.scalate</groupId>

public/biopet-utils/pom.xml

@@ -62,7 +62,7 @@
         <dependency>
             <groupId>com.github.samtools</groupId>
             <artifactId>htsjdk</artifactId>
-            <version>1.132</version>
+            <version>1.141</version>
         </dependency>
         <dependency>
             <groupId>org.scala-lang</groupId>