updating dependencies to current version

updating htsjdk and dataflow
adding vfs2 to resolve dataflow warning

build.gradle

@@ -5,7 +5,7 @@ buildscript {
      }
 
     dependencies {
-        classpath 'org.kt3k.gradle.plugin:coveralls-gradle-plugin:2.0.1'
+        classpath 'org.kt3k.gradle.plugin:coveralls-gradle-plugin:2.3.1'
     }
 }
 
@@ -72,24 +72,25 @@ check.dependsOn installApp
 dependencies {
     compile files("${System.properties['java.home']}/../lib/tools.jar")
 
-    compile 'com.github.samtools:htsjdk:1.130'
-    compile 'com.google.cloud.genomics:google-genomics-dataflow:v1beta2-0.6'
+    compile 'com.github.samtools:htsjdk:1.131'
+    compile 'com.google.cloud.genomics:google-genomics-dataflow:v1beta2-0.8'
     compile 'com.google.cloud.genomics:gatk-tools-java:1.0'
-    compile 'org.apache.logging.log4j:log4j-api:2.1'
-    compile 'org.apache.logging.log4j:log4j-core:2.1'
-    compile 'org.apache.commons:commons-lang3:3.3.2'
-    compile 'org.apache.commons:commons-math3:3.4'
+    compile 'org.apache.logging.log4j:log4j-api:2.2'
+    compile 'org.apache.logging.log4j:log4j-core:2.2'
+    compile 'org.apache.commons:commons-lang3:3.4'
+    compile 'org.apache.commons:commons-math3:3.5'
     compile 'org.apache.commons:commons-collections4:4.0'
+    compile 'org.apache.commons:commons-vfs2:2.0'
     compile 'commons-io:commons-io:2.4'
     compile 'org.reflections:reflections:0.9.9'
     compile 'net.sf.jopt-simple:jopt-simple:4.9-beta-1'
     compile 'com.google.guava:guava:18.0'
-    compile 'com.google.cloud.dataflow:google-cloud-dataflow-java-sdk-all:0.3.150326'
-    compile 'com.google.apis:google-api-services-genomics:v1beta2-rev33-1.20.0'
-    compile 'com.google.cloud.genomics:google-genomics-utils:v1beta2-0.22'
+    compile 'com.google.cloud.dataflow:google-cloud-dataflow-java-sdk-all:0.4.150414'
+    compile 'com.google.apis:google-api-services-genomics:v1beta2-rev39-1.20.0'
+    compile 'com.google.cloud.genomics:google-genomics-utils:v1beta2-0.23'
     compile 'com.google.appengine.tools:appengine-gcs-client:0.4.4'
 
-    testCompile 'org.testng:testng:6.8.8'
+    testCompile 'org.testng:testng:6.8.21'
     //needed for DataflowAssert
     testCompile 'org.hamcrest:hamcrest-all:1.3'
     testCompile 'junit:junit:4.12'