Update to Queue/GATK 3.2

.gitignore

bam-metrics/pom.xml

...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

...c/biopet/pipelines/bammetrics/scripts/CoverageStats.scala

biopet-framework/pom.xml

.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala

...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala

...n/scala/nl/lumc/sasc/biopet/core/BiopetQCommandLine.scala

...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

...main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala

...n/scala/nl/lumc/sasc/biopet/core/apps/BedToInterval.scala

.../scala/nl/lumc/sasc/biopet/core/apps/BiopetFlagstat.scala

...n/scala/nl/lumc/sasc/biopet/core/apps/FastqSplitter.scala

...c/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala

.../scala/nl/lumc/sasc/biopet/core/config/Configurable.scala

...ork/src/main/scala/nl/lumc/sasc/biopet/function/Cat.scala

...work/src/main/scala/nl/lumc/sasc/biopet/function/Ln.scala

.../src/main/scala/nl/lumc/sasc/biopet/function/Pbzip2.scala

...lumc/sasc/biopet/function/PythonCommandLineFunction.scala