Merge branch 'develop' of git.lumc.nl:biopet/biopet into feature-yamsvp

.idea/misc.xml

...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

...lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala

...umc/sasc/biopet/extensions/gatk/VariantRecalibrator.scala

...ala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

...rces/nl/lumc/sasc/biopet/scripts/sync_paired_end_reads.py

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

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

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

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

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala

...in/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala

...c/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala

...rc/main/scala/nl/lumc/sasc/biopet/scripts/FastqSync.scala

.../src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala

...c/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala

...rc/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala

.../test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala

...ala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala