Merge branch 'develop' into feature-small_rna

docs/general/config.md

docs/tools/SamplesTsvToJson.md

...e/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala

...sc/biopet/core/extensions/PythonCommandLineFunction.scala

...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

...a/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala

...lumc/sasc/biopet/extensions/samtools/fix_iupac_mpileup.py

...ces/nl/lumc/sasc/biopet/extensions/varscan/fix_mpileup.py

.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala

.../scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala

...asc/biopet/extensions/picard/AddOrReplaceReadGroups.scala

...la/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala

.../nl/lumc/sasc/biopet/extensions/samtools/FixMpileup.scala

...umc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala

public/biopet-tools-extensions/pom.xml

...cala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala

...iopet-tools-extensions/src/test/scala/VcfFilterTest.scala

...ain/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala

...in/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala

...ls/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala