Merge remote-tracking branch 'origin/develop' into feature-gatk_et_option

.../nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala

...cala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

...umc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala

...asc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala

...scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala

...sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala

public/src/src/test/resources/log4j.properties

public/toucan/pom.xml

...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala

public/yamsvp/pom.xml

.../scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala

.../nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala

.../nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala

...n/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala