Merge branch 'develop' into feature-small_rna

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

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

...ala/nl/lumc/sasc/biopet/extensions/pindel/PindelVCF.scala

public/biopet-public-package/pom.xml

...in/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala

.../nl/lumc/sasc/biopet/extensions/tools/ValidateFastq.scala

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

.../main/scala/nl/lumc/sasc/biopet/tools/ValidateFastq.scala

public/biopet-tools/src/test/resources/paired01c.fq

...t/scala/nl/lumc/sasc/biopet/tools/ValidateFastqTest.scala

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

...s/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala

...c/test/scala/nl/lumc/sasc/biopet/utils/BamUtilsTest.scala

.../sasc/biopet/pipelines/flexiprep/CheckValidateFastq.scala

...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

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

...nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala

...l/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala

public/shiva/src/test/resources/paired01.bam

public/shiva/src/test/resources/paired01.bam.bai