Merge branch 'develop' into feature-wipereads

.idea/libraries/Maven__org_mockito_mockito_all_1_9_5.xml

Biopet.iml

biopet-framework/BiopetFramework.iml

biopet-framework/pom.xml

...ain/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala

...l/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala

...umc/sasc/biopet/extensions/svcallers/BreakdancerVCF.scala

.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala

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

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

.../nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala

...scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala

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

...n/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala

...scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala

.../lumc/sasc/biopet/extensions/svcallers/breakdancer2vcf.py

biopet-framework/src/test/resources/paired01a.fq

biopet-framework/src/test/resources/paired01b.fq

biopet-framework/src/test/resources/single01.fq

.../lumc/sasc/biopet/tools/ExtractAlignedFastqUnitTest.scala