Merge branch 'waiyi' into 'master'

biopet-framework/nb-configuration.xml

biopet-framework/nbactions-yamsvp.xml

biopet-framework/pom.xml

...c/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala

...cala/nl/lumc/sasc/biopet/extensions/aligners/Stampy.scala

...la/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala

...mc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala

.../lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala

...umc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala

.../lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala

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

...ala/nl/lumc/sasc/biopet/extensions/svcallers/Clever.scala

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

...asc/biopet/extensions/svcallers/pindel/PindelCaller.scala

...asc/biopet/extensions/svcallers/pindel/PindelConfig.scala

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

...mc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala

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

.../src/main/scripts/nl/lumc/sasc/biopet/scripts/seq_stat.py