Merge branch 'develop' into feature-FilterOnMappingQualityCarp

...la/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala

...mc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala

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

...l/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala

...l/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala

...in/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala

...scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala

.../nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala

...cala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala

public/biopet-extensions/src/test/resources/log4j.properties

...umc/sasc/biopet/extensions/picard/picard.alignmentMetrics

...l/lumc/sasc/biopet/extensions/picard/picard.dedup.metrics

...mc/sasc/biopet/extensions/picard/picard.insertsizemetrics

...test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala

...scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala

...rc/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala

...xtensions/picard/CollectAlignmentSummaryMetricsTest.scala

...opet/extensions/picard/CollectInsertSizeMetricsTest.scala

...mc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala

public/pom.xml