Merge branch 'develop' of git.lumc.nl:biopet/biopet into feature-gears

...src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala

.../src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala

...ain/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala

...ns/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala

...src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala

...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala

...c/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala

.../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala

...src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala

.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala

...in/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala

.../src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala

...la/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala

...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala

...la/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala

...mc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala