Merge branch 'develop' into feature-pipeable

docs/tools/SamplesTsvToJson.md

public/biopet-framework/pom.xml

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

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

...cala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala

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

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

...in/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala

...rk/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala

...c/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala

.../src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala

...k/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala

...src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala

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

...k/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala

public/biopet-framework/src/test/resources/chrQ2.vcf

public/biopet-framework/src/test/resources/chrQ2.vcf.gz