Added --precise flag to getStatistics.R script to increase precision of statistics.

We need this for the MiSeq... Ask Eddy de Boer (or Lennart or me) for more details.
fixed a nasty bash array bug in MergeBam and some minor changes
Merge pull request #157 from RoanKanninga/master

fixed a nasty bash array bug in MergeBam and some minor changes
Merge pull request #158 from Gerbenvandervries/master

Bugfixes for PE RNA samples, and layout changes to the QC report
fixed the workflow
Added pppv protocol, added parameter to paramfiles, added ppv to workflow
fixed Pindel protocol
Merge branch 'master' of https://github.com/molgenis/molgenis-pipelines
Merge pull request #159 from RoanKanninga/master

fixed the workflow + Pindel fix
Merge pull request #160 from dirkdeweerd/master

Added pppv protocol, added parameter to paramfiles, added ppv to workflow
Merge branch 'master' of https://github.com/molgenis/molgenis-pipelines
bugfixing
added CoverageGATK step
added some small things to the SnpEff step (WIP)
Merge pull request #161 from RoanKanninga/master

bugfixing + adding CoverageGATK step
some bugfixes in coverageGATK
Merge pull request #162 from RoanKanninga/master

some bugfixes in coverageGATK
added max GC threads + FastQC fixing (Illumina 1.5 to 1.9 issue)
removed some duplicated code in FastQC
removed