added fastQC job. Not used at the moment because pipeline starts from chunks. If this changes to non chunked then fastqc job can be used. Or chunks can be joined to use the fastQC job.
Merge branch 'master' of https://github.com/WimS83/mappingPipeLine.git
disabled checking of amount of reads after mapping. This does not work wit already split or gzipped input and also does not work for bwa-mem. Also takes time. 

If Merge bam works then mapping should have worked for all reads / chunks.
added flexible forward en reverse identifier string for illumina PE read group.
made bqsr option more clear, also a bed file can be used. Added getters and setters for forward en reverse identifier for Illumina PE readgroup.
Merge branch 'master' of https://github.com/WimS83/mappingPipeLine.git