Move Gentrap-specific scripts and their wrappers to the Gentrap package

...c/sasc/biopet/pipelines/gentrap/scripts/aggr_base_count.R

.../nl/lumc/sasc/biopet/pipelines/gentrap/scripts/bam_rna.py

.../nl/lumc/sasc/biopet/pipelines/gentrap/scripts/gc_dist.py

...lumc/sasc/biopet/pipelines/gentrap/scripts/insert_dist.py

...mc/sasc/biopet/pipelines/gentrap/scripts/parse_cuffcmp.py

.../lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py

...lumc/sasc/biopet/pipelines/gentrap/scripts/rna_metrics.py

...scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

...sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala

...mc/sasc/biopet/pipelines/gentrap/scripts/Hist2Count.scala