Remove old unused code

...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/hist2count.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

.../nl/lumc/sasc/biopet/pipelines/gentrap/scripts/plot_pca.R

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

.../biopet/pipelines/gentrap/templates/pdf/gentrap_front.png

.../lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib.tex

...sc/biopet/pipelines/gentrap/templates/pdf/lib_mapping.tex

...sc/biopet/pipelines/gentrap/templates/pdf/lib_seqeval.tex

...lumc/sasc/biopet/pipelines/gentrap/templates/pdf/main.tex

...mc/sasc/biopet/pipelines/gentrap/templates/pdf/sample.tex

...biopet/pipelines/gentrap/templates/pdf/sample_mapping.tex

...umc/sasc/biopet/pipelines/gentrap/CufflinksProducer.scala

...c/biopet/pipelines/gentrap/extensions/CustomVarScan.scala

...c/sasc/biopet/pipelines/gentrap/extensions/Pdflatex.scala

.../biopet/pipelines/gentrap/extensions/RawBaseCounter.scala