switched to most recent version of STAR
Adapted python stub to the latest STAR SOP

- extended and reformatted arg-parser to give users better information
  on the available options
- added more possibilities to add read group information to the BAM
  header (@RG line) based on direct input or a tcga xml file.
- replaced downstream usage of samtools with alternatives that are part
  of STAR (sorting, multiple input fast files)
- allowed alignment of single end read sets
- added additional decompression setting for bzips