Implemented 2-pass alignment

- replaced STAR 2-pass alignment with equivalent workaround until
  2-pass alignment with including annotated junctions is available
- added option to allow for a weak RG check that replaces that generates
  a generic read group label in case one input file is given but the
  metadata contains several read groups
- minor changes to in parameter default settings
Added option to use metadata spreadsheet as input.

- added two new command line options to specify a metadata
  spreadsheet file and an analysis id to align instead of an xml
- added sanity checks for command line parameters
- fixed some comments in the code