merge from devel for release 0.08

Production changes:
   1. viv.pl - added checking of input/output connections between nodes, enforcing IN and OUT naming conventions for "ports"
   2. vtfp-.pl - now allows an incoming edge/data source to be connected to multiple targets in a subgraph (VTLIB node) [note: static data only, not yet for streamed data]
   3. update of current bwa_mem and tophat2 templates to contain fixmate, adddupmarksupport, and upgrade to bamstreamingmarkduplicates; also addition of calibration_pu to produce error files for QC