vtfp.pl now evaluates subst directives in the subst_param section
added cfgdatadir path to included alignment_common.json
decided against introducing a new file extension (spf) for now, so renaming alignment_common.spf to alignment_common.json.
amended subgraph files to correctly pick up the shared params in alignment_common.json.
corrected some flags for tophat2 command
corrected specification of flagstat_file file name
elements in the subst_param section should be identified by id, but PARAM-type nodes were using the name attribute instead. Corrected (vtfp.pl) code and templates.
Initial attempt at adding "form" for yhuman separation option to stage2