Merge pull request #62 from dkj/devel

run teepot with -v option
This is the vtfp.pl which handled the new subst_param format. Old-style templates can no longer be proceesed with this.
templates converted to new subst_params format
vtlib templates modified to use the new subst_param format
added alignment_common.spf file containing common subst_param definitions
now added alignment_common.spf file containing common subst_param definitions
removed unused template file
only set stdin/stdout to /dev/null for a node if attribute use_STDIN/use_STDOUT is not true
moved alignment_common.spf to its rightful place in data/vtlib
viv.pl - removed commented code
vtfp.pl - added -template_path flag to allow specification default location of template files
vtfp.pl - updated template_path handling
alignment_common.spf - removed duplicate aligner_numthreads declaration
moved creation of output files from alignment_wtsi_stage2_template to the final_output_prep subgraph.
final_output_prep now has one bam input and one bam output.