Merge pull request #1 from wtsi-npg/devel

update from wtsi-npg
Merge remote-tracking branch 'wtsi/devel' into devel
vtfp.pl: initial version of subgraph handling
viv.pl: tidying
Exampless for subgraphs (VTFILE nodes)
subgraphs - use of multiple VTFILE nodes using the same vtf file, no recursive VTFILE processing yet
Some examples of use of the VTFILE node to specify subgraphs in a vtf file. Accidentally reintroduced adapter reinsert bug (incorrect combination of bamreset/bamadapterfind/bam12auxmerge/... options), but I hope they will still be useful examples.
viv.pl - addded flags to specify insertion of RAFILE nodes at runtime (cl options processing only so far)
vtfp.pl - fixed bug in walk() - now correctly records attrib_names of subst_params with repeated names
alignment_postphixaln.vtf - corrected default path to AlignmentFilter.jar (from devel version to live)
README.visualisation - removed explicit hostnames in URL example
add subst_map attribute to VTFILE nodes to allow "local" values to override the global subst_param values (provides a form of parameterisation).

correct mistaken failure of nested required subst_param
removed some questionable example files
Resolved conflict

Merge branch 'subgraphs' of https://github.com/dozy/p4 into dozy-subgraphs

Conflicts:
	bin/vtfp.pl
Merge branch 'dozy-subgraphs' into devel