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
Merge pull request #21 from wtsi-npg/master

pull request from wtsi master to devel - release 0.05
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
Adding vtf file for running the SNAP aligner on a sample
Merge pull request #23 from jidur/snap

Adding vtf file for running the SNAP aligner on a sample
example vtf files aligning sequence data from illumina2bam through bwa mem alignment to production of final bam and cram files. Bamcheck and flagstats, no spatial filtering.
corrected repeated subst_param names which were causing failure to output cram, bamcheck and flagstat files correctly for both target and phix
Merge pull request #24 from dozy/bwa_mem_example

Bwa mem example
Confirming my own pull request - but these are all new files, and they are only examples
Added new dependency to Build file
Added new dependencies
add keep-fasta-order option to tophat2