Merge pull request #1 from wtsi-npg/devel

update from wtsi-npg
Merge remote-tracking branch 'wtsi/devel' into devel
Merge pull request #8 from wtsi-npg/devel

Merge devel to master for release 0.02
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
Merge pull request #13 from wtsi-npg/devel

fix naming convention for bed files in tophat2 vtf
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 #17 from dkj/devel

bammarkduplicates revert & easily identify forks whilst waiting on open of fifo
Added Build Script
Added Build Script
Added git versioning to Build file
Use VERSION in log files
Merge pull request #1 from dkj/use_version

Use VERSION in log files
Merge pull request #19 from stepf/devel

Added Build File and recording version in deployed scripts and in log files
Merge pull request #18 from dkj/devel

Improve efficiency by using mbuffer in place of tee feeding bwa
Merge pull request #20 from wtsi-npg/devel

pull request from wtsi devel to master - release 0.05
Merge pull request #21 from wtsi-npg/master

pull request from wtsi master to devel - release 0.05