Merge pull request #48 from andrewjpage/master

versioning
Merge pull request #50 from andrewjpage/master

Fastml integration
Merge pull request #51 from andrewjpage/master

strip off input params when testing if exec is in path
Merge pull request #52 from andrewjpage/master

make drawer work with empty tracks
Merge pull request #53 from andrewjpage/master

snp branch output and prefiltering aln
Merge pull request #54 from andrewjpage/master

readme
Merge branch 'master' of github.com:sanger-pathogens/gubbins into fastml_no_gaps