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
insert gaps into internal node sequences
make vcf format valid for pyvcf
length of array
identify gaps
Merge branch 'master' of github.com:sanger-pathogens/gubbins into fastml_no_gaps
use no gaps as input to fastml
fill out gaps at end
dont overwrite gapped position array
remove PyVCF and use custom parsing of ALT, massive speedup
Merge pull request #55 from andrewjpage/fastml_no_gaps

Fastml no gaps