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