Do a 'union' haplotype of multiple definition files.

[rambaut]

As an option for the haplotype command (perhaps --combination?), take the union of all the mutations in the current set of constellation files and create a single haplotype string of that. One string could be the actual states (amino acid, nucleotide, deletion) a second string could be composed of letters denoting which constellation it matches at that site (with - to denote reference and perhaps a digit to denote how many constellations it matches in case of multiple matches).

This could link to Issue #10 - optional interspersion statistic to detect recombination

[rmcolq]

See commit cae6e1c