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cov-lineages / scorpio

serious constellations of reoccurring phylogenetically-independent origin
GNU General Public License v3.0
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Do a 'union' haplotype of multiple definition files. #26

Closed rambaut closed 2 years ago

rambaut commented 3 years ago

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 commented 3 years ago

See commit cae6e1cc2e43a6055d1ce5463c4cb0d9d2002535