Could be used for detecting possible recombinants: when some alts come up for 2 different constellations - could do a stat as to how interspersed they are i.e. (if A and B are the constellations): "AAABBB" has the least possible interspersion, ABABAB has the maximum interspersion.
(the former is possibly recombination, the latter possibly contamination or co-infection).
Since constellations are currently typed independently, this would need to run after intial classification step, possibly including only the best two classifications (although care where constellations differ by 1 mutation eg cB.1.1.7, cB.1.1.7+E484K)
Could be used for detecting possible recombinants: when some alts come up for 2 different constellations - could do a stat as to how interspersed they are i.e. (if A and B are the constellations): "AAABBB" has the least possible interspersion, ABABAB has the maximum interspersion. (the former is possibly recombination, the latter possibly contamination or co-infection).
Since constellations are currently typed independently, this would need to run after intial classification step, possibly including only the best two classifications (although care where constellations differ by 1 mutation eg cB.1.1.7, cB.1.1.7+E484K)