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Allele counting #48
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Allele counting #48
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knows the max value of an allelic state. The use of AlleleCountsMatrix will vastly speed up certain calculations for large data sets.
at the last site processed. The result is improved performance due not not processing "empty" parts of the alphabet space.
and addition of AlleleCountMatrix.
used to construct it.
if character state is encountered that is > matrix.max_allele
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Given the emphasis on performance, StateCounts is getting replaced with AlleleCountMatrix. This makes the overall design very similar to scikit-allel, but with more flexible handling of reference state encoding.