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Mention third PoPoolation Tajima D bug in doc
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lczech committed May 26, 2024
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4 changes: 3 additions & 1 deletion lib/genesis/population/function/diversity_pool_functions.hpp
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Expand Up @@ -77,12 +77,14 @@ enum class TajimaDenominatorPolicy
/**
* @brief Replicate the original behaviour of PoPoolation <= 1.2.2.
*
* There are two major bugs (as far as we are aware) in the PoPoolation implementation
* There are three major bugs (as far as we are aware) in the PoPoolation implementation
* up until (and including) version 1.2.2:
*
* 1. They compute the empirical pool size (expeted number of individuals sequenced) as
* n_base(), based on pool size alone, and do not take the read depth into account at all.
* 2. They do not use alpha star, but set it to be equal to beta star instead.
* 3. To compute window averages, they use the number of SNPs in the window, instead of the
* number of all valid positions in the window.
*
* Using this option, one can voluntarily activate these bugs here as well, in order to get
* results that are comparable with PoPoolation results.
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