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Support multiple alleles #11

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jeromekelleher opened this issue May 24, 2022 · 2 comments · May be fixed by #142
Open

Support multiple alleles #11

jeromekelleher opened this issue May 24, 2022 · 2 comments · May be fixed by #142
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enhancement New feature or request

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@jeromekelleher
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In the simplest case, the reference panel can contain values > 1. Initial version can assume that mutation rates among the k existing alleles are equal. We should keep the possibility open of providing arbitrary transition matrix between states.

May be as easy to do in the first pass as a kxk uniform transition matrix that we create, and then worry about making a parameter later.
@astheeggeggs
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we currently consider the simplest case, whereby multiple alleles are allowed at a given site but where mutation probabilities to each are equal.

@szhan szhan added the enhancement New feature or request label Jun 17, 2024
This was referenced Jul 1, 2024
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@szhan
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szhan commented Jul 2, 2024

It should be now easy to switch the emission probability matrix to support multiple alleles.

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Support multiple allelic states szhan/lshmm
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@jeromekelleher @szhan @astheeggeggs