The greedy_caller function is used to find an initial genotype for the CallingMCMC.fit() method.
In version 0.5.0 the greedy_caller function is hard-coded to use int8 which results in an overflow when there are > 128 unique haplotypes which does occur in some situations. The mcmc_sampler itself infers the genotype_trace dtype from the input (initial) genotype. The genotype trace itself is shape (n_chains n_steps ploidy) and hence is unlikely to be a problem so there is no reason not to use int64 here.
timothymillar
commented
3 years ago
The
greedy_callerfunction is used to find an initial genotype for theCallingMCMC.fit()method. In version 0.5.0 thegreedy_callerfunction is hard-coded to use int8 which results in an overflow when there are > 128 unique haplotypes which does occur in some situations. The mcmc_sampler itself infers the genotype_trace dtype from the input (initial) genotype. The genotype trace itself is shape (n_chains n_steps ploidy) and hence is unlikely to be a problem so there is no reason not to use int64 here.