Precompute A/B Counts and Biallelic Summary Func #14
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Precompute A/B counts for each sample set. We were previously computing them redundantly each for each site pair in our results matrix. The precomputation happens in a function called `get_mutation_sample_sets`, which takes our list of sets (`tsk_bitset_t`) for each mutation and intersects the samples with a particular mutation with the sample sets passed in by the user. The result is an expanded list of sets with one set per mutation per sample set. During this operation, we compute the number of samples containing the given allele for each mutation, avoiding the need to perform redundant count operations on the data. In addition to precomputation, we add a non-normalized version of `compute_general_two_site_stat_result` for situations where we're computing stats from biallelic loci. We dispatch the computation of the result based on the number of alleles in the two loci we're comparing. If the number of alleles in both loci is 2, then we simply perform an LD computation on the derived alleles for the two loci. As a result, we remove the need to compute a matrix of LD values, then take a weighted sum. This is much more efficient and means that we only run the full multiallelic LD routine on sites that are multiallelic.
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Precompute A/B counts for each sample set. We were previously computing them redundantly each for each site pair in our results matrix. The precomputation happens in a function called
get_mutation_sample_sets, which takes our list of sets (tsk_bitset_t) for each mutation and intersects the samples with a particular mutation with the sample sets passed in by the user. The result is an expanded list of sets with one set per mutation per sample set. During this operation, we compute the number of samples containing the given allele for each mutation, avoiding the need to perform redundant count operations on the data.In addition to precomputation, we add a non-normalized version of
compute_general_two_site_stat_resultfor situations where we're computing stats from biallelic loci. We dispatch the computation of the result based on the number of alleles in the two loci we're comparing. If the number of alleles in both loci is 2, then we simply perform an LD computation on the derived alleles for the two loci. As a result, we remove the need to compute a matrix of LD values, then take a weighted sum. This is much more efficient and means that we only run the full multiallelic LD routine on sites that are multiallelic.