remove unused cpp functions for hwe

EvolEcolGroup · Jun 16, 2024 · 16cf5a0 · 16cf5a0
1 parent 6054c9b
commit 16cf5a0
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Showing 8 changed files with 631 additions and 476 deletions.
diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -25,14 +25,6 @@ SNPHWE2 <- function(obs_hets, obs_hom1, obs_hom2, midp) {
     .Call(`_tidypopgen_SNPHWE2`, obs_hets, obs_hom1, obs_hom2, midp)
 }
 
-SNPHWE_t <- function(obs_hets, obs_hom1, obs_hom2, thresh) {
-    .Call(`_tidypopgen_SNPHWE_t`, obs_hets, obs_hom1, obs_hom2, thresh)
-}
-
-SNPHWE_midp_t <- function(obs_hets, obs_hom1, obs_hom2, thresh) {
-    .Call(`_tidypopgen_SNPHWE_midp_t`, obs_hets, obs_hom1, obs_hom2, thresh)
-}
-
 increment_as_counts <- function(k, k2, na_mat, dos_mat, BM, rowInd, colInd) {
     invisible(.Call(`_tidypopgen_increment_as_counts`, k, k2, na_mat, dos_mat, BM, rowInd, colInd))
 }

diff --git a/R/vcf_to_fbm.R b/R/vcf_to_fbm.R
@@ -95,6 +95,7 @@ vcf_to_fbm <- function(
     gt <- vcfR::extract.gt(temp_vcf)
     gt <- gt[bi,,drop=FALSE]
     if (nrow(gt)>1){
+      # @TODO we could parallelise here
       gt <- t(apply(gt,2,poly_indiv_dosage, max_ploidy=max_ploidy))
     } else if (nrow(gt)==1){ # if we only have one marker
       gt <- matrix(apply(gt,2,poly_indiv_dosage, max_ploidy=max_ploidy),ncol=1)