Fix sumstat_file() with ms (#190)

* Fix #188

* Use Rcpp native routines registration

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: coala
-Version: 0.5.1
+Version: 0.5.2
 License: MIT + file LICENSE
 Title: A Framework for Coalescent Simulation
 Authors@R: c(

NEWS.md

@@ -1,3 +1,10 @@
+coala 0.5.2
+===========
+
+* Fix sumstat_file() with ms (#188). Thanks to @acottin for reporting this issue!
+
+
+
 coala 0.5.1
 ===========
 

R/RcppExports.R

@@ -1,99 +1,99 @@
-# Generated by using Rcpp::compileAttributes() -> do not edit by hand
-# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
-
-parse_ms_positions <- function(line) {
-    .Call(coala_parse_ms_positions, line)
-}
-
-parse_ms_output <- function(file_names, sample_size, loci_number) {
-    .Call(coala_parse_ms_output, file_names, sample_size, loci_number)
-}
-
-parse_seqgen_output <- function(output, individuals, locus_length, locus_number, outgroup_size, calc_segsites = TRUE) {
-    .Call(coala_parse_seqgen_output, output, individuals, locus_length, locus_number, outgroup_size, calc_segsites)
-}
-
-generate_trio_trees <- function(trees, trio_dists, file_names) {
-    .Call(coala_generate_trio_trees, trees, trio_dists, file_names)
-}
-
-#' @describeIn segsites Creates segregating sites
-#'
-#' @param snps The SNP Matrix (see Details).
-#' @param positions A numeric vector indicating the relative positions of each
-#'   SNP on the locus (see Details).
-#' @param trio_locus If the locus consists of a locus trio (see Details).
-#' @param check Whether non-segregating sites are removed from the segregating
-#'   sites (\code{TRUE}) or not (\code{FALSE}).
-#' @export
-#'
-create_segsites <- function(snps, positions, trio_locus = numeric(0), check = TRUE) {
-    .Call(coala_create_segsites, snps, positions, trio_locus, check)
-}
-
-#' @describeIn segsites Returns the SNP matrix from a segregating sites
-#'  object.
-#'
-#' @param segsites The segregating sites object
-#' @export
-get_snps <- function(segsites) {
-    .Call(coala_get_snps, segsites)
-}
-
-#' @describeIn segsites Returns the SNP's positions from a segregating
-#'   sites  object.
-#' @export
-get_positions <- function(segsites) {
-    .Call(coala_get_positions, segsites)
-}
-
-#' @describeIn segsites Sets the SNP's positions in a segregating
-#'   sites object.
-#' @export
-set_positions <- function(segsites, positions) {
-    .Call(coala_set_positions, segsites, positions)
-}
-
-#' @describeIn segsites Returns the trio locus positions from a
-#'   segregating sites  object.
-#' @export
-get_trio_locus <- function(segsites) {
-    .Call(coala_get_trio_locus, segsites)
-}
-
-#' @describeIn segsites Sets the trio locus in a segregating sites
-#'   object.
-#' @export
-set_trio_locus <- function(segsites, trio_locus) {
-    .Call(coala_set_trio_locus, segsites, trio_locus)
-}
-
-calc_four_gamete_stat <- function(seg_sites_list, individuals, locus_length, ploidy = 1L) {
-    .Call(coala_calc_four_gamete_stat, seg_sites_list, individuals, locus_length, ploidy)
-}
-
-#' Calculates the Joint Site Frequency Spectrum
-#'
-#' @param segsites_list List of segregating sites
-#' @param ind_per_pop A list of integer vector, where each entry gives the
-#'   index of the haploids that belong the corresponding population.
-#'
-#' @author Paul Staab & Dirk Metzler
-#' @return The Joint Site Frequency Spectrum, as a matrix.
-#' @keywords internal
-calc_jsfs <- function(segsites_list, ind_per_pop) {
-    .Call(coala_calc_jsfs, segsites_list, ind_per_pop)
-}
-
-calc_mcmf <- function(seg_sites, individuals, has_trios = TRUE, expand_mcmf = FALSE, type_expand = 1L, ploidy = 1L, locus_length = matrix(0)) {
-    .Call(coala_calc_mcmf, seg_sites, individuals, has_trios, expand_mcmf, type_expand, ploidy, locus_length)
-}
-
-calc_nucleotide_div <- function(segsites_list, individuals) {
-    .Call(coala_calc_nucleotide_div, segsites_list, individuals)
-}
-
-unphase_segsites <- function(seg_sites_list, ploidy, samples_per_ind) {
-    .Call(coala_unphase_segsites, seg_sites_list, ploidy, samples_per_ind)
-}
-
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+parse_ms_positions <- function(line) {
+    .Call(`_coala_parse_ms_positions`, line)
+}
+
+parse_ms_output <- function(file_names, sample_size, loci_number) {
+    .Call(`_coala_parse_ms_output`, file_names, sample_size, loci_number)
+}
+
+parse_seqgen_output <- function(output, individuals, locus_length, locus_number, outgroup_size, calc_segsites = TRUE) {
+    .Call(`_coala_parse_seqgen_output`, output, individuals, locus_length, locus_number, outgroup_size, calc_segsites)
+}
+
+generate_trio_trees <- function(trees, trio_dists, file_names) {
+    .Call(`_coala_generate_trio_trees`, trees, trio_dists, file_names)
+}
+
+#' @describeIn segsites Creates segregating sites
+#'
+#' @param snps The SNP Matrix (see Details).
+#' @param positions A numeric vector indicating the relative positions of each
+#'   SNP on the locus (see Details).
+#' @param trio_locus If the locus consists of a locus trio (see Details).
+#' @param check Whether non-segregating sites are removed from the segregating
+#'   sites (\code{TRUE}) or not (\code{FALSE}).
+#' @export
+#'
+create_segsites <- function(snps, positions, trio_locus = numeric(0), check = TRUE) {
+    .Call(`_coala_create_segsites`, snps, positions, trio_locus, check)
+}
+
+#' @describeIn segsites Returns the SNP matrix from a segregating sites
+#'  object.
+#'
+#' @param segsites The segregating sites object
+#' @export
+get_snps <- function(segsites) {
+    .Call(`_coala_get_snps`, segsites)
+}
+
+#' @describeIn segsites Returns the SNP's positions from a segregating
+#'   sites  object.
+#' @export
+get_positions <- function(segsites) {
+    .Call(`_coala_get_positions`, segsites)
+}
+
+#' @describeIn segsites Sets the SNP's positions in a segregating
+#'   sites object.
+#' @export
+set_positions <- function(segsites, positions) {
+    .Call(`_coala_set_positions`, segsites, positions)
+}
+
+#' @describeIn segsites Returns the trio locus positions from a
+#'   segregating sites  object.
+#' @export
+get_trio_locus <- function(segsites) {
+    .Call(`_coala_get_trio_locus`, segsites)
+}
+
+#' @describeIn segsites Sets the trio locus in a segregating sites
+#'   object.
+#' @export
+set_trio_locus <- function(segsites, trio_locus) {
+    .Call(`_coala_set_trio_locus`, segsites, trio_locus)
+}
+
+calc_four_gamete_stat <- function(seg_sites_list, individuals, locus_length, ploidy = 1L) {
+    .Call(`_coala_calc_four_gamete_stat`, seg_sites_list, individuals, locus_length, ploidy)
+}
+
+#' Calculates the Joint Site Frequency Spectrum
+#'
+#' @param segsites_list List of segregating sites
+#' @param ind_per_pop A list of integer vector, where each entry gives the
+#'   index of the haploids that belong the corresponding population.
+#'
+#' @author Paul Staab & Dirk Metzler
+#' @return The Joint Site Frequency Spectrum, as a matrix.
+#' @keywords internal
+calc_jsfs <- function(segsites_list, ind_per_pop) {
+    .Call(`_coala_calc_jsfs`, segsites_list, ind_per_pop)
+}
+
+calc_mcmf <- function(seg_sites, individuals, has_trios = TRUE, expand_mcmf = FALSE, type_expand = 1L, ploidy = 1L, locus_length = matrix(0)) {
+    .Call(`_coala_calc_mcmf`, seg_sites, individuals, has_trios, expand_mcmf, type_expand, ploidy, locus_length)
+}
+
+calc_nucleotide_div <- function(segsites_list, individuals) {
+    .Call(`_coala_calc_nucleotide_div`, segsites_list, individuals)
+}
+
+unphase_segsites <- function(seg_sites_list, ploidy, samples_per_ind) {
+    .Call(`_coala_unphase_segsites`, seg_sites_list, ploidy, samples_per_ind)
+}
+

R/simulator_ms.R

@@ -75,7 +75,7 @@ ms_class <- R6Class("ms", inherit = simulator_class,
       }
 
       # Add the file if needed
-      if (requires_files(model)) output$file <- result$file
+      if (requires_files(model)) output$files <- result$file
       else unlink(result$file)
 
       # Add the simulation cmd