# radiator 1.3.1 2024-04-23

* Updated DArT code that use COUNT files to check more for problematic markers usually stemming from merged project
thierrygosselin · Apr 23, 2024 · 899436d · 899436d
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: radiator
 Type: Package
 Title: RADseq Data Exploration, Manipulation and Visualization using R
-Version: 1.3.0
-Date: 2024-02-22
+Version: 1.3.1
+Date: 2024-04-23
 Encoding: UTF-8
 Authors@R: c(
   person("Thierry", "Gosselin", email = "thierrygosselin@icloud.com", role = c("aut", "cre")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# radiator 1.3.1 2024-04-23
+
+* Updated DArT code that use COUNT files to check more for problematic markers usually stemming from merged projects
+
+
 # radiator 1.3.0 2024-02-22
 
 * Bug fix using coverage and DArT data

diff --git a/R/dart.R b/R/dart.R
@@ -882,8 +882,8 @@ import_dart <- function(
     target.id = strata.df$INDIVIDUALS,
     verbose = TRUE)
 
-  # Check for problematic DArT 2 rows ------------------------------------------
-  if (dart.format == "2rows") {
+  # Check for problematic DArT 2 rows and counts --------------------------------
+  if (dart.format == "2rows" || dart.format == "counts") {
     n.markers <- length(unique(data$MARKERS))
     if (n.markers != nrow(data) / 2) {
       message("\n\nProblem with DArT file")
@@ -1269,15 +1269,15 @@ dart2gds <- function(
       dplyr::mutate(
         dplyr::across(
           .cols = c(READ_DEPTH, ALLELE_REF_DEPTH, ALLELE_ALT_DEPTH),
-          .fns = replace_by_na, what = 0L
+          .fns = ~ replace_by_na(data = ., what = 0L)
         )
       )
   } else {
     genotypes.meta %<>%
       dplyr::mutate(
         dplyr::across(
           .cols = "ALLELE_REF_DEPTH",
-          .fns = switch_allele_count, dart.group = FALSE
+          .fns = ~ switch_allele_count(x = ., dart.group = FALSE, ref = TRUE)
         )
       ) %>%
       dplyr::mutate(
@@ -1290,7 +1290,7 @@ dart2gds <- function(
 
 
   # genotypes array ----------------------------------------------------------
-    if (gt.vcf) {
+  if (gt.vcf) {
     genotypes.meta %<>%
       dplyr::mutate(
         GT_VCF = dplyr::case_when(

diff --git a/README.md b/README.md
@@ -7,8 +7,8 @@ state and is being actively
 developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
 [![minimal R
 version](https://img.shields.io/badge/R%3E%3D-NA-6666ff.svg)](https://cran.r-project.org/)
-[![packageversion](https://img.shields.io/badge/Package%20version-1.3.0-orange.svg)](commits/master)
-[![Last-changedate](https://img.shields.io/badge/last%20change-2024--02--25-brightgreen.svg)](/commits/master)
+[![packageversion](https://img.shields.io/badge/Package%20version-1.3.1-orange.svg)](commits/master)
+[![Last-changedate](https://img.shields.io/badge/last%20change-2024--04--23-brightgreen.svg)](/commits/master)
 [![R-CMD-check](https://github.com/thierrygosselin/radiator/workflows/R-CMD-check/badge.svg)](https://github.com/thierrygosselin/radiator/actions)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3687060.svg)](https://doi.org/10.5281/zenodo.3687060)
 <!-- badges: end -->

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/get_started.html b/docs/articles/get_started.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/life_cycle.html b/docs/articles/life_cycle.html
diff --git a/docs/articles/rad_genomics_computer_setup.html b/docs/articles/rad_genomics_computer_setup.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -5,5 +5,5 @@ articles:
   get_started: get_started.html
   life_cycle: life_cycle.html
   rad_genomics_computer_setup: rad_genomics_computer_setup.html
-last_built: 2024-01-25T22:34Z
+last_built: 2024-04-23T22:04Z
 
diff --git a/docs/reference/Exposition_pipe_operator.html b/docs/reference/Exposition_pipe_operator.html
diff --git a/docs/reference/allele_count.html b/docs/reference/allele_count.html
diff --git a/docs/reference/allele_frequencies.html b/docs/reference/allele_frequencies.html
diff --git a/docs/reference/assign_defaults.html b/docs/reference/assign_defaults.html
diff --git a/docs/reference/bayescan_one.html b/docs/reference/bayescan_one.html
diff --git a/docs/reference/betas_estimator.html b/docs/reference/betas_estimator.html
diff --git a/docs/reference/blacklist_hw.html b/docs/reference/blacklist_hw.html
diff --git a/docs/reference/boxplot_stats.html b/docs/reference/boxplot_stats.html
diff --git a/docs/reference/calibrate_alleles.html b/docs/reference/calibrate_alleles.html
diff --git a/docs/reference/change_pop_names.html b/docs/reference/change_pop_names.html
diff --git a/docs/reference/check_args_class.html b/docs/reference/check_args_class.html
diff --git a/docs/reference/check_dart.html b/docs/reference/check_dart.html