# radiator 1.3.3 2024-05-15

* Fix issue #188 related to coverage in DArT 1row and 2rows format

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: radiator
 Type: Package
 Title: RADseq Data Exploration, Manipulation and Visualization using R
-Version: 1.3.2
-Date: 2024-04-30
+Version: 1.3.3
+Date: 2024-05-15
 Encoding: UTF-8
 Authors@R: c(
   person("Thierry", "Gosselin", email = "thierrygosselin@icloud.com", role = c("aut", "cre")),

NEWS.md

@@ -1,3 +1,10 @@
+# radiator 1.3.3 2024-05-15
+
+* Fix issue #188 related to coverage in DArT 1row and 2rows format
+
+
+
+
 # radiator 1.3.2 2024-04-30
 
 * works with R 4.3.4

R/gds.R

@@ -971,7 +971,7 @@ extract_genotypes_metadata <- function(
 #' baddly generated. It will say you have Read and allele Depth info, but you don't.
 #' Default: \code{stacks.haplo.check = FALSE}.
 #' @param dart.check (optional, logical) DArT have different reporting for coverage
-#' information.
+#' information. Will no longer report the average coverage stats from 1 and 2-rows DArT format.
 #' Default: \code{dart.check = FALSE}.
 # @keywords internal
 #' @export
@@ -1000,15 +1000,21 @@ check_coverage <- function(gds, genotypes.metadata.check = FALSE, stacks.haplo.c
   # DArT count and 1 and 2 rows have different information...
   if (dart.check && "dart" %in% data.source) {
     if (any(c("2rows", "1row") %in% data.source)) {
-      got.coverage <- extract_markers_metadata(
-        gds,
-        markers.meta.select = c("AVG_COUNT_REF", "AVG_COUNT_SNP"),
-        whitelist = TRUE
-      )
-      if (!is.null(got.coverage)) {
-        got.coverage <- c("AVG_COUNT_REF", "AVG_COUNT_SNP")
-        return(got.coverage)
-      }
+      # got.coverage <- extract_markers_metadata(
+      #   gds,
+      #   markers.meta.select = c("AVG_COUNT_REF", "AVG_COUNT_SNP"),
+      #   whitelist = TRUE
+      # )
+      # if (!is.null(got.coverage)) {
+      #   got.coverage <- c("AVG_COUNT_REF", "AVG_COUNT_SNP")
+      #   return(got.coverage)
+      # }
+      message("Coverage statistics information for 2rows and 1row DArT format is ignored")
+      message("\nradiator cannot generate coverage statistics from source\npotential blacklisted individuals bias the statistics generated by DArT")
+      message("\nrequest DArT count format from DArT")
+
+      got.coverage <- NULL
+      return(got.coverage)
     }#End DART 1row and 2 rows
   }
 
@@ -2162,7 +2168,7 @@ generate_stats <- function(
   # subsample = variant.select
   # exhaustive = FALSE
   # force.stats = TRUE
-  # # path.folder = NULL
+  # path.folder = NULL
   # plot = TRUE
   # digits = 6
   # # file.date = NULL
@@ -2562,7 +2568,7 @@ generate_stats <- function(
         }
 
         if (individuals) {
-          # changing the margin doesnt work with seqarray, the GDS needs to be optimized by sample
+          # changing the margin doesn't work with seqarray, the GDS needs to be optimized by sample
           # this operation is very costly in both time and disk space.
           # faster to do matrix calculations by rows and sums
           # Note to myself: the huge speed gain by using other packages robustbse, Rfast, etc.
@@ -2791,11 +2797,11 @@ generate_stats <- function(
   # NOTE TO MYSELF need to work on including that one with DArT files...--------
   #DArT 1 row and 2rows --------------------------------------------------------
   # if ("dart" %in% data.source && any(c("2rows", "1row") %in% data.source)) {
-  #   depth <- extract_markers_metadata(
-  #     gds,
-  #     markers.meta.select = c("AVG_COUNT_REF", "AVG_COUNT_SNP"),
-  #     whitelist = TRUE
-  #   )
+    # depth <- extract_markers_metadata(
+      # gds,
+      # markers.meta.select = c("AVG_COUNT_REF", "AVG_COUNT_SNP"),
+      # whitelist = TRUE
+    # )
   #   markers <- ind <- FALSE
   #
   #   if (is.null(depth)) return(NULL)

README.md

@@ -5,8 +5,8 @@
 [![Project Status: Active – The project has reached a stable, usable
 state and is being actively
 developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
-[![packageversion](https://img.shields.io/badge/Package%20version-1.3.2-orange.svg)](commits/master)
-[![Last-changedate](https://img.shields.io/badge/last%20change-2024--04--30-brightgreen.svg)](/commits/master)
+[![packageversion](https://img.shields.io/badge/Package%20version-1.3.3-orange.svg)](commits/master)
+[![Last-changedate](https://img.shields.io/badge/last%20change-2024--05--15-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)
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