**v.0.3.7**

* fixed a bug in `write_vcf`, the function was using REF/ALT coding in integer
not character format. This function is used inside `vcf_imputation` and
sometimes inside `genomic_converter`. Thanks to @jeansebastienmoore for
highlighting the problem.

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: stackr
 Type: Package
 Title: GBS/RADseq Data Exploration, Manipulation and Visualization using R
-Version: 0.3.6
-Date: 2016-09-09
+Version: 0.3.7
+Date: 2016-09-12
 Encoding: UTF-8
 Authors@R: c(
   person("Thierry", "Gosselin", email = "thierrygosselin@icloud.com", role = c("aut", "cre")),

R/global_variables.R

@@ -13,7 +13,8 @@ if (getRversion() >= "2.15.1") {
       "FASTA_REF", "BP", "Chr", "Locus", "Locus ID", "Col", "PP", "ALLELE_GROUP",
       "PROBLEM", "IND_LEVEL_POLYMORPHISM", "HOM", "HET", "N_GENOT", "DIPLO",
       "FREQ_ALLELES", "HOM_E", "HOM_O", "FH", "HET_O", "HET_E", "PI", "pi",
-      "MONOMORPHIC", "POLYMORPHIC", "CONSENSUS", "PARALOGS", "Seg Dist")
+      "MONOMORPHIC", "POLYMORPHIC", "CONSENSUS", "PARALOGS", "Seg Dist", 
+      "REF.x", "ALT.x", "REF.y", "ALT.y")
   )
 }
 # 'GL', 'GL_MAX', 'GL_MIN', 'MIN_REF', 'MIN_ALT', 'READ_DEPTH_MAX', 

R/write_vcf.R

@@ -79,6 +79,13 @@ write_vcf <- function(data, pop.info = FALSE, filename = NULL) {
     input <- left_join(input, ref.alt.alleles.change, by = c("MARKERS", "INDIVIDUALS"))
   }
 
+  # remove duplicate REF/ALT column
+  if (tibble::has_name(input, "REF.x")) {
+    input <- input %>% select(-c(REF.x, ALT.x)) %>% 
+      rename(REF = REF.y, ALT = ALT.y)
+  }
+
+
   # Include CHROM, LOCUS, POS --------------------------------------------------
   if (!tibble::has_name(input, "CHROM")) {
     input <- mutate(
@@ -90,7 +97,7 @@ write_vcf <- function(data, pop.info = FALSE, filename = NULL) {
   }
 
   # Remove the POP_ID column ---------------------------------------------------
-  if (tibble::has_name(input, "POP_ID") & (!pop.info)) {
+  if (tibble::has_name(input, "POP_ID") || (!pop.info)) {
     input <- select(.data = input, -POP_ID)
   }
 
@@ -137,6 +144,22 @@ write_vcf <- function(data, pop.info = FALSE, filename = NULL) {
     )
   }
 
+  # Transform the REF/ALT format back to A/C/G/T
+  output <- output %>% 
+    mutate(
+      REF = stringi::stri_replace_all_fixed(
+        str = REF,
+        pattern = c("001", "002", "003", "004"),
+        replacement = c("A", "C", "G", "T"),
+        vectorize_all = FALSE),
+      ALT = stringi::stri_replace_all_fixed(
+        str = ALT,
+        pattern = c("001", "002", "003", "004"),
+        replacement = c("A", "C", "G", "T"),
+        vectorize_all = FALSE)
+    )
+
+  # Keep the required columns
   output <- output %>% 
     arrange(CHROM, LOCUS, POS) %>%
     ungroup() %>%

README.md

@@ -91,6 +91,13 @@ citation("stackr")
 ## New features
 Change log, version, new features and bug history now lives in the [NEWS.md file] (https://github.com/thierrygosselin/stackr/blob/master/NEWS.md)
 
+**v.0.3.7**
+* fixed a bug in `write_vcf`, the function was using REF/ALT coding in integer 
+not character format. This function is used inside `vcf_imputation` and 
+sometimes inside `genomic_converter`. Thanks to @jeansebastienmoore for 
+highlighting the problem.
+
+
 **v.0.3.6**
 * fixed a bug in `vcf_imputation`, the function now calls `genomic_converter` 
 with all the bells and whistles of that function (updated vcf import and imputations modules)