Fix bug in encode_geno()

- use of nchar() didn't work right if allele_codes was a data frame
rqtl · Mar 25, 2021 · 3cad8d0 · 3cad8d0
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: qtl2convert
-Version: 0.22-7
-Date: 2020-06-30
+Version: 0.23-1
+Date: 2021-03-25
 Title: Convert Data among QTL Mapping Packages
 Description: Functions to convert data structures among the 'qtl2', 'qtl', and 'DOQTL' packages for mapping quantitative trait loci (QTL).
 Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>)

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,14 @@
+## qtl2convert 0.23-1 (2021-03-25)
+
+### Bug fixes
+
+- Needed to fix use of `nchar()` in `encode_geno()` as it no longer
+  works properly with data frames.
+
+
 ## qtl2convert 0.22-7 (2020-06-30)
 
-## Minor changes
+### Minor changes
 
 Cosmetic changes to prepare for posting to CRAN:
 

diff --git a/R/encode_geno.R b/R/encode_geno.R
@@ -32,7 +32,7 @@ function(geno, allele_codes, output_codes=c("-", "A", "H", "B"), cores=1)
     stopifnot(ncol(allele_codes) == 2)
 
     if(any(is.na(allele_codes))) stop("allele_codes can't have missing values")
-    if(any(nchar(allele_codes)>1)) stop("allele_codes should be single characters")
+    if(any(apply(allele_codes, 2, nchar) > 1)) stop("allele_codes should be single characters")
 
     if(!is.matrix(geno)) geno <- as.matrix(geno)
     if(!is.matrix(allele_codes)) allele_codes <- as.matrix(allele_codes)