encode_geno() now gives a warning if allele_codes have >1 character

- Issue rqtl#16
kbroman · Sep 25, 2019 · 34c43dd · 34c43dd
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: qtl2convert
-Version: 0.21-2
-Date: 2019-09-24
+Version: 0.21-3
+Date: 2019-09-25
 Title: Convert Data among R/qtl2, R/qtl, and DOQTL
 Description: Functions to convert data structures among the R/qtl2, R/qtl, and DOQTL packages.
 Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>)

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-## qtl2convert 0.21 (2019-09-24)
+## qtl2convert 0.21 (2019-09-25)
 
 ### New features
 
@@ -19,6 +19,9 @@
 
 - Fix bug for the case `marker_column=NULL`.
 
+- `encode_geno()` now gives a warning if any allele codes have >1 character.
+  ([Issue #16](https://github.com/rqtl/qtl2convert/issues/16))
+
 
 ## qtl2convert 0.20 (2019-06-03)
 

diff --git a/R/encode_geno.R b/R/encode_geno.R
@@ -31,6 +31,9 @@ function(geno, allele_codes, output_codes=c("-", "A", "H", "B"), cores=1)
     stopifnot(nrow(geno) == nrow(allele_codes))
     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(!is.matrix(geno)) geno <- as.matrix(geno)
     if(!is.matrix(allele_codes)) allele_codes <- as.matrix(allele_codes)
 

diff --git a/tests/testthat/test-encode_geno.R b/tests/testthat/test-encode_geno.R
@@ -21,6 +21,12 @@ test_that("encode_geno works", {
 
     expect_equal(encode_geno(geno, cbind(codes[,2], codes[,1])), expected2)
 
+    # errors: multiple characters, NAs
+    expect_error(encode_geno(geno, cbind(paste0(codes[,1], codes[,1]), codes[,2])))
+    expect_error(encode_geno(geno, cbind(codes[,1], paste0(codes[,2], codes[,2]))))
+    codes[1,2] <- NA
+    expect_error(encode_geno(geno, codes))
+
 })