Bug fix in VCF2RADdata if no geno field specified.

lvclark · May 13, 2019 · f77b525 · f77b525
1 parent 4800792
commit f77b525
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/R/data_import.R b/R/data_import.R
@@ -631,7 +631,8 @@ VCF2RADdata <- function(file, phaseSNPs = TRUE, tagsize = 80, refgenome = NULL,
     VariantAnnotation::vcfFixed(svparam) <- 
       c(VariantAnnotation::vcfFixed(svparam), "ALT")
   }
-  if(is.na(VariantAnnotation::vcfGeno(svparam))){
+  if(length(VariantAnnotation::vcfGeno(svparam)) > 0 && 
+     is.na(VariantAnnotation::vcfGeno(svparam)[1])){
     stop("geno field must be provided in svparam.")
   }
   if(!identical(VariantAnnotation::vcfGeno(svparam), "AD")){