From f77b5252a5a3d32d40960d5ea12f4241b6c343a7 Mon Sep 17 00:00:00 2001
From: "Lindsay V. Clark" <lvclark@illinois.edu>
Date: Mon, 13 May 2019 15:49:47 -0500
Subject: [PATCH] Bug fix in VCF2RADdata if no geno field specified.

---
 R/data_import.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/data_import.R b/R/data_import.R
index d0db1fd..c1e805e 100644
--- 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")){