bug fix for VCFR2AF

Author: JimWhiting91

R/summarise_window_parallelism.R

@@ -15,6 +15,7 @@ summarise_window_parallelism <- function(window_id,
   # Make the final_out table
   final_out <- data.frame(window_id=NA,
                           eigenvector=NA,
+                          eigenvalue=NA,
                           parallel_lineages=NA,
                           parallel_pops=NA,
                           antiparallel_pops=NA)
@@ -28,6 +29,7 @@ summarise_window_parallelism <- function(window_id,
     # Output
     out <- data.frame(window_id=window_id,
                       eigenvector=paste0("Eig",eigN),
+                      eigenvalue=eigen_res[[window_id]]$eigenvals[eigN],
                       parallel_lineages = length(loadings[abs(loadings) > loading_cutoff]))
 
     # Catch cases where all parallel but negative

R/vcfR2AF.R

@@ -25,7 +25,7 @@ vcfR2AF <- function(vcf,
   gt <- extract.gt(vcf)
 
   # Convert to numbers using the appropriate separator
-  geno_format <- strsplit(gt[1,1],"")[[1]][2]
+  geno_format <- strsplit(na.omit(gt[1,])[1],"")[[1]][2]
   gt[gt == paste0("0",geno_format,"0")] <- 0
   gt[gt == paste0("0",geno_format,"1")] <- 0.5
   gt[gt == paste0("1",geno_format,"1")] <- 1