input of vcfcomp can be saved RDS file

R/vcf-compare.R

@@ -5,7 +5,7 @@
 #' \code{vcfcomp} implements various statisitcs to compare two VCF/BCF files,
 #' e.g. report genotype concocrdance, correlation stratified by allele frequency.
 #' 
-#' @param test path to the first VCF/BCF file referred as test.
+#' @param test path to the first VCF/BCF file referred as test, or saved RDS file.
 #'
 #' @param truth path to the second VCF/BCF file referred as truth, or saved RDS file.
 #'
@@ -78,7 +78,9 @@ vcfcomp <- function(test, truth,
     formats[1] <- "GT"
   }
   collapse <- ifelse(stats=="pse", FALSE, TRUE)
-  d1 <- vcftable(test, format = formats[1], setid = TRUE, collapse = collapse, ...)
+  d1 <- tryCatch( { suppressWarnings(readRDS(test)) }, error = function(e) {
+    vcftable(test, format = formats[1], setid = TRUE, collapse = collapse, ...)
+  } )
   d2 <- tryCatch( { suppressWarnings(readRDS(truth)) }, error = function(e) {
     vcftable(truth, format = formats[2], setid = TRUE, collapse = collapse, ...)
   } )