add BP check

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MungeSumstats
 Type: Package
 Title: Standardise summary statistics from GWAS
-Version: 1.7.18
+Version: 1.7.19
 Authors@R:
     c(person(given = "Alan",
            family = "Murphy",

R/check_bp_range.R

@@ -10,9 +10,10 @@
 check_bp_range <- function(sumstats_dt, path, ref_genome,log_folder_ind, 
                          imputation_ind,check_save_out, tabix_index, nThread, 
                          log_files) {
-    chr_max<- CHR <- seqlengths <- .SD <- NULL
+    BP<- chr_max<- CHR <- seqlengths <- .SD <- NULL
     col_headers <- names(sumstats_dt)
-    if ("BP" %in% col_headers) {
+    #need CHR to get chrom lengths
+    if ("BP" %in% col_headers && "CHR" %in% col_headers) {
         message("Checking for incorrect base-pair positions")
         #load chromosome lengths
         if (toupper(ref_genome) == "GRCH37") {

R/read_vcf.R

@@ -15,6 +15,7 @@
 #' \item{c("<sample_id1>","<sample_id2>",...) : }{
 #' Only user-selected samples will be used (case-insensitive).}
 #' }
+#' @param which Genomic ranges to be added if supplied. Default is NULL.
 #' @param use_params
 #' When \code{TRUE} (default), increases the speed of reading in the VCF by
 #' omitting columns that are empty based on the head of the VCF (NAs only).