Update url and fix bugs

R/extraction_1KG.R

@@ -111,8 +111,8 @@ get_vcf <- function(chrom, start, end, pop = NA, path = "", web = TRUE) {
         # These are variants filtered by Brian Browning, the developer of BEAGLE.
         data_url = paste(sep = "",
                          "http://tabix.iobio.io/?cmd=-h%20%27",
-                         "http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/",
-                         "individual_chromosomes/chr", chrom, ".1kg.phase3.v5a.vcf.gz",
+                         "http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/b37.vcf/",
+                         "chr", chrom, ".1kg.phase3.v5a.vcf.gz",
                          "%27%20", chrom, ":", start, "-", end
         )
         # Download the data from the server.
@@ -161,7 +161,7 @@ get_vcf <- function(chrom, start, end, pop = NA, path = "", web = TRUE) {
     
     # Convert the genotypes to a numeric matrix.
     retval$geno <- t(apply(retval$geno, 1, function(row) {
-        as.numeric(do.call(cbind, strsplit(row, "|", fixed = TRUE)))
+        as.numeric(do.call(cbind, strsplit(unlist(row), "[/|]")))
     }))
     
     rownames(retval$geno) <- retval$meta$ID