fread.gzipped: update function to check compression based on file con…

…tent and allow to decompress .bgz files

R/backbone.R

@@ -10,20 +10,26 @@ fread.gzipped<-function(filepath,...){
 
 
   # decompress first, fread can't read gzipped files
-  if (R.utils::isGzipped(filepath)){
+  if (R.utils::isGzipped(filepath, method = "content")){
 
     if(.Platform$OS.type == "unix") {
-      filepath=paste("gunzip -c",filepath)
+      # being on unix we can pass comand
+      cmd = paste("gunzip -c",filepath)  
+      ## Read in the file
+      fread(cmd = cmd,...)
     } else {
+      # on windows we have to decompress first
+      ext = if( endsWith(filepath,".bgz") )  "bgz" else "gz"
       filepath <- R.utils::gunzip(filepath,temporary = FALSE, overwrite = TRUE,
-                                  remove = FALSE)
+                                  remove = FALSE, ext = ext, FUN = gzfile)
+      ## Read in the file
+      fread(file = filepath,...)
     }
 
 
   }
 
-  ## Read in the file
-  fread(filepath,...)
+
 
 }
 # reads a table in a fast way to a dataframe