From 9dc5721c58471b1c427fc838f386a47e195f1d6a Mon Sep 17 00:00:00 2001
From: alexg9010 <alex.gos90@gmail.com>
Date: Thu, 17 Jan 2019 12:54:19 +0100
Subject: [PATCH] fread.gzipped: update function to check compression based on
 file content and allow to decompress .bgz files

---
 R/backbone.R | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/R/backbone.R b/R/backbone.R
index 82a5678b..91187818 100644
--- a/R/backbone.R
+++ b/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