removed debug message

[biopieces.git] / code_ruby / lib / maasha / filesys.rb

diff --git a/code_ruby/lib/maasha/filesys.rb b/code_ruby/lib/maasha/filesys.rb
index 81190f532d6ee54281d85d923168e5fd703c51fe..02a8a842f1157a9824052c589795c1630580ff90 100644 (file)
--- a/code_ruby/lib/maasha/filesys.rb
+++ b/code_ruby/lib/maasha/filesys.rb
@@ -22,8 +22,6 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-# require 'zlib'
-# require 'bzip2'
 require 'open3'
 
 # Error class for all exceptions to do with Filesys.
@@ -50,10 +48,8 @@ class Filesys
     if mode == 'w'
       case options[:compress]
       when :gzip
-        # ios = Zlib::GzipWriter.new File.open(file, mode, options)
         ios, = Open3.pipeline_w("gzip -f", out: file)
       when :bzip, :bzip2
-        # ios = Bzip2::Writer.new File.open(file, mode, options)   # TODO being pissed with buggy bzip2 gem.
         ios, = Open3.pipeline_w("bzip2 -c", out: file)
       else 
         ios = File.open(file, mode, options)
@@ -62,15 +58,15 @@ class Filesys
       if file == '-'
         ios = STDIN
       else
-        case `file -L #{file}`
+        case `file -Lk #{file}`
         when /gzip/
-          # ios = Zlib::GzipReader.new File.open(file, mode, options)
-          ios = IO.popen("zcat #{file}")
+          ios = IO.popen("gzip -cd #{file}", :external_encoding=>"EUC-JP")
         when /bzip/
-          # ios = Bzip2::Reader.new File.open(file, mode, options)   # TODO this method is buggy, investigate
           ios = IO.popen("bzcat #{file}")
-        else
+        when /ASCII/
           ios = File.open(file, mode, options)
+        else
+          raise "Unknown file type: #{`file -L #{file}`}"
         end
       end
     end