gzip fiddling

[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 4bb7b8f7d17fd4b88b90da6d64a0aa33be527d8d..eadb53649e785a4144e82f63a3b607e2b314d49e 100644 (file)
--- a/code_ruby/lib/maasha/filesys.rb
+++ b/code_ruby/lib/maasha/filesys.rb
@@ -22,8 +22,9 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-require 'zlib'
-require 'bzip2'
+# require 'zlib'
+# require 'bzip2'
+require 'open3'
 
 # Error class for all exceptions to do with Filesys.
 class FilesysError < StandardError; end
@@ -49,9 +50,11 @@ class Filesys
     if mode == 'w'
       case options[:compress]
       when :gzip
-        ios = Zlib::GzipWriter.new File.open(file, mode, options)
+        # 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)
+        # 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)
       end
@@ -59,11 +62,13 @@ class Filesys
       if file == '-'
         ios = STDIN
       else
-        case `file #{file}`
+        case `file -L #{file}`
         when /gzip/
-          ios = Zlib::GzipReader.new File.open(file, mode, options)
+          # ios = Zlib::GzipReader.new File.open(file, mode, options)
+          ios = IO.popen("gzip -cd #{file}")
         when /bzip/
-          ios = Bzip2::Reader.new File.open(file, mode, options)
+          # ios = Bzip2::Reader.new File.open(file, mode, options)   # TODO this method is buggy, investigate
+          ios = IO.popen("bzcat #{file}")
         else
           ios = File.open(file, mode, options)
         end