temporary fix of bzip2 read problem

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2220 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/lib/maasha/filesys.rb b/code_ruby/lib/maasha/filesys.rb
index 4bb7b8f7d17fd4b88b90da6d64a0aa33be527d8d..6a6067fbc859bb3df62a7f4eda547c0f44d8070c 100644 (file)
--- a/code_ruby/lib/maasha/filesys.rb
+++ b/code_ruby/lib/maasha/filesys.rb
@@ -63,7 +63,8 @@ class Filesys
         when /gzip/
           ios = Zlib::GzipReader.new File.open(file, mode, options)
         when /bzip/
         when /gzip/
           ios = Zlib::GzipReader.new File.open(file, mode, options)
         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
         else
           ios = File.open(file, mode, options)
         end