From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 26 Sep 2013 09:43:24 +0000 (+0000)
Subject: temporary fix of bzip2 read problem
X-Git-Url: https://git.donarmstrong.com/?p=biopieces.git;a=commitdiff_plain;h=3ce24a349c10a76d3e837e08b81259204ab870fe

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 4bb7b8f..6a6067f 100644
--- 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/
-          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