From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 18 Mar 2011 15:18:19 +0000 (+0000)
Subject: polishing stdin for ruby code
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=26cb0176a14e6c7bb789444afd39195b6763890e;p=biopieces.git

polishing stdin for ruby code

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1292 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_python/Cjung/Args.pyc b/code_python/Cjung/Args.pyc
index ddc36fc..66b245e 100644
Binary files a/code_python/Cjung/Args.pyc and b/code_python/Cjung/Args.pyc differ
diff --git a/code_ruby/Maasha/lib/biopieces.rb b/code_ruby/Maasha/lib/biopieces.rb
index 44f0d22..2ab9aa7 100644
--- a/code_ruby/Maasha/lib/biopieces.rb
+++ b/code_ruby/Maasha/lib/biopieces.rb
@@ -453,7 +453,7 @@ class OptionHandler
   def options_check_files(cast)
     if cast[:type] == 'files!' and @options.has_key? cast[:long]
       @options[cast[:long]].each do |path|
-        raise ArgumentError, "No such file: '#{path}'" unless File.file? path
+        raise ArgumentError, "File not readable: '#{path}'" unless File.readable? path
       end
     end
   end
diff --git a/code_ruby/Maasha/lib/fastq.rb b/code_ruby/Maasha/lib/fastq.rb
index fc2863a..2988785 100644
--- a/code_ruby/Maasha/lib/fastq.rb
+++ b/code_ruby/Maasha/lib/fastq.rb
@@ -34,7 +34,11 @@ class Fastq
   # Class method allowing open to be used on (zipped) files.
   # See File.open.
   def self.open(*args)
-    ios = self.zopen(*args)
+    if File.pipe? *args.first
+      ios = self.new(File.open(*args))
+    else
+      ios = self.zopen(*args)
+    end
 
     if block_given?
       begin