From 26cb0176a14e6c7bb789444afd39195b6763890e Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 18 Mar 2011 15:18:19 +0000
Subject: [PATCH] polishing stdin for ruby code

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1292 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_python/Cjung/Args.pyc        | Bin 5364 -> 5601 bytes
 code_ruby/Maasha/lib/biopieces.rb |   2 +-
 code_ruby/Maasha/lib/fastq.rb     |   6 +++++-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/code_python/Cjung/Args.pyc b/code_python/Cjung/Args.pyc
index ddc36fc600f13f1a86a119e0c8fadcd00d0064e1..66b245e94a16f34c4cd693215c8322410309cd50 100644
GIT binary patch
delta 835
zcma))F;Bu!6h`kY&^}55i>M4FI3P)*k(4+%kf?z~OdLc8=LU#?6{5w6iGvBV(@R|4
zjSDvJu8wXJC*$OZ@dtPt5EqBn^tK)P&iUTgejD%0%>4?hufyu@fHmZF5dgAIw{vP8
z*3Im()jO}-Hr*|!VP$vPPS>(+Zn71AFR$Vif0MUTdBCm$O$N;%^Z`0yz?u)XOSJ%0
z+6a7I`4q*LG7N*L(NvLwNHj7{fyQ~EOYZ@?WVqwEYz{O0k)?fPaEGjcVv4d_M8<Da
z11<if8mScc3D}gNr9x*0kd7L9*(J&@0S|;e#K0y?^Q4w2PLg}+1HZ|0^l%Y}OA^tE
zK!!d-<)FPl_OUuNR!^*Fnk{A>Y31CSN7w)8^a%)^oTC5P)k)Y9<I}F(L}XL2T$3%i
z*U>$}w?~@6=k=7TOl#sBdLjbg_loj?L^b7kRc{GLo!yTTi&lf<{WTydxX9zNBVmB+
P#-0V!Q#0uBLA>w-91Y%U

delta 601
zcmaE;{Y8`G;wN6NjZrS%8#yxA1PmA$81yspb5r$m6BCOw5+^6}s!ra?X3AJQ`8}JX
zj3onO2|Gh32SX+&Lo)+IJ{JRH3NwSdM+z%L@MM4Xm)P|;awyxdGIBEV0C6%S&;}+T
zW&>hpATB-!Br4W3lmLxe&cIm1z>vwvkjVrxzLt@phLIs(dGZ4emCfv&8I0JC-@zr%
z$U6B3mnLJ}WF~G+85sr^pkY8GvbY%Xc^MdiAcYa+NG6~oy|^D^ni9xk<H!ba8pwI9
zFsJDQ8I>XoAUA=X1vI9aks&xdPXuTM#C#5j`5>b&^5kF|oyZ%gZwN9*5Md0^Yd|w3
z;bx$_@d<A+ra^%`s+$+^*<%lb%^Cs$SY<RP9~G46f`_%i<adG+JiuTDdWV?-=pD1k
iB0^bMEt`B?NRUx(@=c*^tkRo%g->9$QFZb>QD*?iK#I8l

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
-- 
2.39.5