From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 7 Feb 2012 14:34:26 +0000 (+0000)
Subject: added raw data reading to read_fasta and read_fastq
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=144447a01acd669161794a3ca0d034bf99323840;p=biopieces.git

added raw data reading to read_fasta and read_fastq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1748 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/read_fasta b/bp_bin/read_fasta
index b267d30..82a69a2 100755
--- a/bp_bin/read_fasta
+++ b/bp_bin/read_fasta
@@ -38,8 +38,10 @@ casts << {:long=>'num',     :short=>'n', :type=>'uint',   :mandatory=>false, :de
 options = Biopieces.options_parse(ARGV, casts)
 
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
-  input.each_record do |record|
-    output.puts record
+  unless options[:data_in].first == '-'
+    input.each_record do |record|
+      output.puts record
+    end
   end
 
   num  = 0
diff --git a/bp_bin/read_fastq b/bp_bin/read_fastq
index 923a3b0..8fec43b 100755
--- a/bp_bin/read_fastq
+++ b/bp_bin/read_fastq
@@ -44,8 +44,10 @@ num  = 0
 last = false
 
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
-  input.each_record do |record|
-    output.puts record
+  unless options[:data_in].first == '-'
+    input.each_record do |record|
+      output.puts record
+    end
   end
 
   if options.has_key? :data_in