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 b267d3006f127e04dd7ee99f5b9b14265f8307eb..82a69a2424d9daa4f849b812edb6c8dee477386e 100755 (executable)
--- 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 923a3b057c7198b9792a799fa82e4b2102d26f8a..8fec43bb6724288b527378f53c1cafde228443dc 100755 (executable)
--- 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