From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 11 Apr 2012 08:07:42 +0000 (+0000)
Subject: cleanup in read_fastq
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=1bbce2c1cc18d213a113a4763c21e5a14c3d992a;p=biopieces.git

cleanup in read_fastq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1791 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/read_fastq b/bp_bin/read_fastq
index 4a94957..acc68d6 100755
--- a/bp_bin/read_fastq
+++ b/bp_bin/read_fastq
@@ -31,7 +31,7 @@
 require 'maasha/biopieces'
 require 'maasha/fastq'
 
-allowed_enc = 'auto,sanger,solexa,illumina13,illumina15,illumina18'
+allowed_enc = 'auto,sanger,solexa,illumina1.3,illumina1.5,illumina1.8'
 
 casts = []
 casts << {:long=>'data_in',  :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil,    :allowed=>nil,         :disallowed=>nil}
@@ -40,9 +40,8 @@ casts << {:long=>'encoding', :short=>'e', :type=>'string', :mandatory=>false, :d
 
 options = Biopieces.options_parse(ARGV, casts)
 
-num      = 0
-last     = false
-encoding = options[:encoding]
+num  = 0
+last = false
 
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   unless options[:data_in].first == '-'
@@ -51,8 +50,10 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
     end
   end
 
-  if options.has_key? :data_in
+  if options[:data_in]
     options[:data_in].each do |file|
+      encoding = options[:encoding].downcase.delete('.')
+
       Fastq.open(file, mode='r') do |fastq|
         fastq.each do |entry|
           if encoding == 'auto'
@@ -69,7 +70,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
           output.puts entry.to_bp
           num += 1
 
-          if options.has_key? :num and options[:num] == num
+          if options[:num] == num
             last = true
             break
           end