X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fscores_to_dec;h=2d91c2bda001f24767f1208d5930291fe24d014b;hb=dfe922540177aeaad25c2da595b9bac1a2205c27;hp=c5e7c1e2361788f51471f99886d11a400ca33948;hpb=494dc53ebd515b1e3e9b91bbebf43059899ca4ce;p=biopieces.git

diff --git a/bp_bin/scores_to_dec b/bp_bin/scores_to_dec
index c5e7c1e..2d91c2b 100755
--- a/bp_bin/scores_to_dec
+++ b/bp_bin/scores_to_dec
@@ -28,10 +28,8 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-
 require 'maasha/biopieces'
-
-ILLUMINA_BASE = 64
+require 'maasha/seq'
 
 # Expading class Hash with possibly evil monkey patch.
 class Hash
@@ -40,7 +38,7 @@ class Hash
   def scores2dec!
     if self.has_key? :SCORES
       self[:SCORES].gsub! /./ do |score|
-        score = (score.ord - ILLUMINA_BASE).to_s + ";"
+        score = (score.ord - Seq::SCORE_BASE).to_s + ";"
       end
 
       self[:SCORES].chomp! ";"
@@ -50,14 +48,12 @@ class Hash
   end
 end
 
-casts = []
-
-bp = Biopieces.new
+options = Biopieces.options_parse(ARGV)
 
-options = bp.parse(ARGV, casts)
-
-bp.each_record do |record|
-  bp.puts record.scores2dec!
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    output.puts record.scores2dec!
+  end
 end