rewrite of FASTQ internals

[biopieces.git] / bp_bin / scores_to_dec

diff --git a/bp_bin/scores_to_dec b/bp_bin/scores_to_dec
index b93587f3db97f5af3557e853b2472aaa549063d8..b69f37c950fecc3afa0c24a494dd17283b100fd8 100755 (executable)
--- a/bp_bin/scores_to_dec
+++ b/bp_bin/scores_to_dec
@@ -30,29 +30,19 @@
 
 require 'maasha/biopieces'
 require 'maasha/seq'
-
-# Expading class Hash with possibly evil monkey patch.
-class Hash
-  # Method to convert scores from ASCII encode string to
-  # a semi-colon seperated string of decimal values.
-  def scores2dec!
-    if self[:SCORES]
-      self[:SCORES].gsub! /./ do |score|
-        score = (score.ord - Seq::SCORE_BASE).to_s + ";"
-      end
-
-      self[:SCORES].chomp! ";"
-    end
-
-    self
-  end
-end
+require 'narray'
 
 options = Biopieces.options_parse(ARGV)
 
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   input.each_record do |record|
-    output.puts record.scores2dec!
+    if record[:SCORES]
+      na  = NArray.to_na(record[:SCORES], "byte")
+      na -= Seq::SCORE_BASE
+      record[:SCORES] = na.to_a.join("; ")
+    end
+
+    output.puts record
   end
 end