making changes to accomodate Illumina18 qual scores

[biopieces.git] / code_ruby / lib / maasha / align.rb

diff --git a/code_ruby/lib/maasha/align.rb b/code_ruby/lib/maasha/align.rb
index cdab55b0394d6fa7d00785123f95afa076653b55..32532fe26be362277eb36670ffa400aea7df5066 100755 (executable)
--- a/code_ruby/lib/maasha/align.rb
+++ b/code_ruby/lib/maasha/align.rb
@@ -223,7 +223,7 @@ class Align
     def na_add_entries
       @entries.each_with_index do |entry, i|
         @na_seq[true, i]  = NArray.to_na(entry.seq.downcase.tr(TR_NUC, TR_HEX), "byte")
-        @na_qual[true, i] = NArray.to_na(entry.qual, "byte") - SCORE_ILLUMINA if @has_qual
+        @na_qual[true, i] = NArray.to_na(entry.qual, "byte") - SCORE_BASE if @has_qual
       end
     end
 
@@ -336,7 +336,7 @@ class Align
 
     # Method to calculate a consensus quality from a Consensus object.
     def consensus_qual
-      (@na_qual.mean(1).round.to_type("byte") + SCORE_ILLUMINA).to_s
+      (@na_qual.mean(1).round.to_type("byte") + SCORE_BASE).to_s
     end
   end
 end