fixing up backtrack code

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

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index d13cdaba9dde6cb68ff5c44f93a9759d5d6174d1..57d70b27cc5b5cd0b29cb88a20be7f3c9cec3a0c 100644 (file)
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -78,7 +78,6 @@ class SeqError < StandardError; end
 class Seq
   #include Patscan
   include PatternMatcher
-  include BackTrack
   include Digest
   include Trim
 
@@ -538,8 +537,21 @@ class Seq
     self
   end
 
+  # Method that determines if a quality score string can be
+  # absolutely identified as base 33.
+  def qual_base33?
+    self.qual.match(/[!-:]/)
+  end
+
+  # Method that determines if a quality score string can be
+  # absolutely identified as base 64.
+  def qual_base64?
+    self.qual.match(/[K-h]/)
+  end
+
   # Method to convert quality scores inbetween formats.
   # Sanger     base 33, range  0-40 
+  # 454        base 64, range  0-40 
   # Solexa     base 64, range -5-40 
   # Illumina13 base 64, range  0-40 
   # Illumina15 base 64, range  3-40 
@@ -550,6 +562,7 @@ class Seq
 
       case from.downcase
       when "sanger"     then na_qual -= 33
+      when "454"        then na_qual -= 64
       when "solexa"     then na_qual -= 64
       when "illumina13" then na_qual -= 64
       when "illumina15" then na_qual -= 64
@@ -559,6 +572,7 @@ class Seq
 
       case to.downcase
       when "sanger"     then na_qual += 33
+      when "454"        then na_qual += 64
       when "solexa"     then na_qual += 64
       when "illumina13" then na_qual += 64
       when "illumina15" then na_qual += 64