X-Git-Url: https://git.donarmstrong.com/?p=biopieces.git;a=blobdiff_plain;f=code_ruby%2Flib%2Fmaasha%2Fseq%2Ftrim.rb;h=8efabf9c8fe24309fdd8c3c9496e06266b1f9a91;hp=a11159bd5cfd065c7f4f1a89ec540d591f01047f;hb=dfe922540177aeaad25c2da595b9bac1a2205c27;hpb=44f810b56c353bfe302469a8313b0aada285b27e

diff --git a/code_ruby/lib/maasha/seq/trim.rb b/code_ruby/lib/maasha/seq/trim.rb
index a11159b..8efabf9 100644
--- a/code_ruby/lib/maasha/seq/trim.rb
+++ b/code_ruby/lib/maasha/seq/trim.rb
@@ -34,7 +34,7 @@ module Trim
   def quality_trim_right(min_qual, min_len = 1)
     check_trim_args(min_qual)
 
-    pos = trim_right_pos_c(self.qual, self.length, min_qual, min_len, SCORE_BASE)
+    pos = trim_right_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
     self.subseq(0, pos)
   end
@@ -44,7 +44,7 @@ module Trim
   def quality_trim_right!(min_qual, min_len = 1)
     check_trim_args(min_qual)
 
-    pos = trim_right_pos_c(self.qual, self.length, min_qual, min_len, SCORE_BASE)
+    pos = trim_right_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
     self.subseq!(0, pos)
   end
@@ -54,7 +54,7 @@ module Trim
   def quality_trim_left(min_qual, min_len = 1)
     check_trim_args(min_qual)
 
-    pos = trim_left_pos_c(self.qual, self.length, min_qual, min_len, SCORE_BASE)
+    pos = trim_left_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
     self.subseq(pos)
   end
@@ -64,7 +64,7 @@ module Trim
   def quality_trim_left!(min_qual, min_len = 1)
     check_trim_args(min_qual)
 
-    pos = trim_left_pos_c(self.qual, self.length, min_qual, min_len, SCORE_BASE)
+    pos = trim_left_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
     self.subseq!(pos)
   end
@@ -74,8 +74,8 @@ module Trim
   def quality_trim(min_qual, min_len = 1)
     check_trim_args(min_qual)
 
-    pos_right = trim_right_pos_c(self.qual, self.length, min_qual, min_len, SCORE_BASE)
-    pos_left  = trim_left_pos_c(self.qual, self.length, min_qual, min_len, SCORE_BASE)
+    pos_right = trim_right_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
+    pos_left  = trim_left_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
     pos_left = pos_right if pos_left > pos_right
 
@@ -87,8 +87,8 @@ module Trim
   def quality_trim!(min_qual, min_len = 1)
     check_trim_args(min_qual)
 
-    pos_right = trim_right_pos_c(self.qual, self.length, min_qual, min_len, SCORE_BASE)
-    pos_left  = trim_left_pos_c(self.qual, self.length, min_qual, min_len, SCORE_BASE)
+    pos_right = trim_right_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
+    pos_left  = trim_left_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
     pos_left = pos_right if pos_left > pos_right
 
@@ -102,8 +102,8 @@ module Trim
   def check_trim_args(min_qual)
     raise TrimError, "no sequence"      if self.seq.nil?
     raise TrimError, "no quality score" if self.qual.nil?
-    unless (SCORE_MIN .. SCORE_MAX).include? min_qual
-      raise TrimError, "minimum quality value: #{min_qual} out of range #{SCORE_MIN} .. #{SCORE_MAX}"
+    unless (Seq::SCORE_MIN .. Seq::SCORE_MAX).include? min_qual
+      raise TrimError, "minimum quality value: #{min_qual} out of range #{Seq::SCORE_MIN} .. #{Seq::SCORE_MAX}"
     end
   end