X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=code_ruby%2Flib%2Fmaasha%2Fseq%2Ftrim.rb;h=2ca94542b65c3ed3e6d536b460095295b1f13181;hb=3656f15bb59e2eb7eff628bae117db6479b2f03f;hp=2be3e56800a518a25ce5da5665053b0951d4de8e;hpb=a5d19041b1dcfe481eef2747058f63173a36aaf3;p=biopieces.git

diff --git a/code_ruby/lib/maasha/seq/trim.rb b/code_ruby/lib/maasha/seq/trim.rb
index 2be3e56..2ca9454 100644
--- a/code_ruby/lib/maasha/seq/trim.rb
+++ b/code_ruby/lib/maasha/seq/trim.rb
@@ -40,7 +40,7 @@ module Trim
 
     pos = trim_right_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
-    self.subseq(0, pos)
+    self[0, pos]
   end
 
   # Method to progressively trim a Seq object sequence from the right end until
@@ -50,7 +50,10 @@ module Trim
 
     pos = trim_right_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
-    self.subseq!(0, pos)
+    self.seq  = self.seq[0, pos]
+    self.qual = self.qual[0, pos] if self.qual
+
+    self
   end
 
   # Method to progressively trim a Seq object sequence from the left end until
@@ -60,7 +63,7 @@ module Trim
 
     pos = trim_left_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
-    self.subseq(pos)
+    self[pos .. -1]
   end
 
   # Method to progressively trim a Seq object sequence from the left end until
@@ -70,7 +73,10 @@ module Trim
 
     pos = trim_left_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
-    self.subseq!(pos)
+    self.seq  = self.seq[pos .. -1]
+    self.qual = self.qual[pos .. -1] if self.qual
+
+    self
   end
 
   # Method to progressively trim a Seq object sequence from both ends until a
@@ -83,7 +89,7 @@ module Trim
 
     pos_left = pos_right if pos_left > pos_right
 
-    self.subseq(pos_left, pos_right - pos_left)
+    self[pos_left ... pos_right]
   end
 
   # Method to progressively trim a Seq object sequence from both ends until a
@@ -96,7 +102,10 @@ module Trim
 
     pos_left = pos_right if pos_left > pos_right
 
-    self.subseq!(pos_left, pos_right - pos_left)
+    self.seq  = self.seq[pos_left ... pos_right]
+    self.qual = self.qual[pos_left ... pos_right] if self.qual
+
+    self
   end
 
   # Method to locate a pattern in a sequence and trim all sequence to the left