From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 20 Nov 2012 09:00:05 +0000 (+0000)
Subject: added uchime to usearch
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=87faa77bda25d25d60e486ad35da199bd9299678;p=biopieces.git

added uchime to usearch

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1991 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/usearch.rb b/code_ruby/lib/maasha/usearch.rb
index c821cac..2a3365b 100644
--- a/code_ruby/lib/maasha/usearch.rb
+++ b/code_ruby/lib/maasha/usearch.rb
@@ -85,6 +85,13 @@ class Usearch
 		execute
   end
 
+  # Method to execute uchime chimera detection.
+  def uchime
+    @command << "usearch --uchime #{@infile} --db #{@options[:database]} --uchimeout #{@outfile}"
+
+    execute
+  end
+
   # Method to execute ustar alignment.
   def ustar
     command = %Q{grep "^[SH]" #{@outfile} > #{@outfile}.sub}