added max_diversity swith to findsim.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1845 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/findsim_seq b/bp_bin/findsim_seq
index fec7772269aed40b6fd0bccde1bf1b9a78faeaa3..5622cec8b0a6d0d129546843bbf3aecf8cd169cd 100755 (executable)
--- a/bp_bin/findsim_seq
+++ b/bp_bin/findsim_seq
@@ -34,14 +34,15 @@ require 'maasha/fasta'
 require 'maasha/findsim'
 
 casts = []
-casts << {:long=>'database',    :short=>'d', :type=>'file!', :mandatory=>true,  :default=>nil, :allowed=>nil,           :disallowed=>nil}
-casts << {:long=>'kmer',        :short=>'k', :type=>'uint',  :mandatory=>false, :default=>8,   :allowed=>"4,5,6,7,8,9", :disallowed=>nil}
-casts << {:long=>'step',        :short=>'s', :type=>'uint',  :mandatory=>false, :default=>1,   :allowed=>nil,           :disallowed=>"0"}
-casts << {:long=>'min_score',   :short=>'m', :type=>'float', :mandatory=>false, :default=>0.5, :allowed=>nil,           :disallowed=>nil}
-casts << {:long=>'max_hits',    :short=>'h', :type=>'uint',  :mandatory=>false, :default=>7,   :allowed=>nil,           :disallowed=>"0"}
-casts << {:long=>'query_ids',   :short=>'Q', :type=>'flag',  :mandatory=>false, :default=>nil, :allowed=>nil,           :disallowed=>nil}
-casts << {:long=>'subject_ids', :short=>'S', :type=>'flag',  :mandatory=>false, :default=>nil, :allowed=>nil,           :disallowed=>nil}
-casts << {:long=>'realign',     :short=>'r', :type=>'flag',  :mandatory=>false, :default=>nil, :allowed=>nil,           :disallowed=>nil}
+casts << {:long=>'database',      :short=>'d', :type=>'file!', :mandatory=>true,  :default=>nil, :allowed=>nil,           :disallowed=>nil}
+casts << {:long=>'kmer',          :short=>'k', :type=>'uint',  :mandatory=>false, :default=>8,   :allowed=>"4,5,6,7,8,9", :disallowed=>nil}
+casts << {:long=>'step',          :short=>'s', :type=>'uint',  :mandatory=>false, :default=>1,   :allowed=>nil,           :disallowed=>"0"}
+casts << {:long=>'min_score',     :short=>'m', :type=>'float', :mandatory=>false, :default=>0.5, :allowed=>nil,           :disallowed=>nil}
+casts << {:long=>'max_hits',      :short=>'h', :type=>'uint',  :mandatory=>false, :default=>7,   :allowed=>nil,           :disallowed=>"0"}
+casts << {:long=>'max_diversity', :short=>'h', :type=>'uint',  :mandatory=>false, :default=>5,   :allowed=>nil,           :disallowed=>nil}
+casts << {:long=>'query_ids',     :short=>'Q', :type=>'flag',  :mandatory=>false, :default=>nil, :allowed=>nil,           :disallowed=>nil}
+casts << {:long=>'subject_ids',   :short=>'S', :type=>'flag',  :mandatory=>false, :default=>nil, :allowed=>nil,           :disallowed=>nil}
+casts << {:long=>'realign',       :short=>'r', :type=>'flag',  :mandatory=>false, :default=>nil, :allowed=>nil,           :disallowed=>nil}
 
 options    = Biopieces.options_parse(ARGV, casts)
 tmpdir     = Biopieces.mktmpdir