X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Ffindsim_seq;h=edfe980f5cb1e63c8bbef2851bdbd4a41baa302b;hb=59a8d4cedcc4477492d40270f50e6ef34ded4741;hp=eeb26552dbedd9ffff2a6efe8ac064d713aac8d1;hpb=2e250e33293415e15ba5068f0e4e5317246ab2d6;p=biopieces.git

diff --git a/bp_bin/findsim_seq b/bp_bin/findsim_seq
index eeb2655..edfe980 100755
--- a/bp_bin/findsim_seq
+++ b/bp_bin/findsim_seq
@@ -34,13 +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=>'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=>20,  :allowed=>nil,           :disallowed=>"0"}
+casts << {:long=>'max_diversity', :short=>'M', :type=>'float', :mandatory=>false, :default=>nil, :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