From aaaca4f941716d8c2d54ecfebd493ecc23d954af Mon Sep 17 00:00:00 2001 From: martinahansen Date: Mon, 25 Jun 2012 09:02:40 +0000 Subject: [PATCH] added max_diversity swith to findsim.rb git-svn-id: http://biopieces.googlecode.com/svn/trunk@1845 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/findsim_seq | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/bp_bin/findsim_seq b/bp_bin/findsim_seq index fec7772..5622cec 100755 --- 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 -- 2.39.2