From 2e250e33293415e15ba5068f0e4e5317246ab2d6 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Wed, 18 Apr 2012 09:06:27 +0000 Subject: [PATCH] changed record_scores to max_hits refactoring git-svn-id: http://biopieces.googlecode.com/svn/trunk@1800 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/findsim_seq | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/bp_bin/findsim_seq b/bp_bin/findsim_seq index d6879cc..eeb2655 100755 --- a/bp_bin/findsim_seq +++ b/bp_bin/findsim_seq @@ -34,13 +34,13 @@ 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=>'report_scores', :short=>'r', :type=>'uint', :mandatory=>false, :default=>7, :allowed=>nil, :disallowed=>"0"} -casts << {:long=>'min_score', :short=>'m', :type=>'float', :mandatory=>false, :default=>0.5, :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=>'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} options = Biopieces.options_parse(ARGV, casts) tmpdir = Biopieces.mktmpdir -- 2.39.5