added word_size switch to blast_seq_pair

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2127 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/blast_seq_pair b/bp_bin/blast_seq_pair
index ca1d543533a8056f62d0eeff6ed22cdc92f2fbef..73c74154a7340809fbe0784726dc83791f1dc071 100755 (executable)
--- a/bp_bin/blast_seq_pair
+++ b/bp_bin/blast_seq_pair
@@ -61,6 +61,7 @@ class Blast
     commands << "-j #{@infile2}"
     commands << "-o #{@outfile}"
     commands << "-p #{@program}"
+    commands << "-W #{options[:word_size]}" if options[:word_size]
     commands << "-D 1" # tabular output
     commands << "-e #{options[:e_val]}"
     commands << (options[:megablast] ? "-m T" : "-m F")
@@ -147,6 +148,7 @@ casts << {:long=>'e_val',     :short=>'e', :type=>'float',  :mandatory=>false, :
 casts << {:long=>'filter',    :short=>'f', :type=>'string', :mandatory=>false, :default=>'no', :allowed=>'yes,no',    :disallowed=>nil}
 casts << {:long=>'megablast', :short=>'m', :type=>'flag',   :mandatory=>false, :default=>nil,  :allowed=>nil,         :disallowed=>nil}
 casts << {:long=>'no_gaps',   :short=>'G', :type=>'flag',   :mandatory=>false, :default=>nil,  :allowed=>nil,         :disallowed=>nil}
+casts << {:long=>'word_size', :short=>'w', :type=>'uint',   :mandatory=>false, :default=>nil,  :allowed=>nil,         :disallowed=>nil}
 
 options = Biopieces.options_parse(ARGV, casts)