fixed type cast bug

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1396 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/analyze_assembly b/bp_bin/analyze_assembly
index b30517ac0fc322fbe9f97e3101ee108f048a4f22..a946d2c17b48d4742f45aae1bbc3d2cb7aa353f0 100755 (executable)
--- a/bp_bin/analyze_assembly
+++ b/bp_bin/analyze_assembly
@@ -35,10 +35,10 @@ require 'prodigal'
 require 'pp'
 
 casts = []
-casts << {:long=>'gene_cov',  :short=>'g', :type=>'flag',      :mandatory=>false, :default=>nil,      :allowed=>nil,           :disallowed=>nil}
-casts << {:long=>'full',      :short=>'p', :type=>'procedure', :mandatory=>true,  :default=>'single', :allowed=>'single,meta', :disallowed=>nil}
-casts << {:long=>'no_stream', :short=>'x', :type=>'flag',      :mandatory=>false, :default=>nil,      :allowed=>nil,           :disallowed=>nil}
-casts << {:long=>'data_out',  :short=>'o', :type=>'file',      :mandatory=>false, :default=>nil,      :allowed=>nil,           :disallowed=>nil}
+casts << {:long=>'gene_cov',  :short=>'g', :type=>'flag',   :mandatory=>false, :default=>nil,      :allowed=>nil,           :disallowed=>nil}
+casts << {:long=>'procedure', :short=>'p', :type=>'string', :mandatory=>true,  :default=>'single', :allowed=>'single,meta', :disallowed=>nil}
+casts << {:long=>'no_stream', :short=>'x', :type=>'flag',   :mandatory=>false, :default=>nil,      :allowed=>nil,           :disallowed=>nil}
+casts << {:long=>'data_out',  :short=>'o', :type=>'file',   :mandatory=>false, :default=>nil,      :allowed=>nil,           :disallowed=>nil}
 
 bp = Biopieces.new
 

diff --git a/bp_bin/find_genes b/bp_bin/find_genes
index f0d64c8365300b3c970dd43fd6f6f7c1ed67f9e1..367b9766763d85fe21dc9b8a080c764e3b168926 100755 (executable)
--- a/bp_bin/find_genes
+++ b/bp_bin/find_genes
@@ -34,8 +34,8 @@ require 'fasta'
 require 'prodigal'
 
 casts = []
-casts << {:long=>'full', :short=>'f', :type=>'flag',      :mandatory=>false, :default=>nil,      :allowed=>nil,           :disallowed=>nil}
-casts << {:long=>'full', :short=>'p', :type=>'procedure', :mandatory=>true,  :default=>'single', :allowed=>'single,meta', :disallowed=>nil}
+casts << {:long=>'full',      :short=>'f', :type=>'flag',   :mandatory=>false, :default=>nil,      :allowed=>nil,           :disallowed=>nil}
+casts << {:long=>'procedure', :short=>'p', :type=>'string', :mandatory=>true,  :default=>'single', :allowed=>'single,meta', :disallowed=>nil}
 
 bp = Biopieces.new