rename switch to something more appropriate

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1447 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/assemble_seq_idba b/bp_bin/assemble_seq_idba
index e6a1290e7431c3293f7551d880fcbf5edd40a910..1f392e91184b94de637b43e7e4a4b32648db5085 100755 (executable)
--- a/bp_bin/assemble_seq_idba
+++ b/bp_bin/assemble_seq_idba
@@ -40,7 +40,7 @@ casts << {:long=>'count_min',  :short=>'c', :type=>'uint', :mandatory=>false, :d
 casts << {:long=>'cover',      :short=>'C', :type=>'uint', :mandatory=>false, :default=>0,   :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'pairs_min',  :short=>'p', :type=>'uint', :mandatory=>false, :default=>5,   :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'prefix_len', :short=>'P', :type=>'uint', :mandatory=>false, :default=>3,   :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'clean',      :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'clean',      :short=>'X', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
 
 options = Biopieces.options_parse(ARGV, casts)
 

diff --git a/bp_bin/assemble_seq_velvet b/bp_bin/assemble_seq_velvet
index 7569811eba6537c4af52e5c21fb70207375bb057..71fc5c129c9972320fdc3d8d79976eca32fcfc58 100755 (executable)
--- a/bp_bin/assemble_seq_velvet
+++ b/bp_bin/assemble_seq_velvet
@@ -148,7 +148,7 @@ casts << {:long=>'kmer_min',   :short=>'k', :type=>'uint',   :mandatory=>true,
 casts << {:long=>'kmer_max',   :short=>'K', :type=>'uint',   :mandatory=>true,  :default=>31,          :allowed=>nil,   :disallowed=>nil}
 casts << {:long=>'cov_cutoff', :short=>'c', :type=>'list',   :mandatory=>true,  :default=>cov_cutoffs, :allowed=>nil,   :disallowed=>nil}
 casts << {:long=>'exp_cov',    :short=>'e', :type=>'float',  :mandatory=>true,  :default=>'auto',      :allowed=>nil,   :disallowed=>nil}
-casts << {:long=>'clean',      :short=>'x', :type=>'flag',   :mandatory=>false, :default=>nil,         :allowed=>nil,   :disallowed=>nil}
+casts << {:long=>'clean',      :short=>'X', :type=>'flag',   :mandatory=>false, :default=>nil,         :allowed=>nil,   :disallowed=>nil}
 
 options = Biopieces.options_parse(ARGV, casts)