added --clean to assemble_seq_idba

[biopieces.git] / bp_bin / assemble_seq_idba

diff --git a/bp_bin/assemble_seq_idba b/bp_bin/assemble_seq_idba
index 812fe5fb81cd0975b195aa317f0a0f346bd35b55..f3a29afe7178eb6099b281b32b4f7e4a32aa4593 100755 (executable)
--- a/bp_bin/assemble_seq_idba
+++ b/bp_bin/assemble_seq_idba
@@ -41,6 +41,7 @@ casts << {:long=>'count_min',   :short=>'c', :type=>'uint',   :mandatory=>false,
 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}
 
 bp = Biopieces.new
 
@@ -86,6 +87,9 @@ unless File.size(file_fasta) == 0
   end
 end
 
+FileUtils.remove_entry_secure options[:directory] if options[:clean]
+
+
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