fixed to_i bug in pcr_seq

[biopieces.git] / bp_bin / assemble_seq_idba

diff --git a/bp_bin/assemble_seq_idba b/bp_bin/assemble_seq_idba
index 2b655431a8a0154c4af8bc7005a8cf527668d24a..bd8b4a819b8986ccfe6f9c968f9f65bbb264043b 100755 (executable)
--- a/bp_bin/assemble_seq_idba
+++ b/bp_bin/assemble_seq_idba
@@ -34,6 +34,7 @@ require 'maasha/fasta'
 casts = []
 casts << {:long=>'directory',  :short=>'d', :type=>'dir',  :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'scaffold',   :short=>'s', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'metagenome', :short=>'m', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'kmer_min',   :short=>'k', :type=>'uint', :mandatory=>false, :default=>25,  :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'kmer_max',   :short=>'K', :type=>'uint', :mandatory=>false, :default=>50,  :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'count_min',  :short=>'c', :type=>'uint', :mandatory=>false, :default=>2,   :allowed=>nil, :disallowed=>nil}
@@ -76,7 +77,13 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
 
                commands = []
                commands << "nice -n 19"
-               commands << "idba"
+
+    if options[:metagenome]
+                 commands << "metaidba"
+    else
+                 commands << "idba"
+    end
+
                commands << "--read #{file_fasta}"
                commands << "--output #{prefix}"
                commands << "--scaffold" if options[:scaffold]