fixed encoding bug in read_454

[biopieces.git] / bp_bin / blast_seq_pair

diff --git a/bp_bin/blast_seq_pair b/bp_bin/blast_seq_pair
index ca1d543533a8056f62d0eeff6ed22cdc92f2fbef..854ee424c3201110c9fb48f1dfcbe085737a884b 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)
 
@@ -173,14 +175,14 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
         end
 
         got1  = true
-        type1 = Seq.new(nil, record[:SEQ][0 ... 100]).type_guess
+        type1 = Seq.new(seq: record[:SEQ][0 ... 100]).type_guess
       elsif got2.nil?
         Fasta.open(infile2, "w") do |fasta_io|
           fasta_io.puts seq.to_fasta
         end
 
         got2  = true
-        type2 = Seq.new(nil, record[:SEQ][0 ... 100]).type_guess
+        type2 = Seq.new(seq: record[:SEQ][0 ... 100]).type_guess
       end
 
       if got1 and got2