X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fpatscan_seq;h=28f028dec433ccb5ac8ccd32c6d4ba59b9d08a0d;hb=5526cf56fc20602b9be197db8b1a9a44502791ab;hp=f408bd677f5c31ad1aaaeb1371c15f8db104ab34;hpb=2a8f4b16e21e5e0b2d268775b035c5f0651e888d;p=biopieces.git

diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
index f408bd6..28f028d 100755
--- a/bp_bin/patscan_seq
+++ b/bp_bin/patscan_seq
@@ -51,7 +51,7 @@ class Patscan
       args << "scan_for_matches"
       args << "-c"                         if options[:comp]
       args << "-p"                         if options[:seq_type] == :protein
-      args << "-o"                         if options[:overlap]
+      args << "-o 1"                       if options[:overlap]
       args << "-n #{options[:max_misses]}" if options[:max_misses]
       args << "-m #{options[:max_hits]}"   if options[:max_hits]
       args << File.join(@tmp_dir, "#{i}.pat")
@@ -161,7 +161,7 @@ seq_name_hash  = {}
 seq_type       = nil
 
 Biopieces.open(options[:stream_in], tmp_file) do |input, output|
-  Fasta.open(in_file, mode="w") do |fasta_io|
+  Fasta.open(in_file, "w") do |fasta_io|
     input.each_record do |record|
       if record[:SEQ_NAME]
         seq_name_hash[seq_name_count] = record[:SEQ_NAME]