X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fpatscan_seq;h=a209bc6f104fb004fc5aba4d48b4d5eda2d17029;hb=847dcea71d11154d6636abc7257d2ff1af83bcde;hp=f408bd677f5c31ad1aaaeb1371c15f8db104ab34;hpb=5eda8ede42e0096ad55f1470b8eef3b03eefb38f;p=biopieces.git

diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
index f408bd6..a209bc6 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")