made find_adaptor ignore too short sequences

[biopieces.git] / bp_bin / find_adaptor

diff --git a/bp_bin/find_adaptor b/bp_bin/find_adaptor
index 0534572bd4ff08669f934a57d1d1bfc9a64d9486..4fd559dd281b45b06b372134e6215cc600ef55a2 100755 (executable)
--- a/bp_bin/find_adaptor
+++ b/bp_bin/find_adaptor
@@ -88,10 +88,10 @@ end
 
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   input.each do |record|
-    if record[:SEQ] and record[:SEQ].length > 0
+    if record[:SEQ]
       entry = Seq.new_bp(record)
 
-      if options[:forward]
+      if options[:forward] and record[:SEQ].length >= options[:forward].length
         if m = entry.patmatch(options[:forward], 0, fmis, fins, fdel)
           record[:ADAPTOR_POS_LEFT] = m.pos
           record[:ADAPTOR_LEN_LEFT] = m.length
@@ -120,7 +120,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
         end
       end
 
-      if options[:reverse]
+      if options[:reverse] and record[:SEQ].length >= options[:reverse].length
         if m = entry.patmatch(options[:reverse], 0, rmis, rins, rdel)
           record[:ADAPTOR_POS_RIGHT] = m.pos
           record[:ADAPTOR_LEN_RIGHT] = m.length