added tests to remove_primers

[biopieces.git] / bp_bin / remove_primers

diff --git a/bp_bin/remove_primers b/bp_bin/remove_primers
index 108f5856746485329dbc812daf56d07693b42f33..9c8457ccb527bd50281e2a202dc47ae1003959f6 100755 (executable)
--- a/bp_bin/remove_primers
+++ b/bp_bin/remove_primers
@@ -47,6 +47,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
     if record.has_key? :SEQ
       seq = Seq.new_bp(record)
       pos = 0
+      len = 0
 
       if forward = seq.patscan(options[:forward].to_s, pos, options[:mismatches], options[:insertions], options[:deletions])
         record[:FORWARD_POS] = forward.last.pos
@@ -61,10 +62,16 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
         record[:REVERSE_LEN] = reverse.first.length
         pos = 0
         len = reverse.first.pos
-        seq.subseq!(pos, len) if len > 0
+
+        if len == 0
+          seq.seq  = ""
+          seq.qual = "" if seq.qual
+        else
+          seq.subseq!(pos, len)
+        end
       end
 
-      if pos > 0
+      if forward or reverse
         record.merge!(seq.to_bp)
       end