adding bzip2 support in ruby

[biopieces.git] / bp_bin / remove_primers

diff --git a/bp_bin/remove_primers b/bp_bin/remove_primers
index 720d943ee6db515b49980342afb96a8717a0fa22..1f7b7b216ab3fc9f089848b9303771d62d36a77f 100755 (executable)
--- a/bp_bin/remove_primers
+++ b/bp_bin/remove_primers
@@ -32,6 +32,9 @@
 require 'pp'
 require 'maasha/biopieces'
 require 'maasha/seq'
+require 'maasha/seq/backtrack'
+
+include BackTrack
 
 casts = []
 casts << {:long=>'forward',    :short=>'f', :type=>'string', :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}
@@ -44,7 +47,7 @@ options = Biopieces.options_parse(ARGV, casts)
 
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   input.each do |record|
-    if record.has_key? :SEQ
+    if record[:SEQ]
       forward = false
       reverse = false
       seq = Seq.new_bp(record)