X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fremove_primers;h=88c1a81c3351df23fca647bec6d131d5b64e9dd9;hb=eb15b4040e0ceba1c3df40b7f0a597c469771cee;hp=5f26eb6051a3bc2092c5c6a1dc882be7dd2f1efc;hpb=3d51113401b585dc2fc813cbe67f8250e2bcfd43;p=biopieces.git

diff --git a/bp_bin/remove_primers b/bp_bin/remove_primers
index 5f26eb6..88c1a81 100755
--- a/bp_bin/remove_primers
+++ b/bp_bin/remove_primers
@@ -32,6 +32,7 @@
 require 'pp'
 require 'maasha/biopieces'
 require 'maasha/seq'
+require 'maasha/seq/backtrack'
 
 include BackTrack
 
@@ -46,12 +47,15 @@ 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)
 
-      seq.patscan(options[:forward].to_s, 0, options[:mismatches], options[:insertions], options[:deletions]) do |match|
+      seq.patscan(options[:forward].to_s,
+                  max_mismatches: options[:mismatches],
+                  max_insertions: options[:insertions],
+                  max_deletions:  options[:deletions]) do |match|
         record[:FORWARD_POS] = match.pos
         record[:FORWARD_LEN] = match.length
         pos = match.pos + match.length
@@ -61,7 +65,10 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
         break
       end
 
-      seq.patscan(options[:reverse].to_s, 0, options[:mismatches], options[:insertions], options[:deletions]) do |match|
+      seq.patscan(options[:reverse].to_s,
+                  max_mismatches: options[:mismatches],
+                  max_insertions: options[:insertions],
+                  max_deletions:  options[:deletions]) do |match|
         record[:REVERSE_POS] = match.pos
         record[:REVERSE_LEN] = match.length
         pos = 0