refactored backtrack methods to use options hash in method invocations

[biopieces.git] / bp_bin / remove_primers

diff --git a/bp_bin/remove_primers b/bp_bin/remove_primers
index 1f7b7b216ab3fc9f089848b9303771d62d36a77f..88c1a81c3351df23fca647bec6d131d5b64e9dd9 100755 (executable)
--- a/bp_bin/remove_primers
+++ b/bp_bin/remove_primers
@@ -52,7 +52,10 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
       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
@@ -62,7 +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