renamed patternmatcher to dynamic

[biopieces.git] / bp_bin / find_adaptor

diff --git a/bp_bin/find_adaptor b/bp_bin/find_adaptor
index 9b6a3d215884bb96ccf36e38f37839f9ca6df2b9..bf4f372d12a0ad110100dd5ddc221d1bc208fb68 100755 (executable)
--- a/bp_bin/find_adaptor
+++ b/bp_bin/find_adaptor
@@ -170,18 +170,17 @@ class Pattern
 end
 
 casts = []
-casts << {:long=>'forward',     :short=>'f', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'forward_rc',  :short=>'F', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'reverse',     :short=>'r', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'reverse_rc',  :short=>'R', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'len_forward', :short=>'l', :type=>'uint',   :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>'0'}
-casts << {:long=>'len_reverse', :short=>'L', :type=>'uint',   :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>'0'}
-casts << {:long=>'mismatches',  :short=>'m', :type=>'uint',   :mandatory=>false, :default=>10,  :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'insertions',  :short=>'i', :type=>'uint',   :mandatory=>false, :default=>5,   :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'deletions',   :short=>'d', :type=>'uint',   :mandatory=>false, :default=>5,   :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'cpus',        :short=>'c', :type=>'uint',   :mandatory=>false, :default=>1,   :allowed=>nil, :disallowed=>'0'}
-
-BASE_PER_FILE = 10_000_000
+casts << {:long=>'forward',       :short=>'f', :type=>'string', :mandatory=>false, :default=>nil,        :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'forward_rc',    :short=>'F', :type=>'string', :mandatory=>false, :default=>nil,        :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'reverse',       :short=>'r', :type=>'string', :mandatory=>false, :default=>nil,        :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'reverse_rc',    :short=>'R', :type=>'string', :mandatory=>false, :default=>nil,        :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'len_forward',   :short=>'l', :type=>'uint',   :mandatory=>false, :default=>nil,        :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'len_reverse',   :short=>'L', :type=>'uint',   :mandatory=>false, :default=>nil,        :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'mismatches',    :short=>'m', :type=>'uint',   :mandatory=>false, :default=>10,         :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'insertions',    :short=>'i', :type=>'uint',   :mandatory=>false, :default=>5,          :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'deletions',     :short=>'d', :type=>'uint',   :mandatory=>false, :default=>5,          :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'cpus',          :short=>'c', :type=>'uint',   :mandatory=>false, :default=>1,          :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'bases_per_file',:short=>'b', :type=>'uint',   :mandatory=>false, :default=>10_000_000, :allowed=>nil, :disallowed=>'0'}
 
 options = Biopieces.options_parse(ARGV, casts)
 
@@ -235,7 +234,7 @@ Biopieces.open(options[:stream_in], file_records) do |input, output|
       count_seq += 1;
       bases      += record[:SEQ].length
 
-      if bases > BASE_PER_FILE
+      if bases > options[:bases_per_file]
         out_fa.close
         bases       = 0
         count_file += 1