added duplicate_record biopiece

[biopieces.git] / bp_bin / denoise_seq

diff --git a/bp_bin/denoise_seq b/bp_bin/denoise_seq
index ff557b431a6d6d57d152c5e7f69dd8202fbd60a6..5e67ab8b57633592f99d26fc9910a36dbdfa51cd 100755 (executable)
--- a/bp_bin/denoise_seq
+++ b/bp_bin/denoise_seq
@@ -37,8 +37,11 @@ require 'maasha/align'
 require 'maasha/usearch'
 
 casts = []
-casts << {:long=>'identity',    :short=>'i', :type=>'float', :mandatory=>true, :default=>0.97, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'cluster_min', :short=>'c', :type=>'uint',  :mandatory=>true, :default=>2,    :allowed=>nil, :disallowed=>"0"}
+casts << {:long=>'identity',      :short=>'i', :type=>'float', :mandatory=>true, :default=>0.97, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'cluster_min',   :short=>'c', :type=>'uint',  :mandatory=>true, :default=>2,    :allowed=>nil, :disallowed=>"0"}
+casts << {:long=>'frequency_min', :short=>'f', :type=>'uint',  :mandatory=>true, :default=>2,    :allowed=>nil, :disallowed=>"0"}
+casts << {:long=>'quality_min',   :short=>'q', :type=>'uint',  :mandatory=>true, :default=>20,   :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'consensus_min', :short=>'C', :type=>'float', :mandatory=>true, :default=>0.2,  :allowed=>nil, :disallowed=>nil}
 
 options          = Biopieces.options_parse(ARGV, casts)
 tmpdir           = Biopieces.mktmpdir
@@ -95,6 +98,8 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
 
   uc.each_alignment do |align|
     if align.members >= options[:cluster_min]
+      align.options = options
+
       alignment_to_fastq(align.entries, index)
 
       cons          = align.consensus