major upgrade of denoise_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1759 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/denoise_seq b/bp_bin/denoise_seq
index 5e67ab8b57633592f99d26fc9910a36dbdfa51cd..0129c47f2fb0b081ac888d6583359289feb3da63 100755 (executable)
--- a/bp_bin/denoise_seq
+++ b/bp_bin/denoise_seq
@@ -37,11 +37,13 @@ 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=>'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}
+casts << {:long=>'cluster_ident', :short=>'i', :type=>'float', :mandatory=>true,  :default=>0.97, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'cluster_min',   :short=>'c', :type=>'uint',  :mandatory=>true,  :default=>1,    :allowed=>nil, :disallowed=>"0"}
+casts << {:long=>'sequence_min',  :short=>'s', :type=>'uint',  :mandatory=>true,  :default=>1,    :allowed=>nil, :disallowed=>"0"}
+casts << {:long=>'residue_min',   :short=>'r', :type=>'float', :mandatory=>true,  :default=>0.3,  :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'gap_max',       :short=>'g', :type=>'float', :mandatory=>true,  :default=>0.4,  :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'quality_min',   :short=>'q', :type=>'uint',  :mandatory=>true,  :default=>10,   :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'quality_mean',  :short=>'Q', :type=>'uint',  :mandatory=>true,  :default=>15,   :allowed=>nil, :disallowed=>nil}
 
 options          = Biopieces.options_parse(ARGV, casts)
 tmpdir           = Biopieces.mktmpdir
@@ -49,6 +51,8 @@ fastq_file       = File.join(tmpdir, "test.fq")
 fasta_file       = File.join(tmpdir, "test.fna")
 fasta_file_align = File.join(tmpdir, "test.aln.fna")
 
+options[:identity] = options[:cluster_ident]
+
 def alignment_to_fastq(entries, index)
   entries.each do |entry|
     cluster, ident, name = entry.seq_name.split('|')