fixed defaults and key names

[biopieces.git] / bp_bin / assemble_pairs2

diff --git a/bp_bin/assemble_pairs2 b/bp_bin/assemble_pairs2
index f6d2f28594056689190bbb5e34d66ae183132836..3741222a0f2a03e9983f1d390017d4870bd092e0 100755 (executable)
--- a/bp_bin/assemble_pairs2
+++ b/bp_bin/assemble_pairs2
@@ -35,7 +35,7 @@ require 'maasha/seq/assemble'
 require 'pp'
 
 casts = []
-casts << {:long=>'mismatches',  :short=>'m', :type=>'uint', :mandatory=>false, :default=>10,  :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'mismatches',  :short=>'m', :type=>'uint', :mandatory=>false, :default=>5,   :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'overlap_min', :short=>'o', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>"0"}
 casts << {:long=>'overlap_max', :short=>'p', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>"0"}
 
@@ -68,7 +68,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
           new_record = merged.to_bp
 
           if merged.seq_name =~ /overlap=(\d+):hamming=(\d+)$/
-            new_record[:OVERLAP]      = $1
+            new_record[:OVERLAP_LEN]  = $1
             new_record[:HAMMING_DIST] = $2
           end