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"}
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