casts = []
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_min', :short=>'o', :type=>'uint', :mandatory=>false, :default=>1, :allowed=>nil, :disallowed=>"0"}
casts << {:long=>'overlap_max', :short=>'p', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>"0"}
options = Biopieces.options_parse(ARGV, casts)
if merged
new_record = merged.to_bp
- if merged.seq_name =~ /overlap=(\d+):hamming=(\d+)$/
- new_record[:OVERLAP_LEN] = $1
- new_record[:HAMMING_DIST] = $2
+ if merged.seq_name =~ /overlap=(\d+)$/
+ new_record[:OVERLAP_LEN] = $1
end
output.puts new_record