casts << {long: 'no_sort', short: 'n', type: 'flag', mandatory: false, default: nil, allowed: nil, disallowed: nil}
casts << {long: 'comp', short: 'c', type: 'flag', mandatory: false, default: nil, allowed: nil, disallowed: nil}
casts << {long: 'identity', short: 'i', type: 'float', mandatory: true, default: 0.9, allowed: nil, disallowed: nil}
+casts << {long: 'cpus', short: 'C', type: 'uint', mandatory: false, default: 1, allowed: nil, disallowed: "0"}
options = Biopieces.options_parse(ARGV, casts)
Biopieces.open(file_records, options[:stream_out]) do |input, output|
input.each_record do |record|
if record[:SEQ_NAME] and record[:SEQ]
- if hash[record[:SEQ_NAME].to_sym]
- us = hash[record[:SEQ_NAME].to_sym]
+ seq_name = record[:SEQ_NAME].split(/\s+/).first.to_sym
+ if us = hash[seq_name]
record[:CLUSTER] = us[:CLUSTER].to_i
record[:IDENT] = us[:IDENT].to_i
record[:IDENT] = '*' if us[:TYPE] == 'S'