Biopieces.open(options[:stream_in], file_records) do |input, output|
input.each do |record|
- if record.has_key? :SEQ
+ if record[:SEQ]
na_mask = NArray.int(record[:SEQ].length) unless na_mask
na_seq = NArray.to_na(record[:SEQ], "byte")
na_mask += na_seq.eq('-'.ord)
Biopieces.open(file_records, options[:stream_out]) do |input, output|
input.each do |record|
- if sum > 0 and record.has_key? :SEQ
+ if sum > 0 and record[:SEQ]
na_seq = NArray.to_na(record[:SEQ], "byte")
record[:SEQ] = na_seq[na_mask].to_s
record[:SEQ_LEN] = record[:SEQ].length