Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
input.each do |record|
- if record[:SEQ] and record[:SEQ].length > 0
+ if record[:SEQ]
entry = Seq.new_bp(record)
- if options[:forward]
+ if options[:forward] and record[:SEQ].length >= options[:forward].length
if m = entry.patmatch(options[:forward], 0, fmis, fins, fdel)
record[:ADAPTOR_POS_LEFT] = m.pos
record[:ADAPTOR_LEN_LEFT] = m.length
end
end
- if options[:reverse]
+ if options[:reverse] and record[:SEQ].length >= options[:reverse].length
if m = entry.patmatch(options[:reverse], 0, rmis, rins, rdel)
record[:ADAPTOR_POS_RIGHT] = m.pos
record[:ADAPTOR_LEN_RIGHT] = m.length