last = false
Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
- unless options[:data_in].first == '-'
+ unless options[:data_in] and options[:data_in].first == '-'
input.each_record do |record|
output.puts record
end
Fastq.open(file, mode='r') do |fastq|
fastq.each do |entry|
if encoding == 'auto'
- if entry.qual.match(/[!-:]/) # sanger or illumina18
+ if entry.qual_base33? # sanger or illumina18
encoding = 'illumina18'
- elsif entry.qual.match(/[K-h]/) # solexa or illumina13 or illumina15
+ elsif entry.qual_base64? # solexa or illumina13 or illumina15
encoding = 'illumina13'
else
raise SeqError, "Could not auto-detect quality score encoding"