require 'maasha/biopieces'
require 'maasha/fastq'
-allowed_enc = 'auto,sanger,solexa,illumina13,illumina15,illumina18'
+allowed_enc = 'auto,sanger,solexa,illumina1.3,illumina1.5,illumina1.8'
casts = []
casts << {:long=>'data_in', :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
options = Biopieces.options_parse(ARGV, casts)
-num = 0
-last = false
-encoding = options[:encoding]
+num = 0
+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
end
- if options.has_key? :data_in
+ if options[:data_in]
options[:data_in].each do |file|
+ encoding = options[:encoding].downcase.delete('.')
+
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"
output.puts entry.to_bp
num += 1
- if options.has_key? :num and options[:num] == num
+ if options[:num] == num
last = true
break
end