# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-# Identify paired end orphan in records with sequence data.
+# Find paired end orphan in records with sequence data.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
input.each_record do |record|
- records << record
+ if record[:SEQ_NAME]
+ records << record
- if records.size == 2
- if Illumina.name_match?(records.first[:SEQ_NAME], records.last[:SEQ_NAME])
- records.first[:TYPE] = "paired"
- records.last[:TYPE] = "paired"
+ if records.size == 2
+ if Illumina.name_match?(records.first[:SEQ_NAME], records.last[:SEQ_NAME])
+ records.first[:TYPE] = "paired"
+ records.last[:TYPE] = "paired"
- output.puts records.first
- output.puts records.last
+ output.puts records.first
+ output.puts records.last
- records = []
- else
- records.first[:TYPE] = "orphan"
- output.puts records.first
+ records = []
+ else
+ records.first[:TYPE] = "orphan"
+ output.puts records.first
- records.shift
+ records.shift
+ end
end
end
end