name = $1.to_sym
pair = $2.to_i
else
- $stderr.puts "WARNING: Unmatched sequence name: #{record[:SEQ_NAME]}" if options[:verbose]
+ $stderr.puts "WARNING: Unmatched sequence name: #{record[:SEQ_NAME]}"
end
if pair == 1
if hash2[name]
+ record[:ORDER] = "paired"
+ hash2[name][:ORDER] = "paired"
output.puts record
output.puts hash2[name]
end
elsif pair == 2
if hash1[name]
+ hash1[name][:ORDER] = "paired"
+ record[:ORDER] = "paired"
output.puts hash1[name]
output.puts record
end
end
end
-end
-if options[:verbose]
- $stderr.puts "Unmatched names with 1st read pair: #{hash1.size}"
- $stderr.puts "Unmatched names with 2nd read pair: #{hash2.size}"
+ hash1.each_value do |record|
+ record[:ORDER] = "orphan 1"
+ output.puts record
+ end
+
+ hash2.each_value do |record|
+ record[:ORDER] = "orphan 2"
+ output.puts record
+ end
end
+
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<