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#!/usr/bin/env ruby
class Fixer
def initialize
end
def run left, right, prefix
leftout = ""
rightout = ""
buffersize = 200000
buffer = 0
data = {}
cont = true
lh = File.open(left)
rh = File.open(right)
lout = File.open("#{prefix}-fixed.1.fastq", "w")
rout = File.open("#{prefix}-fixed.2.fastq", "w")
count=0
name1 = lh.readline.chomp rescue nil
name2 = rh.readline.chomp rescue nil
while cont
seq1 = lh.readline rescue nil
plus1 = lh.readline rescue nil
quals1 = lh.readline rescue nil
seq2 = rh.readline rescue nil
plus2 = rh.readline rescue nil
quals2 = rh.readline rescue nil
if name1
shortname1 = name1[0..-3]
if data[shortname1]
leftout << "#{name1}\n#{seq1}+\n#{quals1}"
rightout << data[shortname1][1]
buffer+=1
data.delete(shortname1)
if buffer>=buffersize
lout.write leftout
leftout=""
rout.write rightout
rightout=""
buffer=0
end
else
data[shortname1]=[]
data[shortname1][0]="#{name1}\n#{seq1}+\n#{quals1}"
end
end
if name2
shortname2 = name2[0..-3]
if data[shortname2]
leftout << data[shortname2][0]
rightout << "#{name2}\n#{seq2}+\n#{quals2}"
buffer+=1
data.delete(shortname2)
if buffer>=buffersize
lout.write leftout
leftout=""
rout.write rightout
rightout=""
buffer=0
end
else
data[shortname2]=[]
data[shortname2][1]="#{name2}\n#{seq2}+\n#{quals2}"
end
end
name1 = lh.readline.chomp rescue nil
name2 = rh.readline.chomp rescue nil
if name1==nil and name2==nil
cont=false
end
end
lout.write leftout
rout.write rightout
lout.close
rout.close
File.open("#{prefix}-fixed.single.fastq", "w") do |out|
data.each do |name, list|
if list
if list[0]
out.write list[0]
end
if list[1]
out.write list[1]
end
end
end
end
end
end
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