The source code is located here:
This program takes the two files of each corresponding read pair, checks that both reads in each pair pass illumina's quality filter, and outputs them both into their two respective .fastq files if they both pass the quality filter. The reads that pass illumina's quality filter can still be pretty crappy so simply excluding the ones that do not pass illumina's quality filter does not necessarily make them high quality reads.
illuminaToFastq <in_pair1> <in_pair2> <out_pair1> <out_pair2>
Feel free to modify the source as seen fit.