As new Illumina software (GA 1.3+) has changed quality score encoding, I've written a small patch which adds 'ill2sanger' function, to convert new illumina fastq files into sanger fastq.
It applies to maq-0.7.1. Essentially it takes the illumina score and adds 2. The function to read fastq files (defined in seq.c) removes 33 to this score, so that the overall operation is removal of 31 from illumina score
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