[BioC] mismatch & replacement

[Daniel.Berner at unibas.ch]

Hi list
1. I have a large fastq file containing solexa reads that start with a  
barcode (identifier to separate individuals). I now want to filter  
that large data set according to the barcodes using ShortRead. I  
understand that this is easily done with grep() when one wants a  
perfect barcode match. However, I want to allow ONE single wrong  
nucleotide within the barcode, at any position. Is there an efficient  
way to filter by barcode while allowing a mismatch?

2. Is there a way to modify nucleotides in ShortRead objects? E.g., to  
replace a G by an A at position 3 for ALL sequences in the object?

Thanks!
Daniel