I am working with PacBio data in fastq format. The PacBio software outputs fastqs that contain quality scores ranging all the way up to Q=93, encoded as the ASCII 33+93 = `~`.
This is causing a problem within the ShortRead package, because the fastq quality score alphabet is hardcoded to extend only to ASCII 33+92='}' (see below for the problematic code). As a result, all ShortRead functions that work with quality scores ignore the Q=93 scores.
Is there a workaround for this problem that does not require case-by-case rewriting of ShortRead functions (e.g. somehow substituting the S4 method to return the 32:126 alphabet)? And why are quality scores cut-off at 92?
> selectMethod("alphabet", "FastqQuality") Method Definition: function (x, ...) rawToChar(as.raw(32:125), TRUE) <environment: namespace:ShortRead> Signatures: x target "FastqQuality" defined "FastqQuality"