Support the FastQ format that combines sequence and quality. See:
Of course, this is yet another vaguely defined pseudo-standard with conflicting definitions. Of course Solexa had to go and invent a different, but indistinguishably so, way to do it:
Currently, we only support the non-Solexa FastQ, adding/subtracting 33 for the quality values.
As far as I know, FastQ is only used for nucleotide sequences, never amino acid.