[Bioc-devel] phred qualities

On 06/27/2012 08:02 AM, Kasper Daniel Hansen wrote:

Phred qualities are usually presented as ascii-encode numbers with an
offset of either 32 or 64. Some packages returns this as a
BStringSet. I can convert a character vector "charvec" to a list of
integers using code like
sapply(charvec, function(xx) charToRaw(xx) - 33L)

Do we have fast(er) ways of doing this, when charvec is really long
and not necessarily with the same number of chars in each string? I
am thinking of implementing the sapply() above in C (directly
vectorizing it), but surely someone has done something like that
somewhere.

I think you get this with XStringSet, e.g., PhredQuality, with

x = PhredQuality(c("HH", "III"))
y = as.numeric(unlist(x)) - 33L

z = relist(y, x)

Martin

Kasper