[BioC] shortread base quality

David Vilanova vilanew at gmail.com
Mon Aug 27 16:53:54 CEST 2012

Excellent Martin,
Works well.

One quick question, my scores range from -29 to 8. This is normally an 
illumina 1.9 format (as detected by fastqc program) .
Is there a quick way to ckeck within shortread which encoding has been 
used by shortRead and which version of illumina was recognized (like 
what fastqc does).

On 08/27/2012 03:44 PM, Martin Morgan wrote:
> q = quality(rfq)
> w = width(q)
> m = matrix(NA_integer_, length(q), max(width(q)))
> for (i in seq(min(w), max(w)))
>     m[w==i, 1:i] = as(q[w==i], "matrix")

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