Read quality can be "Phred + 64" encoded

[hukai916]

Hi developers,

I noticed that the current implementation only considers "Phred + 33" encoding for read qualities, however, "Phred + 64" encoding is also commonly used.

In particular, the following line is only compatible if the read quality is "Phred + 33" encoded.

UMIc/R/casesWorkflows.R

Line 61 in 8b9228f

quality <- as(quality(reads1), "matrix")

Will changing it to the following, and remove all + 33 help?

quality <- apply(as.matrix(quality(reads1)@quality), c(1,2), FUN = utf8ToInt)

Thanks!

--Kai

[npechl]

Thank you for your suggestion!

We will work on adding this attribute in a future version of the tool.

Regards,
Nikos