check_encoding {FastqCleaner}R Documentation

Check quality encoding

Description

Check quality encoding

Usage

check_encoding(x = NULL, custom = NULL)

Arguments

x

Quality values

custom

custom encoding from the following:

'Sanger' ——–> expected range: [0, 40]

'Illumina1.8' ——–> expected range: [0, 41]

'Illumina1.5' ——–> expected range: [0, 40]

'Illumina1.3' ——–> expected range: [3, 40]

'Solexa' ——–> expected range: [-5, 40]

Value

List with encoding information

Author(s)

Leandro Roser learoser@gmail.com

Examples


require(Biostrings)

x <- list(PhredQuality(0:40), SolexaQuality(-5:40), IlluminaQuality(3:40))
x <- lapply(x, function(i)utf8ToInt(as.character(i)[1]))
lapply(x, check_encoding)
 
SolexaQuality(0:40)
IlluminaQuality(0:40)

[Package FastqCleaner version 1.10.0 Index]