R/readBaseQuality.R

In ShortRead: FASTQ input and manipulation

.readBaseQuality_Solexa <-
    function(dirPath, seqPattern=character(0), prbPattern=character(0),
             ...)
{
    prbs <- readPrb(dirPath, pattern=prbPattern, ...)
    ShortReadQ(
        sread = readXStringColumns(
          dirPath, pattern=seqPattern,
          colClasses=c(rep(list(NULL), 4), list("DNAString")))[[1]],
        quality=prbs,
        id=BStringSet(as.character(seq_len(length(prbs)))))
}

.readBaseQuality_character <-
    function(dirPath, seqPattern=character(0), prbPattern=character(0),
             type=c("Solexa"), ...)
{
    if (missing(type))
        .arg_missing_err("type", "readBaseQuality,character-method",
                         "help(\"readBaseQuality,character-method\")")
    if (!is.character(type) || length(type) != 1)
        .arg_mismatch_type_err("type", "character(1)")
    vals <- eval(formals(.readBaseQuality_character)$type,
                 getNamespace("ShortRead"))
    if (!type %in% vals)
        .arg_mismatch_value_err("type", type, vals)
    tryCatch({
        switch(type,
               Solexa=.readBaseQuality_Solexa(dirPath,
                 seqPattern=seqPattern, prbPattern=prbPattern,...))
    }, error=function(err) {
        if (is(err, "SRError")) stop(err)
        else {
            seqpat <- paste(seqPattern, collapse=" ")
            prbpat <- paste(prbPattern, collapse=" ")
            txt <- paste("'%s' failed to parse files",
                         "dirPath: '%s'",
                         "seqPattern: '%s'",
                         "prbPattern: '%s'",
                         "type: '%s'",
                         "error: %s", sep="\n  ")
            msg <- sprintf(txt, "readBaseQuality", dirPath,
                           seqpat, prbpat, type,
                           conditionMessage(err))
            .throw(SRError("Input/Output", msg))
        }
    })
}

setMethod(readBaseQuality, "character", .readBaseQuality_character)