filterFastq {ShortRead} | R Documentation

## Filter fastq from one file to another

### Description

`filterFastq` filters reads from source to destination file(s) applying a filter to reads in each file. The filter can be a function or FilterRules instance; operations are done in a memory-efficient manner.

### Usage

    filterFastq(files, destinations, ..., filter = FilterRules(),
        compress=TRUE, yieldSize = 1000000L)

### Arguments

`files` | a character vector of valid file paths.
`destinations` | a character vector of destinations, recycled to be the same length as `files`. `destinations` must not already exist.
`...` | Additional arguments, perhaps used by a `filter` function.
`filter` | A simple function taking as it's first argument a `ShortReadQ` instance and returning a modified `ShortReadQ` instance (e.g., with records or nucleotides removed), or a `FilterRules` instance specifying which records are to be removed.
`compress` | A logical(1) indicating whether the file should be gz-compressed. The default is `TRUE`.
`yieldSize` | Number of fastq records processed in each call to `filter`; increase this for (marginally) more efficient I/O at the expense of increased memory use.

### Author(s)

Martin Morgan mtmorgan@fhcrc.org

### Examples

    ## path to a convenient fastq file
    sp <- SolexaPath(system.file('extdata', package='ShortRead'))
    fl <- file.path(analysisPath(sp), "s_1_sequence.txt")

    ## filter reads to keep those with GC < 0.7
    fun <- function(x) {
        gc <- alphabetFrequency(sread(x), baseOnly=TRUE)[,c("G", "C")]
        x[rowSums(gc) / width(x) < .7]
    }
    filterFastq(fl, tempfile(), filter=fun)

    ## trimEnds,character-method uses filterFastq internally
    trimEnds(fl, "V", destinations=tempfile())

[Package ShortRead version 1.45.4 Index]