readsff: Read SFF-formatted files into SffReads or SffReadsQ objects

Description Usage Arguments Value Author(s) Examples

Description

readSff reads all sff files specified in filenames, returning an R object of type SffReads or SffReadsQ which acts and behaves similarly to the ShortRead and ShortReadQ classes from package ShortRead

Usage

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readSff(filenames, use.qualities=TRUE, use.names=TRUE,
    clipMode = c("full", "adapter", "quality", "raw"), verbose=TRUE)

Arguments

filenames

File or files to be read in.

use.qualities

logical(1) indicating whether to include quality values in the returned object.

use.names

logical(1) indicating whether to return read names, not yet implemented

clipMode

character(1) indicating the clipMode of the returned object.

verbose

logical(1) indicating whether to return verbose output.

Value

A SffReads or SffReadsQ object.

Author(s)

Matt Settles <msettles@uidaho.edu>

Examples

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sff <- readSff(system.file("extdata","Small454Test.sff",package="rSFFreader"))


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