\name{readSolexaFastq}

\alias{readSolexaFastQ}
\alias{readSolexaFastA}

\title{Read Solexa fastq and fasta-style files}

\description{
  These function illustrates how to read a Solexa fasta- and fastq-style
  file into a \code{DNAStringSet} or \code{SolexaSequenceQ} object.
}

\usage{
readSolexaFastQ(filepaths)
readSolexaFastA(filepaths)
}
\arguments{
  \item{filepaths}{
    A character vector containing file paths.
  }
}
\details{
  Each sequence in a Solexa fastq file consists of four lines. The first
  and third are identifiers (identical in each record), the second line
  is the sequence, and the fourth line the ASCII-encoded base quality
  score. For example:

\preformatted{
@HWI-EAS88_1_1_1_1001_499
GGACTTTGTAGGATACCCTCGCTTTCCTTCTCCTGT
+HWI-EAS88_1_1_1_1001_499
]]]]]]]]]]]]Y]Y]]]]]]]]]]]]VCHVMPLAS
}

  \code{readSolexaFastq} parses one or more files in this format into a
  single \code{SolexaSequenceQ} object.

  Solexa fasta files are nearly standard, except that uncalled bases
  are encoded as \code{.} instead of \code{-}.
}
\value{
  \code{readSolexaFastA} returns a \code{DNAStringSet} class represnting
  all reads. \code{readSolexaFastQ} returns a \code{SolexaSequenceQ}
  class representing reads, their quality scores, and the read names.
}
\seealso{
  \code{\linkS4class{SolexaSequenceQ}}
}
\examples{
aFile <- system.file('extdata', 's_5.fasta',
                     package='BiostringsCinterfaceDemo')
sa <- readSolexaFastQ(aFile)
sa

qFile <- system.file('extdata', 's_1_sequence.txt',
                     package='BiostringsCinterfaceDemo')
sq <- readSolexaFastQ(qFile)
sq
}
\keyword{manip}