\name{writeSimContFastq}
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\alias{writeSimContFastq}
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\title{writeSimContFastq: Create FASTQ files with simulated k-mer sequences}
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\description{Writes compressed FASTQ files where sequence sections contain
    concatenated k-mers which are uniformly distributed in the range of k-mers
    for given k.
    A fraction of the reads can be contaminated with one or more deterministic
    k-mers.}
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\usage{ writeSimContFastq(k=6, nk=5, nSeq=10, pos=1,
        kIndex=1, nContam=nSeq, filename="simc.fq.gz")}
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\arguments{
    \item{k}{\code{numeric}. Length of k-mer. Default value is 6.}
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    \item{nk}{\code{numeric}. Number of k-mers in each FASTQ read. Default
        value is 5.}
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    \item{nSeq}{\code{numeric}. Number of simulated reads in FASTQ-file. 
        Default value is 10.}
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    \item{pos}{\code{numeric}. Determines at which position in sequence the 
        k-mer is inserted. 1-based (1=first position).}
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    \item{kIndex}{\code{numeric}. k-mer index of inserted k-mer.
        The k-mer index can be retreaved for a given k-mer with 'kMerIndex'.}
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    \item{nContam}{\code{numeric}. Absolute number of contaminated reads.
        The k-mer's are inserted at the firsts 'nContam' reads
        of the sequence array.}
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    \item{filename}{\code{character}. Name of written (compressed) FASTQ file.}
}
\details{The read headers are consequtive numbered. The phred quality values 
    are equally set to 46 (='.') which represents a phred value of 13. This
    function is not designed for routine use. The random content FASTQ files
    can be used in order to measure the separation capabilities of hierarchical
    clustering mechanisms.}
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\value{None.}
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\references{
Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM
The sanger FASTQ file format for sequences with quality scores and
    the Solexa/Illumina FASTQ variants.
Nucleic Acids Research 2010 Vol.38 No.6 1767-1771}
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\author{Wolfgang Kaisers}
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% Examples
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\examples{
\dontrun{writeSimContFastq()}
}
\keyword{writeSimContFastq}