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add seqTools package

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqTools@95415 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 13/10/2014 19:02:34
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+\name{writeSimContFastq}
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+%
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+\alias{writeSimContFastq}
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+%
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+\title{writeSimContFastq: Create FASTQ files with simulated k-mer sequences}
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+%
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+\description{Writes compressed FASTQ files where sequence sections contain
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+    concatenated k-mers which are uniformly distributed in the range of k-mers
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+    for given k.
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+    A fraction of the reads can be contaminated with one or more deterministic
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+    k-mers.}
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+%
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+\usage{ writeSimContFastq(k=6, nk=5, nSeq=10, pos=1,
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+        kIndex=1, nContam=nSeq, filename="simc.fq.gz")}
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+%
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+\arguments{
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+    \item{k}{\code{numeric}. Length of k-mer. Default value is 6.}
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+    %
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+    \item{nk}{\code{numeric}. Number of k-mers in each FASTQ read. Default
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+        value is 5.}
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+    %
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+    \item{nSeq}{\code{numeric}. Number of simulated reads in FASTQ-file. 
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+        Default value is 10.}
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+    %
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+    \item{pos}{\code{numeric}. Determines at which position in sequence the 
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+        k-mer is inserted. 1-based (1=first position).}
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+    %
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+    \item{kIndex}{\code{numeric}. k-mer index of inserted k-mer.
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+        The k-mer index can be retreaved for a given k-mer with 'kMerIndex'.}
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+    %
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+    \item{nContam}{\code{numeric}. Absolute number of contaminated reads.
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+        The k-mer's are inserted at the firsts 'nContam' reads
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+        of the sequence array.}
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+    %
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+    \item{filename}{\code{character}. Name of written (compressed) FASTQ file.}
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+}
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+\details{The read headers are consequtive numbered. The phred quality values 
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+    are equally set to 46 (='.') which represents a phred value of 13. This
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+    function is not designed for routine use. The random content FASTQ files
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+    can be used in order to measure the separation capabilities of hierarchical
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+    clustering mechanisms.}
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+%
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+\value{None.}
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+%
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+\references{
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+Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM
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+The sanger FASTQ file format for sequences with quality scores and
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+    the Solexa/Illumina FASTQ variants.
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+Nucleic Acids Research 2010 Vol.38 No.6 1767-1771}
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+%
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+\author{Wolfgang Kaisers}
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+% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - %
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+% Examples
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+% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - %
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+\examples{
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+\dontrun{writeSimContFastq()}
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+}
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+\keyword{writeSimContFastq}