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\name{read.maqmap.tags}
\alias{read.maqmap.tags}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{ Read MAQ text alignment output file }
\description{
Reads in MAQ alignment results in text format (that results from "maq mapview" command.)
}
\usage{
read.maqmap.tags(filename, read.tag.names = F, fix.chromosome.names = T)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
\item{filename}{ MAQ text output file }
\item{read.tag.names}{ Whether the tag names should be read in }
\item{fix.chromosome.names}{ Whether to remove ".fa" from the end of
the sequence names }
}
\value{
\item{tags }{ A vector of 5' tag coordinates, with negative values
corresponding to tags mapped to the negative strand. }
\item{quality }{ Number of mismatches }
\item{names }{ Tag names, if \code{read.tag.names} was set }
}
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