\title{Counting reads across intervals}
\description{Counts the number of reads starting at each position across given
genomic intervals}
\usage{count.reads(reads_fn, I, sb=NULL, binary=FALSE, sum.counts=FALSE)}
  \item{reads_fn}{filename of aligned reads in BAM format}
  \item{I}{a GRanges object giving valid genomic intervals}
  \item{sb}{a seqbias object}
  \item{binary}{if \code{TRUE}, return a 0-1 vector, otherwise return a vector
  counting the number of reads mapped to each position}
  \item{sum.counts}{if \code{TRUE} return the total read count for each interval}
  Given an indexed BAM file, this function counts the number of reads starting
  at each position of each provided interval. If a seqbias object is provided
  through the \code{sb} attribute, counts are corrected for sequence bias.
  The total read count for each interval is returned if \code{sum.counts} is
  If \code{binary} is \code{TRUE} a 0-1 vector is returned instead, where
  positions at which no reads are mapped are 0, and those with one or more are
  A list of numeric vectors is returned, one for each interval provided. Each
  vector gives an integer count of the number of reads beginning on that
  The BAM file provided should be indexed with 'samtools index'.
    Daniel Jones
  reads_fn <- system.file( "extra/example.bam", package = "seqbias" )

  I <- GRanges( c('seq1'), IRanges( c(1), c(5000) ), strand = c('-') )

  counts <- count.reads( reads_fn, I )