\name{bam2R}
\alias{bam2R}
\title{Read nucleotide counts...}
\usage{bam2R(file, chr, start, stop, q=25, s=2, head.clip=0, max.depth=1e+06)
}
\description{Read nucleotide counts}
\details{This function reads the nucleotide counts on each position of a .bam alignment. The counts of both strands are reported separately 
and nucleotides below a quality cutoff are masked. It is called by \code{\link{deepSNV}} to parse the alignments of the test and control experiments,
respectively.}
\value{A named \code{\link{matrix}} with rows corresponding to genomic positions and columns for the nucleotide counts (A, T, C, G, -), masked nucleotides (N), (INS)ertions, (DEL)etions, (HEAD)s and (TAIL)s that count how often a read begins and end at the given position, respectively, 
and the sum of alignment (QUAL)ities. 
Counts from matches on the reference strand (s=0) are uppercase, counts on the complement (s=1) are lowercase. The returned matrix has 11 * 2 (strands) = 22 columns and (stop - start + 1) rows.}
\author{gemoritz}
\arguments{\item{file}{The name of the .bam file as a string.}
\item{chr}{The chromosome as a string.}
\item{start}{The start position (1-indexed).}
\item{stop}{The end position (1-indexed).}
\item{q}{An optional cutoff for the nucleotide Phred quality. Default q = 25. Nucleotides with Q < q will be masked by 'N'.}
\item{s}{Optional choice of the strand. Defaults to s = 2 (both).}
\item{head.clip}{Should n nucleotides from the head of reads be clipped? Default 0.}
\item{max.depth}{The maximal depth for the pileup command. Default 1,000,000.}
}
\examples{## Simple example:
counts <- bam2R(file = system.file("extdata", "test.bam", package="deepSNV"), chr="B.FR.83.HXB2_LAI_IIIB_BRU_K034", start = 3120, stop=3140, q = 10)
show(counts)
## Not run: Requires an internet connection, but try yourself.
# bam <- bam2R(file = "http://www.bsse.ethz.ch/cbg/software/deepSNV/data/test.bam", chr="B.FR.83.HXB2_LAI_IIIB_BRU_K034", start = 2074, stop=3585, q=10)
# head(bam)}