\name{BamInput}
\Rdversion{1.1}

\alias{scanBam}
\alias{scanBam,character-method}
\alias{countBam}
\alias{countBam,character-method}
\alias{scanBamHeader}
\alias{scanBamHeader,character-method}
\alias{asBam}
\alias{asBam,character-method}
\alias{indexBam}
\alias{indexBam,character-method}
\alias{filterBam}
\alias{filterBam,character-method}
\alias{sortBam}
\alias{sortBam,character-method}

\title{

  Import, count, index, and other operations on `BAM' (binary alignment)
  files.

}
\description{
  Import binary `BAM' files into a list structure, with facilities for
  selecting what fields and which records are imported.
}
\usage{

scanBam(file, index=file, ..., param=ScanBamParam())

countBam(file, index=file, ..., param=ScanBamParam())

scanBamHeader(files, ...)
\S4method{scanBamHeader}{character}(files, ...)

asBam(file, destination, ...)
\S4method{asBam}{character}(file, destination, ...,
    overwrite=FALSE, indexDestination=TRUE)

filterBam(file, destination, index=file, ...)
\S4method{filterBam}{character}(file, destination, index=file, ...,
    indexDestination=TRUE, param=ScanBamParam())
    
sortBam(file, destination, ...)
\S4method{sortBam}{character}(file, destination, ..., byQname=FALSE, maxMemory=512)

indexBam(files, ...)
\S4method{indexBam}{character}(files, ...)

}

\arguments{

  \item{file}{The character(1) file name of the `BAM' ('SAM' for
    \code{asBam}) file to be processed.}

  \item{files}{The character() file names of the `BAM' file to be
    processed.}

  \item{index}{The character(1) name of the index file of the 'BAM' file
    being processed; this is given \emph{without} the '.bai' extension.}

  \item{destination}{The character(1) file name of the location where
    the sorted or filtered output file will be created. For \code{asBam}
    and \code{sortBam} this is without the \dQuote{.bam} file suffix.}

  \item{\dots}{Additional arguments, passed to methods.}

  \item{overwrite}{A logical(1) indicating whether the destination
    can be over-written if it already exists.}

  \item{indexDestination}{A logical(1) indicating whether the created
    destination file should also be indexed.}
    
  \item{byQname}{A logical(1) indicating whether the sorted destination
    file should be sorted by Query-name (TRUE) or by mapping
    position (FALSE).}
    
  \item{maxMemory}{A numerical(1) indicating the maximal amount of
    memory (in MB) that the function is allowed to use.}

  \item{param}{An instance of \code{\linkS4class{ScanBamParam}}. This
	influences what fields and which records are imported.}

}
\details{

  The \code{scanBam} function parses binary BAM files; text SAM files
  can be parsed using R's \code{\link{scan}} function, especially with
  arguments \code{what} to control the fields that are parsed.

  \code{countBam} returns a count of records consistent with
  \code{param}.

  \code{scanBamHeader} visits the header information in a BAM file,
  returning for each file a list containing elements \code{targets} and
  \code{text}, as described below. The SAM / BAM specification does not
  require that the content of the header be consistent with the content
  of the file, e.g., more targets may be present that are represented by
  reads in the file.

  \code{asBam} converts 'SAM' files to 'BAM' files, equivalent to the
  \code{samtools view -Sb file > destination}. The 'BAM' file is sorted
  and an index created on the destination (with extension '.bai') when
  \code{indexDestination=TRUE}.

  \code{filterBam} parses records in \code{file} satisfying the
  \code{bamWhich} of \code{param}, writing each record satisfying the
  \code{bamFlag} and \code{bamSimpleCigar} criteria of \code{param} to
  file \code{destination}. An index file is created on the destination
  when \code{indexDestination=TRUE}.
  
  \code{sortBam} sorts the BAM file given as its first argument,
  analogous to the \dQuote{samtools sort} function.

  \code{indexBam} creates an index for each BAM file specified,
  analogous to the \sQuote{samtools index} function.
  
  Details of the \code{ScanBamParam} class are provide on its help page;
  several salient points are reiterated here. \code{ScanBamParam} can
  contain a field \code{what}, specifying the components of the BAM
  records to be returned. Valid values of \code{what} are available with
  \code{\link{scanBamWhat}}. \code{ScanBamParam} can contain an argument
  \code{which} that specifies a subset of reads to return. This requires
  that the BAM file be indexed, and that the file be named following
  samtools convention as \code{<bam_filename>.bai}. \code{ScanBamParam}
  can contain an argument \code{tag} to specify which tags will be
  extracted. 

}

\value{

  The \code{scanBam,character-method} returns a list of lists. The outer
  list groups results from each \code{Ranges} list of
  \code{bamWhich(param)}; the outer list is of length one when
  \code{bamWhich(param)} has length 0. Each inner list contains elements
  named after \code{scanBamWhat()}; elements omitted from
  \code{bamWhat(param)} are removed. The content of non-null elements
  are as follows, taken from the description in the samtools API
  documentation:

  \item{qname}{The query name, i.e., identifier, associated with the
	read.}

  \item{flag}{A numeric value summarizing details of the read. See
	\code{\linkS4class{ScanBamParam}} and the \code{flag} argument, and
	\code{scanBamFlag()}.}

  \item{rname}{The name of the reference to which the read is aligned.}

  \item{strand}{The strand to which the read is aligned.}

  \item{pos}{The genomic coordinate at the start of the
	alignment. Coordinates are `left-most', i.e., at the 3' end of a
	read on the '-' strand, and 1-based. The position \emph{excludes}
	clipped nucleotides, even though soft-clipped nucleotides are
	included in \code{seq}.}

  \item{qwidth}{The width of the query, as calculated from the
	\code{cigar} encoding; normally equal to the width of the query
	returned in \code{seq}.}

  \item{mrnm}{The reference to which the mate (of a paired end or mate
	pair read) aligns.}

  \item{mpos}{The position to which the mate aligns.}

  \item{isize}{Inferred insert size for paired end alignments.}

  \item{seq}{The query sequence, in the 5' to 3' orientation. If aligned
	to the minus strand, it is the reverse complement of the original
	sequence.}

  \item{qual}{Phred-encoded, phred-scaled base quality score, oriented
	as \code{seq}.}

  \code{scanBamHeader} returns a list, with one element for each file
  named in \code{files}. The list contains two element. The
  \code{targets} element contains target (reference) sequence
  lengths. The \code{text} element is itself a list with each element a
  list corresponding to tags (e.g., \sQuote{@SQ}) found in the header,
  and the associated tag values.

  \code{asBam} returns the file name of the BAM file.

  \code{sortBam} returns the file name of the sorted file.

  \code{indexBam} returns the file name of the index file created.

  \code{filterBam} returns the file name of the destination file
  created.

}
\references{
  \url{http://samtools.sourceforge.net/}
}
\author{

  Martin Morgan <mtmorgan@fhcrc.org>.  Thomas Unterhiner
  <thomas.unterthiner@students.jku.at> (\code{sortBam}).

}

\seealso{

  \code{\linkS4class{ScanBamParam}}, \code{\link{scanBamWhat}},
  \code{\link{scanBamFlag}}

}
\examples{

fl <- system.file("extdata", "ex1.bam", package="Rsamtools")

res0 <- scanBam(fl)[[1]] # always list-of-lists
names(res0)
length(res0[["qname"]])
lapply(res0, head, 3)
table(width(res0[["seq"]])) # query widths
table(res0[["qwidth"]], useNA="always") # query widths derived from cigar
table(res0[["cigar"]], useNA="always")
table(res0[["strand"]], useNA="always")
table(res0[["flag"]], useNA="always")

which <- RangesList(seq1=IRanges(1000, 2000),
                    seq2=IRanges(c(100, 1000), c(1000, 2000)))
p1 <- ScanBamParam(which=which)
res1 <- scanBam(fl, param=p1)
names(res1)
names(res1[[2]])

p2 <- ScanBamParam(what=c("rname", "strand", "pos", "qwidth"))
res2 <- scanBam(fl, param=p2)
                
p3 <- ScanBamParam(flag=scanBamFlag(isMinusStrand=FALSE))
length(scanBam(fl, param=p3)[[1]])

sorted <- sortBam(fl, tempfile())

## map values(which) to output, e.g., of countBam
gwhich <- as(which, "GRanges")[c(2, 1, 3)]
values(gwhich)[["OriginalOrder"]] <- 1:3
cnt <- countBam(fl, param=ScanBamParam(which=gwhich))
cntVals <- unlist(split(values(gwhich), seqnames(gwhich)))
cbind(cnt, as.data.frame(cntVals))

}

\keyword{ manip }