\name{ScanBcfParam-class}
\Rdversion{1.1}
\docType{class}
\alias{ScanBcfParam}
\alias{ScanBcfParam-class}
\alias{ScanBcfParam,GRanges-method}
\alias{ScanBcfParam,RangedData-method}
\alias{ScanBcfParam,RangesList-method}
\alias{ScanBcfParam,missing-method}
\alias{bcfInfo}
\alias{bcfGeno}
\alias{bcfTrimEmpty}
\alias{bcfWhich}
\alias{show,ScanBcfParam-method}

\title{Parameters for scanning VCF / BCF files}
\description{

  Use \code{ScanBcfParam()} to create a paraemter object influencing the
  \sQuote{INFO} and \sQuote{GENO} fields parsed, and which recrods are
  imported from a BCF file. Use of \code{which} requires that a BCF
  index file (\code{<filename>.bci}) exists.

}

\usage{

ScanBcfParam(info=character(), geno=character(), trimEmpty=TRUE,
             which)
\S4method{ScanBcfParam}{missing}(info=character(), geno=character(), trimEmpty=TRUE,
             which)
\S4method{ScanBcfParam}{RangesList}(info=character(), geno=character(), trimEmpty=TRUE,
             which)
\S4method{ScanBcfParam}{RangedData}(info=character(), geno=character(), trimEmpty=TRUE,
             which)
\S4method{ScanBcfParam}{GRanges}(info=character(), geno=character(), trimEmpty=TRUE,
             which)

## Accessors
bcfInfo(object)
bcfGeno(object)
bcfTrimEmpty(object)
bcfWhich(object)
}

\arguments{

  \item{info}{A character() vector of \sQuote{INFO} fields (see
    \code{\link{scanBcfHeader}}) to be returned. Not currently
    implemented.}

  \item{geno}{A character() vector of \sQuote{GENO} fields (see
    \code{\link{scanBcfHeader}}) to be returned.\code{character(0)}
    returns all fields, \code{NA_character_} returns none.}

  \item{trimEmpty}{A logical(1) indicating whether \sQuote{GENO} fields
    with no values should be returned.}

  \item{which}{An object, for which a method is defined (see usage,
    above), describing the sequences and ranges to be queried. Variants
    whose \code{POS} lies in the interval(s) \code{[start, end)} are
    returned.}

  \item{object}{An instance of class \code{ScanBcfParam}.}

}

\section{Objects from the Class}{

  Objects can be created by calls of the form \code{ScanBcfParam()}.

}
\section{Slots}{
  \describe{
    \item{\code{which}:}{Object of class \code{"RangesList"} indicating
      which reference sequence and coordinate variants must overlap.}
    \item{\code{info}:}{Object of class \code{"character"} indicating
      portions of \sQuote{INFO} to be returned.}
    \item{\code{geno}:}{Object of class \code{"character"} indicating
      portions of \sQuote{GENO} to be returned. }
    \item{\code{trimEmpty}:}{Object of class \code{"logical"} indicating
      whether empty \sQuote{GENO} fields are to be returned.}
  }
}
\section{Functionas and methods}{

  See 'Usage' for details on invocation.

  Constructor:
  \describe{

    \item{ScanBcfParam:}{Returns a \code{ScanBcfParam} object. The
      \code{which} argument to the constructor can be one of several
      types, as documented above.}
  }

  Accessors:
  \describe{

    \item{bcfInfo, bcfGeno, bcfTrimEmpty, bcfWhich:}{Return the
      corresponding field from \code{object}.}

  }

  Methods:
  \describe{

	\item{show}{Compactly display the object.}

  }
}
\author{
  Martin Morgan \url{mtmorgan@fhcrc.org}
}
\seealso{

  \code{\link{scanBcf}}

}

\examples{
p0 <- ScanBcfParam()

## subset of reads based on genomic coordinates
which <- RangesList(seq1=IRanges(1000, 2000),
                    seq2=IRanges(c(100, 1000), c(1000, 2000)))
p1 <- ScanBcfParam(which=which)

## return only specified GENO field(s)
p2 <- ScanBcfParam(geno="GT")

}

\keyword{classes}