1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
|
\name{BcfInput}
\Rdversion{1.1}
\alias{scanBcfHeader}
\alias{scanBcfHeader,character-method}
\alias{scanBcf}
\alias{scanBcf,character-method}
\alias{asBcf}
\alias{asBcf,character-method}
\alias{indexBcf}
\alias{indexBcf,character-method}
\title{
Operations on `BCF' files.
}
\description{
Import, coerce, or index variant call files in text or binary format.
}
\usage{
scanBcfHeader(file, ...)
\S4method{scanBcfHeader}{character}(file, ...)
scanBcf(file, ...)
\S4method{scanBcf}{character}(file, index = file, ..., param=ScanBcfParam())
asBcf(file, dictionary, destination, ...,
overwrite=FALSE, indexDestination=TRUE)
\S4method{asBcf}{character}(file, dictionary, destination, ...,
overwrite=FALSE, indexDestination=TRUE)
indexBcf(file, ...)
\S4method{indexBcf}{character}(file, ...)
}
\arguments{
\item{file}{For \code{scanBcf} and \code{scanBcfHeader}, the
character() file name of the \sQuote{BCF} file to
be processed, or an instance of class \code{\link{BcfFile}}.}
\item{index}{The character() file name(s) of the `BCF' index to be
processed.}
\item{dictionary}{a character vector of the unique \dQuote{CHROM}
names in the VCF file.}
\item{destination}{The character(1) file name of the location where
the BCF output file will be created. For \code{asBcf} this is
without the \dQuote{.bcf} file suffix.}
\item{param}{A instance of \code{\linkS4class{ScanBcfParam}}
influencing which records are parsed and the \sQuote{INFO} and
\sQuote{GENO} information returned.}
\item{...}{Additional arguments, e.g., for
\code{scanBcfHeader,character-method}, \code{mode} of
\code{\link{BcfFile}}.}
\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.}
}
\details{
\code{bcf*} functions are restricted to the GENO fields supported by
\sQuote{bcftools} (see documentation at the url below). The argument
\code{param} allows portions of the file to be input, but requires
that the file be BCF or bgzip'd and indexed as a
\code{\linkS4class{TabixFile}}. For similar functions operating on VCF
files see ?\code{scanVcf} in the \code{VariantAnnotation} package.
}
\value{
\code{scanBcfHeader} returns a list, with one element for each file
named in \code{file}. Each element of the list is itself a list containing
three elements. The \code{reference} element is a character() vector with
names of reference sequences. The \code{sample} element is a character()
vector of names of samples. The \code{header} element is a character()
vector of the header lines (preceeded by \dQuote{##}) present in the VCF
file.
\code{scanBcf} returns a list, with one element per file. Each list has 9
elements, corresponding to the columns of the VCF specification: \code{CHROM},
\code{POS}, \code{ID}, \code{REF}, \code{ALT}\code{QUAL}, \code{FILTER},
\code{INFO}, \code{FORMAT}, \code{GENO}.
The \code{GENO} element is itself a list, with elements corresponding
to fields supported by \sQuote{bcftools} (see documentation at the url below).
\code{asBcf} creates a binary BCF file from a text VCF file.
\code{indexBcf} creates an index into the BCF file.
}
\references{
\url{http://vcftools.sourceforge.net/specs.html} outlines the VCF
specification.
\url{http://samtools.sourceforge.net/mpileup.shtml} contains
information on the portion of the specification implemented by
\code{bcftools}.
\url{http://samtools.sourceforge.net/} provides information on
\code{samtools}.
}
\seealso{
\code{\link{BcfFile}}, \code{\link{TabixFile}}
}
\author{
Martin Morgan <mtmorgan@fhcrc.org>.
}
\examples{
fl <- system.file("extdata", "ex1.bcf", package="Rsamtools",
mustWork=TRUE)
scanBcfHeader(fl)
bcf <- scanBcf(fl)
## value: list-of-lists
str(bcf[1:8])
names(bcf[["GENO"]])
str(head(bcf[["GENO"]][["PL"]]))
example(BcfFile)
}
\keyword{ manip }
|