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
|
\name{Compression}
\Rdversion{1.1}
\alias{bgzip}
\alias{razip}
\title{
File compression for tabix (bgzip) and fasta (razip) files.
}
\description{
These functions compress files for use in other parts of
\pkg{Rsamtools}: \code{bgzip} for tabix files, \code{razip} for
random-access fasta files.
}
\usage{
bgzip(file, dest=sprintf("\%s.bgz", sub("\\\\.gz$", "", file)),
overwrite = FALSE)
razip(file, dest=sprintf("\%s.rz", sub("\\\\.gz$", "", file)),
overwrite = FALSE)
}
\arguments{
\item{file}{A character(1) path to an existing uncompressed or
gz-compressed file. This file will be compressed.}
\item{dest}{A character(1) path to a file. This will be the compressed
file. If \code{dest} exists, then it is only over-written when
\code{overwrite=TRUE}.}
\item{overwrite}{A logical(1) indicating whether \code{dest} should
be over-written, if it already exists.}
}
\value{
The full path to \code{dest}.
}
\references{
\url{http://samtools.sourceforge.net/}
}
\author{
Martin Morgan <mtmorgan@fhcrc.org>
}
\seealso{
\code{\link{TabixFile}}, \code{\link{FaFile}}.
}
\examples{
from <- system.file("extdata", "ex1.sam", package="Rsamtools",
mustWork=TRUE)
to <- tempfile()
zipped <- bgzip(from, to)
}
\keyword{ manip }
|