Compression {Rsamtools} | R Documentation |
File compression for tabix (bgzip) and fasta (razip) files.
IMPORTANT NOTE: Starting with Rsamtools 1.99.0 (Bioconductor 3.9),
razip()
is defunct. Please use bgzip()
instead.
Description
bgzip
compresses tabix (e.g. SAM or VCF) or FASTA files
to a format that allows indexing for later fast random-access.
Usage
bgzip(file, dest=sprintf("%s.bgz", sub("\\.gz$", "", file)),
overwrite = FALSE)
## Defunct!
razip(file, dest=sprintf("%s.rz", sub("\\.gz$", "", file)),
overwrite = FALSE)
Arguments
file |
A character(1) path to an existing uncompressed or gz-compressed file. This file will be compressed. |
dest |
A character(1) path to a file. This will be the compressed
file. If |
overwrite |
A logical(1) indicating whether |
Value
The full path to dest
.
Author(s)
Martin Morgan <mtmorgan@fhcrc.org>
References
http://samtools.sourceforge.net/
See Also
Examples
from <- system.file("extdata", "ex1.sam", package="Rsamtools",
mustWork=TRUE)
to <- tempfile()
zipped <- bgzip(from, to)
[Package Rsamtools version 2.18.0 Index]