R: File compression for tabix (bgzip) and fasta (razip) files.

Compression {Rsamtools}

R Documentation

File compression for tabix (bgzip) and fasta (razip) files.

Description

These functions compress files for use in other parts of Rsamtools: bgzip for tabix files, 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

`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 `dest` exists, then it is only over-written when `overwrite=TRUE`.
`overwrite`	A logical(1) indicating whether `dest` should be over-written, if it already exists.

Value

The full path to dest.

Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

References

http://samtools.sourceforge.net/

Examples


from <- system.file("extdata", "ex1.sam", package="Rsamtools",
                    mustWork=TRUE)
to <- tempfile()
zipped <- bgzip(from, to)

[Package Rsamtools version 1.30.0 Index]