Rsamtools: zip – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

zip

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 `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)

Rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

v2.6.0

Artistic-2.0 | file LICENSE

Authors

Martin Morgan, Hervé Pagès, Valerie Obenchain, Nathaniel Hayden

Initial release

zip