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 `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/

### See Also

`TabixFile`, `FaFile`.

### Examples

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

[Package Rsamtools version 2.2.3 Index]