Codec {DECIPHER} | R Documentation

## Compression/Decompression of Character Vectors

### Description

Compresses character vectors into raw vectors, or decompresses raw vectors into character vectors using a variety of codecs.

### Usage

    Codec(x,
          compression,
          compressRepeats = FALSE,
          processors = 1)

### Arguments

`x` | Either a character vector to be compressed, or a list of raw vectors to be decompressed.
`compression` | The type of compression algorithm to use when `x` is a character vector. This should be (an unambiguous abbreviation of) one of `"nbit"` (for nucleotides), `"qbit"` (for quality scores), `"gzip"`, `"bzip2"`, or `"xz"`. If `compression` is `"nbit"` or `"qbit"` then a second method can be provided for cases when `x` is incompressible. Decompression type is determined automatically. (See details section below.)
`compressRepeats` | Logical specifying whether to compress exact repeats and reverse complement repeats in a character vector input (`x`). Only applicable when `compression` is `"nbit"`. Repeat compression in long DNA sequences generally increases compression by about 2% while requiring three-fold more compression time.
`processors` | The number of processors to use, or `NULL` to automatically detect and use all available processors.

### Details

`Codec` can be used to compress/decompress character vectors using different algorithms. The `"nbit"` and `"qbit"` methods are tailored specifically to nucleotides and quality scores, respectively. These two methods will store the data as plain text (`"ASCII"` format) when it is incompressible. In such cases, a second `compression` method can be given to use in lieu of plain text. For example `compression = c("nbit", "gzip")` will use `"gzip"` compression when `"nbit"` compression is inappropriate.

When performing the reverse operation, decompression, the type of `compression` is automatically detected based on the unique signature ("magic number") added by each compression algorithm.

### Value

If `x` is a character vector to be compressed, the output is a list with one element containing a raw vector per character string. If `x` is a list of raw vectors to be decompressed, then the output is a character vector with one string per list element.

### Author(s)

Erik Wright eswright@pitt.edu

### Examples

    fas <- system.file("extdata", "Bacteria_175seqs.fas", package="DECIPHER")
    dna <- as.character(readDNAStringSet(fas)) # aligned sequences
    object.size(dna)

    # compression
    system.time(x <- Codec(dna, compression="nbit"))
    object.size(x)/sum(nchar(dna)) # bytes per position

    system.time(g <- Codec(dna, compression="gzip"))
    object.size(g)/sum(nchar(dna)) # bytes per position

    # decompression
    system.time(y <- Codec(x))
    stopifnot(dna==y)

    system.time(z <- Codec(g))
    stopifnot(dna==z)

[Package DECIPHER version 2.8.1 Index]