nvBWT : builds the BWT indices of the reference FASTA files — nvBWT • RbowtieCuda
Description: This function can be use to call wrapped nvBWT binary.

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# nvBWT : builds the BWT indices of the reference FASTA files

Source: `R/bowtieCuda.R`
`nvBWT.Rd`

This function can be use to call wrapped `nvBWT` binary.

## Usage

    nvBWT(myinput, output, options = NULL)

## Arguments

myinput

  `Character` vector. A path to a .fa file

output

  `Character` vector. A path to a index file used for the alignment output.

options

  `Character` vector. Options Example: `--verbosity`

## Value

An invisible `Integer` of call status. The value is 0 when there is not any mistakes Otherwise the value is non-zero.

## Details

Available options:

    -v       | --verbosity     int (0-6) [5]     // select the verbosity level
    -m       | --max-length    int       [inf]   // clamp input length
    -b       | --byte-packing  [default]         // output a byte-encoded .pac file
    -w       | --word-packing                    // output a word-encoded .wpac file
                                                 // (more efficient)
    -c       | --crc                             // compute CRCs
    -d       | --device                          // select a cuda device

## References

Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), 357-359.

## Author

Franck RICHARD

## Examples

    td <- tempdir()
    fa_file <- system.file(package='RbowtieCuda', 'extdata', 'bt2', 'refs', 'lambda_virus.fa')
    nvBWT(myinput=fa_file, output=file.path(td, 'index'), options='')
    #> [1] 0