nvBWT : builds the BWT indices of the reference FASTA files

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