Usage
"gsnap"(input_a, input_b, params, output = file.path(getwd(), file_path_sans_ext(basename(input_a), TRUE)), consolidate = TRUE, ...)
Arguments
input_a
A path to the FASTA file containing reads to align against a
GmapGenome object. If the sequencing data is single-end, this
is the only FASTA file used as input.
input_b
If provided, a path to the FASTA file containing the
second set of reads from paired-end sequencing data.
params
A GsnapParam object to configure the behavior of
GSNAP.
output
The output path for the GSNAP alignments. The results
will be saved in dirname(output). If split_output in
params is TRUE, basename(output) is used as the
common stem for the multiple output files. Otherwise, the results
are saved to a single SAM file, its path formed by adding the
“sam” extention to output.
consolidate
If GSNAP is run with multiple worker threads, each
thread will output its own set of files. If consolidate is set to
TRUE, these files will be merged. The default is TRUE.
...
Additional arguments to pass to GSNAP not specifically
supported by the gmapR package.