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#' Run LoFreq for a sample
#'
#' @inheritParams run.vardict.sample
#'
#'
#'
#'
run.lofreq.sample <- function(
tumour.bam,
sample.id,
paired,
normal.bam = NULL,
output.directory = NULL,
output.filename = NULL,
code.directory = NULL,
log.directory = NULL,
config.file = NULL,
job.dependencies = NULL,
quiet = FALSE,
job.name = NULL,
verify.options = !quiet,
job.group = NULL
) {
### INPUT TESTS ###########################################################
# make sure no factors have been passed in
assertthat::assert_that( is.character(tumour.bam) );
assertthat::assert_that( is.character(sample.id) );
assertthat::assert_that( is.null(normal.bam) || is.character(normal.bam));
assertthat::assert_that( is.null(output.directory) || is.character(output.directory) );
if(paired && is.null(normal.bam)) {
stop('paired is set to true but no normal sample BAM has been supplied.');
}
if(!paired && !is.null(normal.bam)) {
stop('Getting mixed signals: paired is set to false but a normal sample BAM has been supplied.');
}
### MAIN ##################################################################
if( verify.options ) {
verify.varitas.options(
varitas.options = config.file,
stages.to.run = 'calling',
variant.callers = 'lofreq'
);
}
# save temporary config file that can be read by Perl
if(is.null(config.file)) {
config.file <- save.config();
}
# sort out whether to pass paired flag to Perl
flags <- NULL;
if(paired) {
flags <- 'paired';
}
script <- system.file('perl', 'run_lofreq.pl', package = get.varitas.options('pkgname') );
command <- make.command.line.call(
main.command = c('perl', script),
options = c(
'tumour_bam' = tumour.bam,
'normal_bam' = normal.bam,
'sample_id' = sample.id,
'config_file' = config.file,
'output_directory' = output.directory,
'output_filename' = output.filename,
'code_directory' = code.directory,
'log_directory' = log.directory,
'job_dependencies' = job.dependencies,
'job_name' = job.name,
'job_group' = job.group
),
flags = flags
);
if( quiet ) {
cat(command, '\n');
} else {
system(command);
}
}
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