#' cavalier: Candidate Variant List Evaluation Report
#'
#' \pkg{cavalier} assists and automates variant interpretation in next-generation sequencing data:
#' 1) filter list of variants and create a short list of candidate variants
#' 2) combine information from multiple sources useful for evaluating and prioritising variants
#' 3) create PDF output for visualing and communicating results
#'
#' @docType package
#' @name cavalier
NULL
# environment to store default options, user settable with function cavalier_options()
cavalier_opts <- new.env()
# set default options
cavalier_opts$cache_dir <- '~/.cavalier'
cavalier_opts$snapshot_dir <- '.igv_snapshots'
cavalier_opts$retry_pause_base <- 5
cavalier_opts$retry_pause_min <- 5
cavalier_opts$retry_times <- 3
cavalier_opts$ref_genome <- 'hg38'
cavalier_opts$xvfb_run_cmd <- 'xvfb-run'
cavalier_opts$igv_cmd <- 'igv.sh'
cavalier_opts$singularity_cmd <- 'singularity'
cavalier_opts$igv_hg38_uri <- 'https://s3.amazonaws.com/igv.org.genomes/hg38/hg38.genome'
cavalier_opts$igv_hg19_uri <- 'https://s3.amazonaws.com/igv.org.genomes/hg19/hg19.genome'
cavalier_opts$gtex_tissues <-
c(
"Adipose - Subcutaneous",
"Artery - Tibial",
"Bladder",
"Breast - Mammary Tissue",
"Brain - Cerebellum",
"Brain - Cortex",
"Colon - Sigmoid",
"Esophagus - Mucosa",
"Heart - Left Ventricle",
"Kidney - Cortex",
"Liver",
"Lung",
"Muscle - Skeletal",
"Nerve - Tibial",
"Ovary",
"Stomach",
"Skin - Sun Exposed (Lower leg)",
"Testis",
"Thyroid",
"Whole Blood")
#' @export
get_cavalier_opt <- function(name = NULL) {
if (is.null(name)) {
return(as.list(cavalier_opts))
}
cavalier_opts[[name]]
}
#' @export
set_cavalier_opt <- function(...) {
dots <- dots_list(...)
assert_that(is_named(dots))
purrr::walk2(names(dots), dots, function(n, v) {
assign(n, v, envir = cavalier_opts)
})
}
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