## ----prereqs,include=FALSE,error=0--------------------------------------------
library(BiocStyle)
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    cache = TRUE,
    out.width = "100%"
)
has_env <- reticulate::virtualenv_exists("vrs_env")
has_gcloud <- AnVILBase::has_avworkspace(
    strict = TRUE, platform = AnVILGCP::gcp()
)
has_envs <- has_env && has_gcloud

## ----install, eval=FALSE------------------------------------------------------
# if (!requireNamespace("BiocManager", quietly = TRUE))
#     install.packages("BiocManager")
# 
# BiocManager::install("AnVILVRS")

## ----load---------------------------------------------------------------------
library(AnVILVRS)
library(reticulate)

## ----setup, eval=FALSE--------------------------------------------------------
# install_AnVILVRS(envname = "vrs_env")

## ----venv, eval=has_env-------------------------------------------------------
# use_virtualenv("vrs_env", required = TRUE)

## ----translate, eval=has_env--------------------------------------------------
# get_vrs_id("chr7-87509329-A-G", "gnomad")
# get_vrs_id("NC_000005.10:80656509:C:TT", "spdi")
# get_vrs_id("NC_000005.10:g.80656510delinsTT", "hgvs")
# get_vrs_id("5 : 80656489 C > T", "beacon")

## ----allele, eval=has_env-----------------------------------------------------
# allele <- get_vrs_allele("5 : 80656489 C > T", "beacon")
# allele

## ----variant_from_allele, eval=has_env----------------------------------------
# get_variant_from_allele(allele, "hgvs")

## ----download, eval=has_envs--------------------------------------------------
# library(readr)
# pop_desc <- get_pop_descriptor()
# read_tsv(
#     file = pop_desc,
#     col_types = cols(
#         population_descriptor_id = col_character(),
#         population_descriptor = col_character(),
#         subject_id = col_character(),
#         country_of_recruitment = col_character(),
#         population_label = col_character()
#     )
# )

## ----seqrepo, eval=FALSE------------------------------------------------------
# get_seqrepo(destdir = tempdir())

## ----get_caf, eval=FALSE------------------------------------------------------
# use_virtualenv("vrs_env", required = TRUE)
# toolkit_dir <- setup_vrs_toolkit()
# vcf <- AnVILVRS:::.get_fixture_vcf()
# vcf_index <- build_vrs_index()
# variant_id <- "chr1-20094-TAA-T"
# vrs_id <- get_vrs_id(variant_id, "gnomad")
# pop_desc <- get_pop_descriptor()
# get_caf(
#     vrs_id = vrs_id,
#     vcf = vcf,
#     vcf_index = vcf_index,
#     phenotype = "USA",
#     pop_desc_file = pop_desc,
#     toolkit_dir = toolkit_dir
# )

## ----session_info-------------------------------------------------------------
sessionInfo()