# =========================
# 01 建立项目文件夹并检查输入
# =========================

source("R/config.R")
source("R/utils.R")

dirs <- c(
  "00_raw_data", "01_target_loci", "02_region_data", "03_harmonised_data",
  "04_coloc_results", "05_regional_plots", "06_tables", "scripts",
  DIR_GWAS_REGIONS, DIR_PQTL_REGIONS, DIR_HARMONISED, DIR_PLOTS_PNG, DIR_PLOTS_PDF
)

invisible(lapply(dirs, ensure_dir))

loci_ok <- file.exists(TARGET_LOCI_XLSX) || file.exists(TARGET_LOCI_TSV)
cat("Target loci file exists:", loci_ok, "\n")

# 读取一次，检查列名
if (loci_ok) {
  loci <- read_loci_file()
  cat("Number of target rows:", nrow(loci), "\n")
  cat("Target loci read successfully:", TRUE, "\n")
}

write_status("01_setup_project", loci_ok, ifelse(loci_ok, "Target loci file found.", "Missing target loci file."))