# =========================
# 项目配置
# =========================

PROJECT_ROOT <- getwd()

# 目标区域文件
TARGET_LOCI_XLSX <- file.path("01_target_loci", "original_coloc_loci.xlsx")
TARGET_LOCI_TSV  <- file.path("01_target_loci", "original_coloc_loci.tsv")

# 标准化后的 GWAS 文件，按你的实际文件名修改
GWAS_STANDARDIZED_FILES <- list(
  VTE = file.path("02_region_data", "VTE_GWAS_standardized.tsv"),
  DVT = file.path("02_region_data", "DVT_GWAS_standardized.tsv"),
  PE  = file.path("02_region_data", "PE_GWAS_standardized.tsv")
)

# FinnGen outcome ID，仅用于表格记录
OUTCOME_MAP <- data.frame(
  Outcome = c("DVT", "PE", "VTE"),
  Outcome_ID = c("finn-b-I9_PHLETHROMBDVTLOW", "finn-b-I9_PULMEMB", "finn-b-I9_VTE"),
  stringsAsFactors = FALSE
)

# 图排版顺序
GENE_ORDER <- c("ABO", "BCAM", "CHST15", "GNS", "TUFT1", "VWF")
OUTCOME_ORDER <- c("DVT", "PE", "VTE")

# 输出文件夹
DIR_GWAS_REGIONS <- file.path("02_region_data", "original_gwas_regions")
DIR_PQTL_REGIONS <- file.path("02_region_data", "original_pqtl_regions")
DIR_HARMONISED   <- file.path("03_harmonised_data", "original_loci_v_final")
DIR_PLOTS_PNG    <- file.path("05_regional_plots", "original_loci_png")
DIR_PLOTS_PDF    <- file.path("05_regional_plots", "original_loci_pdf")
DIR_TABLES       <- "06_tables"

# 画图参数
PLOT_WIDTH_IN  <- 6.5
PLOT_HEIGHT_IN <- 6.5
PLOT_DPI <- 300

# OpenGWAS 查询参数
PQTL_QUERY_CHUNK_SIZE <- 500
SLEEP_SECONDS_BETWEEN_QUERIES <- 0.2