#!/usr/bin/env bash
set -euo pipefail

if [[ $# -lt 2 ]]; then
  echo "Usage: $0 <input_dir> <scaf_suffix> [threads] [bttoxin_db_dir]"
  echo "Example: $0 /home/zly/project/bttoxin-pipeline/tests/test_data .fna 4"
  echo "Example with external DB: $0 /home/zly/project/bttoxin-pipeline/tests/test_data .fna 4 /home/zly/project/bttoxin-pipeline/external_dbs/bt_toxin"
  exit 1
fi

input_dir="$1"
scaf_suffix="$2"
threads="${3:-4}"
bttoxin_db_dir="${4:-}"

cache_dir="$(pwd)/.rattler-cache"
mkdir -p "$cache_dir"
if [[ -n "$bttoxin_db_dir" ]]; then
  if [[ -d "$bttoxin_db_dir" ]]; then
    env_bin="$(RATTLER_CACHE_DIR="$cache_dir" pixi run which BtToxin_Digger | xargs dirname)"
    ln -sfn "$bttoxin_db_dir" "$env_bin/BTTCMP_db/bt_toxin"
  else
    echo "[warn] bttoxin_db_dir not found: $bttoxin_db_dir" >&2
  fi
fi
RATTLER_CACHE_DIR="$cache_dir" pixi run BtToxin_Digger \
  --SeqPath "$input_dir" \
  --SequenceType nucl \
  --Scaf_suffix "$scaf_suffix" \
  --threads "$threads"