for new integration test
run_test() {
    local test_name="$1"
    local command="$2"
    local expected_output="$3"
    
    echo -n "Testing ${test_name}... "
    
    if eval "$command" > temp_output.bed 2>/dev/null; then
        if diff -q temp_output.bed "$expected_output" >/dev/null 2>&1; then
            echo -e "${GREEN}PASS${NC}"
            return 0
        else
            echo -e "${RED}FAIL${NC} (output mismatch)"
            return 1
        fi
    else
        echo -e "${RED}FAIL${NC} (comman