作用：用 nucmer 把组装 contig 比对到参考组装，推导每个 query contig 的主导参考 contig、比对长度、比例与链向，用于排序与定向。
入口：05.1.nucmer.sh → 05.2.contigOrder.py
输入：Gifu_ref.fa（参考）与 Gifu_contig.fa（组装 contig），文件名硬编码并在工作目录解析。
输出：Gifu_scaffold.delta、Gifu_scaffold.filter.delta、Gifu_scaffold.filter.delta.coords、Gifu_scaffold.delta.coords、一张 mummerplot PNG；mummer_analysis_results/dominant_mapping.csv 与 .../query_contig_on_dominant_ref_colored.pdf（+ 蓝、- 红）。
运行：bash 05.1.nucmer.sh，然后 python 05.2.contigOrder.py
工具：MUMmer nucmer --prefix Gifu_scaffold、delta-filter -i 89 -l 1000 -1、show-coords -THrd、mummerplot --layout --png --large（需 gnuplot）；Python 3 + pandas/matplotlib（read_csv(sep='\t', skiprows=5)）。
English
**Purpose**: Align the assembled contigs to a reference with nucmer and derive each query contig's dominant reference contig, aligned length, ratio and strand, for ordering and orientation.
**Entry point**: `05.1.nucmer.sh` → `05.2.contigOrder.py`
**Inputs**: `Gifu_ref.fa` (reference) and `Gifu_contig.fa` (contigs) — hardcoded filenames resolved in the working directory.
**Outputs**: `Gifu_scaffold.delta`, `Gifu_scaffold.filter.delta`, `Gifu_scaffold.filter.delta.coords`, `Gifu_scaffold.delta.coords`, a `mummerplot` PNG; `mummer_analysis_results/dominant_mapping.csv` and `.../query_contig_on_dominant_ref_colored.pdf` (`+` blue, `-` red).
**Run**: `bash 05.1.nucmer.sh`, then `python 05.2.contigOrder.py`
**Tools**: MUMmer `nucmer --prefix Gifu_scaffold`, `delta-filter -i 89 -l 1000 -1`, `show-coords -THrd`, `mummerplot --layout --png --large` (needs gnuplot); Python 3 with pandas and matplotlib (`read_csv(sep='\t', skiprows=5)`).