作用：用自研代码表征 Gifu T2T 组装的端粒：扫描 7 bp 端粒重复单元、换算为 100 bp 窗口密度、在每个染色体末端调用端粒区间、统计其上的 ONT/HiFi 深度并提取跨端粒读段。
入口：run_telomere.sh（内部调用 telomere.py 的 find-tel/coverage/alignments/plot 子命令）。
输入：00_assembly_result/GifuT2T/Lotus_GifuT2T_v1.0.fasta（无 .fai 时先 samtools faidx）；02_assembly/Gifu/08.quality/01.mapping/01.ont/ont_q30.bam 与 .../02.hifi/ccs_q30.bam（无 .bai 时先 samtools index）；环境变量 TELOMERE_*（工作目录、前缀、步骤、Python/samtools/bedtools 路径、输入 FASTA/BAM、bin 大小、绘图侧翼与线程，默认值均为 Gifu 生产值）。
输出：工作目录中以前缀 ${PREFIX}（默认 GifuT2T）命名的表：*.tel_unit.bed、*_tel.100.result+*_tel.100.detail.tsv、*.telomere_coords.tsv、*.telomere_coverage.100bp.tsv+.summary.tsv、*.telomere_alignments.tsv；plots/ 下的端粒长度、末端、覆盖度汇总与读段分布 PDF。
运行：csub run_telomere.sh（全流程）；TELOMERE_STEPS=plot bash run_telomere.sh（仅重绘）；顺序为 find-tel → coverage → alignments → plot；脚本内 SCRIPT_DIR 写死为 ${PROJECT_ROOT}/03_annotation/Gifu/01.tel（csub 会复制脚本），须按实际路径修改。
工具：telomere.py（自研）：bin 100 bp、密度 0.5、单元最大间隔 14 bp、最多 5 个凹陷箱、绘图侧翼 10,000 bp，跨端读段 --min-overlap 50、--max-reads-per-arm 2500、--min-mapq 0；samtools 1.18 faidx、index -@16；Python ``{CONDA_PY3}/bin/python3；bedtools 经 --bedtools 传入；alignments 需 pysam，plot 需 matplotlib。
English
**Purpose**: Characterise the telomeres of the Gifu T2T assembly with in-house code: scan 7-bp telomere repeat units, convert them to 100-bp window density, call the telomere tract at each chromosome end, measure ONT/HiFi depth over the calls and extract spanning reads.
**Entry point**: `run_telomere.sh` (which calls the `find-tel`/`coverage`/`alignments`/`plot` subcommands of `telomere.py`).
**Inputs**: `00_assembly_result/GifuT2T/Lotus_GifuT2T_v1.0.fasta` (`samtools faidx` runs when the `.fai` is missing); `02_assembly/Gifu/08.quality/01.mapping/01.ont/ont_q30.bam` and `.../02.hifi/ccs_q30.bam` (`samtools index` runs when the `.bai` is missing); the `TELOMERE_*` environment variables (workdir, prefix, steps, Python/samtools/bedtools paths, input FASTA/BAMs, bin size, plot flank and threads), each defaulted to the production Gifu value.
**Outputs**: tables in the workdir prefixed with `${PREFIX}` (default `GifuT2T`): `*.tel_unit.bed`, `*_tel.100.result`+`*_tel.100.detail.tsv`, `*.telomere_coords.tsv`, `*.telomere_coverage.100bp.tsv`+`.summary.tsv`, `*.telomere_alignments.tsv`; PDFs under `plots/` for telomere lengths, chromosome ends, coverage summary and read distribution.
**Run**: `csub run_telomere.sh` (full pipeline); `TELOMERE_STEPS=plot bash run_telomere.sh` (re-plot only); the order is `find-tel` → `coverage` → `alignments` → `plot`; `SCRIPT_DIR` is hardcoded to `${PROJECT_ROOT}/03_annotation/Gifu/01.tel` (because `csub` copies the script), so it must be edited to the real path.
**Tools**: `telomere.py` (in-house): bin 100 bp, density 0.5, max unit gap 14 bp, max dip bins 5, plot flank 10,000 bp, spanning reads `--min-overlap 50`, `--max-reads-per-arm 2500`, `--min-mapq 0`; samtools 1.18 `faidx`, `index -@16`; Python ``{CONDA_PY3}`/bin/python3`; bedtools passed through `--bedtools`; `alignments` requires pysam and `plot` requires matplotlib.