作用：用 Barrnap 注释 Gifu T2T 的 rRNA 基因以确定 rDNA 位点，切出各阵列做 StainedGlass 自比对，并统计每个阵列的 18S/5.8S/28S/5S 特征数以得到完整 45S 重复单元数。
入口：barrnap.sh
输入：Lotus_GifuT2T_v1.0.fasta（含随附 .fai，Chr1–Chr6）；区段 BED Chr2_0_3Mbp.bed、Chr2_24_26Mbp.bed、Chr5_14_16Mbp.bed、Chr6_8_10Mbp.bed、Chr6_25_28Mbp.bed；Barrnap 的 rRNA.gff/rRNA.fa；生产 GFF Gifu_rRNA.gff、MG20_rRNA.gff。
输出：rRNA.gff/rRNA.fa；result/*_output.tbl.gz、*_output.bed.gz 及 .fa/.fai/.bed/.fasta/.mmi/.bam 中间文件；results/ 下各阵列的 PDF/PNG 图；阵列组成表打印到标准输出并写入 03_annotation/rDNA_array_summary.tsv（45S 完整单元数 = 阵列内 min(18S, 5.8S, 28S)，阵列坐标硬编码在 count_rDNA.py 中）。
运行：bash barrnap.sh → python3 count_rDNA.py → bash result/process.sh（process.sh 从自身目录读 ../Lotus_GifuT2T_v1.0.fasta 与区段 BED，结果写到当前目录，须在 result/ 下运行）。
工具：Barrnap --kingdom euk --threads 88；minimap2 建索引 -f 1000 -s 400 -ax ava-ont、比对 -t 88 -f 10000 -s 400 -ax ava-ont --dual=yes --eqx；StainedGlass 0.6 samIdentity.py --threads 88 --matches 400 --header、refmt.py --window 2000、aln_plot.R --threads 88；bedtools getfasta、makewindows -w 2000；samtools faidx、sort -m 4G；bgzip、Rscript、python3.13（经 {SOFTWARE_LOCAL}）；count_rDNA.py 仅用标准库。
English
**Purpose**: Annotate the Gifu T2T rRNA genes with Barrnap to define the rDNA loci, extract each array for StainedGlass self-identity analysis, and count the 18S/5.8S/28S/5S features per array to derive the number of complete 45S repeat units.
**Entry point**: `barrnap.sh`
**Inputs**: `Lotus_GifuT2T_v1.0.fasta` (with the shipped `.fai`, Chr1–Chr6); the region BEDs `Chr2_0_3Mbp.bed`, `Chr2_24_26Mbp.bed`, `Chr5_14_16Mbp.bed`, `Chr6_8_10Mbp.bed`, `Chr6_25_28Mbp.bed`; Barrnap's `rRNA.gff`/`rRNA.fa`; the production GFFs `Gifu_rRNA.gff` and `MG20_rRNA.gff`.
**Outputs**: `rRNA.gff`/`rRNA.fa`; `result/*_output.tbl.gz` and `*_output.bed.gz` plus the `.fa`/`.fai`/`.bed`/`.fasta`/`.mmi`/`.bam` intermediates; PDF/PNG plots per array under `results/`; the array composition table on stdout and in `03_annotation/rDNA_array_summary.tsv` (complete 45S units = `min(18S, 5.8S, 28S)` inside each array, with the array coordinates hardcoded in `count_rDNA.py`).
**Run**: `bash barrnap.sh` → `python3 count_rDNA.py` → `bash result/process.sh` (`process.sh` reads `../Lotus_GifuT2T_v1.0.fasta` and the region BEDs from its own directory and writes into the current directory, so it must run inside `result/`).
**Tools**: Barrnap `--kingdom euk --threads 88`; minimap2 index `-f 1000 -s 400 -ax ava-ont`, alignment `-t 88 -f 10000 -s 400 -ax ava-ont --dual=yes --eqx`; StainedGlass 0.6 `samIdentity.py --threads 88 --matches 400 --header`, `refmt.py --window 2000`, `aln_plot.R --threads 88`; bedtools `getfasta`, `makewindows -w 2000`; samtools `faidx`, `sort -m 4G`; `bgzip`, `Rscript`, `python3.13` (through ``{SOFTWARE_LOCAL}``); `count_rDNA.py` is standard library only.