作用：用 StainedGlass 自比对展示 Gifu 着丝粒重复阵列的高阶结构，每条染色体一次：切出单条染色体、切成 2 kb 窗口、minimap2 全比全自比对，再用 StainedGlass 脚本转成 identity 表并绘图。
入口：run_stainglass.sh
输入：各 Gifu_Chr<N>/ 内的 Gifu_Chr<N>_2k.fasta 与其 .fai；get.sh 另需 mg20_cent.fa 与 .fai。
输出：每个 Gifu_Chr<N>/ 内的 Gifu_Chr<N>_2k.mmi、Gifu_Chr<N>.bam、.tbl.gz、.full.tbl.gz、.bed.gz，图件在 results/Gifu_Chr<N>_figures/{pdfs,pngs}/；get.sh 每条染色体写 <id>.fa、<id>.fa.fai、<id>_2k.bed、<id>_2k.fasta。
运行：bash run_stainglass.sh（在 04_stainglass/ 下依次进入 Gifu_Chr1…Gifu_Chr6，每目录内建索引与自比对 → samIdentity.py → bgzip → refmt.py → aln_plot.R）。
工具：StainedGlass 0.6（samIdentity.py --threads 88 --matches 400 --header、refmt.py --window 2000、aln_plot.R --threads 88，工作流脚本来自 SG=~/software/StainedGlass-0.6/workflow/scripts）；minimap2 -f 1000 -s 400 -ax ava-ont 建索引、-t 88 -f 10000 -s 400 -ax ava-ont --dual=yes --eqx 比对；samtools faidx、sort -m 4G；bedtools makewindows -w 2000、getfasta；bgzip、Rscript。
English
**Purpose**: StainedGlass self-alignments showing the higher-order organisation of the Gifu centromeric repeat arrays, one chromosome at a time: each chromosome is cut out, windowed at 2 kb and aligned to itself all-versus-all with minimap2, then converted to identity tables with the StainedGlass scripts and plotted.
**Entry point**: `run_stainglass.sh`
**Inputs**: the 2-kb window FASTA and its `.fai` inside each `Gifu_Chr/` directory (`Gifu_Chr_2k.fasta`, `Gifu_Chr.fa.fai`); `get.sh` additionally needs `mg20_cent.fa` and its `.fai`.
**Outputs**: inside each `Gifu_Chr/` directory `Gifu_Chr_2k.mmi`, `Gifu_Chr.bam`, `.tbl.gz`, `.full.tbl.gz`, `.bed.gz`, with plots under `results/Gifu_Chr_figures/{pdfs,pngs}/`; `get.sh` writes `.fa`, `.fa.fai`, `_2k.bed` and `_2k.fasta` per chromosome.
**Run**: `bash run_stainglass.sh` (from `04_stainglass/`, entering `Gifu_Chr1`…`Gifu_Chr6` in turn; each directory runs index and self alignment → `samIdentity.py` → `bgzip` → `refmt.py` → `aln_plot.R`).
**Tools**: StainedGlass 0.6 (`samIdentity.py --threads 88 --matches 400 --header`, `refmt.py --window 2000`, `aln_plot.R --threads 88`, with the workflow scripts taken from `SG=~/software/StainedGlass-0.6/workflow/scripts`); minimap2 index `-f 1000 -s 400 -ax ava-ont`, alignment `-t 88 -f 10000 -s 400 -ax ava-ont --dual=yes --eqx`; samtools `faidx`, `sort -m 4G`; bedtools `makewindows -w 2000`, `getfasta`; `bgzip`, `Rscript`.