作用：用 read-pair 证据验证区分 Gifu 与 MG20 的 Chr1↔Chr2 易位是真实结构差异而非组装错误，并对多个样本批量分型：同一套 reads 比对到两个基因组，统计跨染色体 pair。
入口：run.sh
输入：trans.conf（3 列制表符分隔、无表头：sample、bam_gifu、bam_mg）及其中列出的 BAM；逐对计数另需坐标排序并建索引的 gifu2gifu.bam、gifu2mg.bam、mg2gifu.bam、mg2mg.bam；区域 Chr1:22829936-22849936（Gifu）与 Chr2:99260160-99280160（MG20）。
输出：bam.list；每样本 {sample}.trans.gifu_anchored.merged_pairs.tsv、{sample}.trans.mg_anchored.merged_pairs.tsv 与 4 个子集 BAM；汇总 lotus_translocation_typing.tsv（sample、n_cross_in_gifu_bam、n_cross_in_mg_bam、call、ratio_MG20、note）；逐对计数在 stdout 出计数表并写 <bam>_chr1_chr2_pairs.txt 等文件。
运行：bash run.sh（须在存放 trans.conf、BAM 与 TSV 的目录中运行；文件末尾的逐对计数命令以注释保留，需单独运行）。
工具：pysam（BAM 访问）、pandas、numpy；samtools index；Python 3（finder 经 subprocess 调用，--min-support 默认 5，两侧都达标为 Mixed，都低于为 Uncertain）；CSUB（-q c01、-n 88）。
English
**Purpose**: Read-pair evidence that the Chr1↔Chr2 translocation distinguishing Gifu from MG20 is a real structural difference rather than a mis-assembly, plus batch typing across samples: the same reads are mapped to both genomes and cross-chromosome pairs are counted.
**Entry point**: `run.sh`
**Inputs**: `trans.conf` (3 tab-separated columns, no header: `sample`, `bam_gifu`, `bam_mg`) and the BAMs it lists; per-pair counting also needs the coordinate-sorted, indexed `gifu2gifu.bam`, `gifu2mg.bam`, `mg2gifu.bam`, `mg2mg.bam`; regions `Chr1:22829936-22849936` (Gifu) and `Chr2:99260160-99280160` (MG20).
**Outputs**: `bam.list`; per sample `{sample}.trans.gifu_anchored.merged_pairs.tsv`, `{sample}.trans.mg_anchored.merged_pairs.tsv` and four subset BAMs; the summary `lotus_translocation_typing.tsv` (`sample`, `n_cross_in_gifu_bam`, `n_cross_in_mg_bam`, `call`, `ratio_MG20`, `note`); per-pair counting prints count tables to stdout and writes files such as `_chr1_chr2_pairs.txt`.
**Run**: `bash run.sh` (must run in the directory holding `trans.conf`, the BAMs and the TSVs; the per-pair counting commands are kept commented at the end of the file and must be run separately).
**Tools**: `pysam` (BAM access), pandas, numpy; `samtools index`; Python 3 (the finder is called through `subprocess`; `--min-support` defaults to 5, both sides at or above it give `Mixed`, below it on both sides gives `Uncertain`); CSUB (`-q c01`, `-n 88`).