作用：对补洞后的组装做长读长与 k-mer 迭代抛光：Winnowmap2 比对、falconc 过滤、Racon 共识、Merfin/bcftools 校正。
入口：bash.sh（调用第三方 polish.sh；build_merylDB.sh 构建 k-mer 库）
输入：ontPolish.iter_2.consensus.fasta（生效调用所用的草图）；HiFi reads ``{PROJ_LOTUS_ZC}/data/Gifu/hifi/Gifu_hifi.fastq.gz；读 k-mer 库 ccs.merylDB。
输出：ccs.merylDB；每轮 <prefix>.iter_N.*（winnowmap.bam、falconc.sam、racon.fasta、merfin 校正 VCF、consensus.fasta）与 .memtime 日志。
运行：bash bash.sh
工具：polish.sh 10 2 ontPolish.iter_2.consensus.fasta <hifi.fastq.gz> ccs.merylDB hifiPolish；meryl count k=21；winnowmap -k 21 -ax map-pb；falconc bam-filter-clipped -F 0x104；racon -L -S；merfin -polish -peak 106.7；bcftools consensus -H 1。
注意：bash.sh 中前缀 ontPolish 的 ONT 运行被注释，生效的 HiFi 运行以它的输出为草图，须先备好该文件；polish.sh 为 third_party/ 下未修改的第三方代码，以绝对路径调用。
English
**Purpose**: Iteratively polish the gap-closed assembly with long reads and k-mers: Winnowmap2 mapping, falconc filtering, Racon consensus and Merfin/bcftools correction.
**Entry point**: `bash.sh` (calls the third-party `polish.sh`; `build_merylDB.sh` builds the k-mer database)
**Inputs**: `ontPolish.iter_2.consensus.fasta` (the draft used by the active call); HiFi reads ``{PROJ_LOTUS_ZC}`/data/Gifu/hifi/Gifu_hifi.fastq.gz`; read k-mer database `ccs.merylDB`.
**Outputs**: `ccs.merylDB`; per iteration `.iter_N.*` (`winnowmap.bam`, `falconc.sam`, `racon.fasta`, the Merfin correction VCF, `consensus.fasta`) and `.memtime` logs.
**Run**: `bash bash.sh`
**Tools**: `polish.sh 10 2 ontPolish.iter_2.consensus.fasta ccs.merylDB hifiPolish`; meryl `count k=21`; winnowmap `-k 21 -ax map-pb`; falconc `bam-filter-clipped -F 0x104`; racon `-L -S`; merfin `-polish -peak 106.7`; bcftools `consensus -H 1`.
**Notes**: The ONT run with prefix `ontPolish` in `bash.sh` is commented out while the active HiFi run takes its output as the draft, so that file must exist first; `polish.sh` is unmodified third-party code under `third_party/`, called by an absolute path.