作用：把 HiFi reads 回贴到 hifiasm primary contig 统计读深与覆盖度，并去除单倍型冗余（haplotig）contig。
入口：02.1.minimap.sh（比对）→ 02.2.purge.sh（去冗余）
输入：Gifu.hifiasm.fasta（步骤 01 输出）；HiFi reads ``{PROJ_LOTUS_ZC}/data/Gifu/hifi/Gifu_hifi.fastq.gz。
输出：aligned.bam、aligned.bam.200.gencov、coverage_stats.csv；去冗余后的 contig FASTA 与 haplotig FASTA（purge_haplotigs purge 的默认名）。
运行：bash 02.1.minimap.sh，然后 bash 02.2.purge.sh
工具：minimap2 -ax map-pb；samtools view -hF 256、sort -@ 20 -m 1G -T tmp.ali；purge_haplotigs readhist -t 88、contigcov -l 15 -m 100 -h 185、purge -t 88 -a 50。
注意：02.2.purge.sh 中 readhist 与 contigcov 处于注释状态、仅 purge 生效，其读取的 aligned.bam.200.gencov 须按原名存在。
English
**Purpose**: Align HiFi reads back to the hifiasm primary contigs to measure read depth and coverage, then purge haplotig (duplicated) contigs.
**Entry point**: `02.1.minimap.sh` (alignment) → `02.2.purge.sh` (purging)
**Inputs**: `Gifu.hifiasm.fasta` (step 01 output); HiFi reads ``{PROJ_LOTUS_ZC}`/data/Gifu/hifi/Gifu_hifi.fastq.gz`.
**Outputs**: `aligned.bam`, `aligned.bam.200.gencov`, `coverage_stats.csv`; the purged contig FASTA and the haplotig FASTA (the `purge_haplotigs purge` default names).
**Run**: `bash 02.1.minimap.sh`, then `bash 02.2.purge.sh`
**Tools**: minimap2 `-ax map-pb`; samtools `view -hF 256`, `sort -@ 20 -m 1G -T tmp.ali`; purge_haplotigs `readhist -t 88`, `contigcov -l 15 -m 100 -h 185`, `purge -t 88 -a 50`.
**Notes**: In `02.2.purge.sh`, `readhist` and `contigcov` are commented out and only `purge` is active, so the `aligned.bam.200.gencov` it reads must exist under that exact name.