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… matrix, meta panel, copy (14 tests)
…mpty/headerless CLI errors, INFO/FORMAT defs, symbolic alleles, natural chrom sort, windowed list virtualization (filter toggle 12.5s→0.6s at 300k variants)
…r-preserving filter, no re-sort), async status-bar stats; PASS filter toggle 44.5s→3.1s, startup 59s→2.8s at 5.7M variants
- Binary quick-scan (first 5000) then background resume: open latency 46s→11ms - GIL-yield tuning (25ms/1000 rows): scroll during scan 2000ms→~200-400ms/press - Hide scrollbar while scanning + lazy restore (5.7M virtual-height recompute stalled UI 3s) - Reuse one binary file handle for detail seek-back reads - Time-throttled batch callbacks + end-of-scan reconciliation (no lost variants) - Async status-bar stats with token guard against exit race Regenerated test/big_chr.vcf: 508MB, 5.7M variants, chr1 coords up to 248,956,641 (>100M). 272 tests pass.
…osition on large files Root causes: - Every 0.5s batch callback rebuilt the window via clear_options(), resetting OptionList scroll state → periodic jump-to-top while browsing - Scrollbar was re-enabled after scan over a 400-option windowed buffer, falsely implying 'drag to bottom = end of data' (bottom showed chr1:17,065, the ~400th variant, not the 5.7M-th at 248,956,641) Fixes: - Batch appends never clear/rebuild: incremental add_options only when the window sits at the data tail and is unfilled; otherwise data-only extend - Scrollbar only shown when the list is fully materialized (<= WINDOW items); large lists rely on position indicator (sub_title 'X / N') + G/g jumps - Mouse wheel on large lists moves the browsing position (window shifts) instead of scrolling inside the 400-option buffer Verified on test/big_chr.vcf (508MB, 5.7M variants): - 8s mid-scan with multiple batches: 0 position jumps - G reaches true last variant chr1:248,956,641, indicator 5,700,000 / 5,700,000 - filter/sort/navigation stable after scan completion 280 tests pass (8 new regressions).
- Search bar (/) now supports chr1:10000 (nearest variant), chr1:10000-20000 and chr1:10000..20000 (first variant in range), with thousands separators and auto-swapped reversed ranges - Binary search on position-ordered view: 0.2ms jump on 5.7M variants (linear fallback for QUAL sort mode); mid-scan searches report indexed count - New AbsoluteScrollbar widget: thumb maps to the FULL view (position and size), click/drag to jump anywhere — replaces the misleading 400-option-buffer scrollbar on large lists - parse_coord_query added to pure parser layer (vcf.py), fully unit-tested - Help panel, search placeholder and README updated 298 tests pass (18 new).
- 修改 on_mount 方法中的注释说明焦点设置功能 - 在应用启动后显式设置焦点到侧栏组件 - 确保 Footer 组件能够显示完整的快捷键信息 - 优化了初始加载时的用户体验和界面响应
- VCF 浏览器右侧详情/基因型矩阵面板支持键盘滚动浏览 （Tab 聚焦，j/k/↑↓/PgUp/PgDn/Space/b/g/G，Esc 返回列表； n/p 保持变异级导航语义不受焦点影响） - issue #4: SequenceView.on_unmount 组件自身关闭持久句柄 （Textual 先卸载子组件，App 级钩子 query 返回空集从未生效） - issue #4: SequenceList 构造/追加改用批量 add_options （逐个 add_option 导致索引耗时退化 25 倍，复核者 A/B 验证 4.4x 提速） - 修复软屏蔽 DNA（RepeatMasker 小写 x）误判为蛋白质 - CLI _check_file 只拒绝目录，恢复 /dev/stdin、命名管道等 Unix 惯用输入 - 新增 clipboard.py 共享分层回退剪贴板（browser/vcf_browser 统一） - 327 项测试全部通过，ruff check src/ 零告警
- VCF 浏览器 App 级 Space/b 绑定与 action_page_down/up、PAGE 常量移除 - DetailPanel 移除 Space/b 绑定（PageUp/PageDown 物理键保留为详情翻页） - 帮助屏与 README 快捷键表同步更新 - 测试同步：Space/b 按下无任何副作用，方向键/PageUp/PageDown/g/G 滚动不受影响
- 新增 _DefaultBrowseGroup(TyperGroup)：首个参数非已知子命令时自动路由到 browse （seqviz test.fa ≡ seqviz browse test.fa；seqviz 无参仍打开当前目录选择器） - browse 改为 hidden 兼容别名，--help 命令列表只保留辅助子命令 （view/stats/head/fqview/config） - 主帮助文案更新：直接跟文件/目录路径即可打开浏览器 - README 同步：快速开始/命令表/各浏览器章节全部改用 seqviz <路径> 用法 - 新增 6 项默认路由测试（文件直达/VCF 路由/不存在路径/无参目录/子命令不被吞/选项不误路由） - 333 项测试全部通过，ruff check src/ 零告警
- 修复 21 个 ruff 错误 (import 排序/清理)，test/** 豁免 RUF059/RUF015 - 类型注解现代化 (Generator[X]、去字符串化)，requires-python >= 3.14 - CI lint 锁定 ruff@0.16.3，移除冗余 Python 安装步骤 - 版本升至 0.7.0rc2，同步 __init__.py / README / TODO.md
- 修复 _types/_qual_order 缓存在后台扫描追加变异后未失效导致的 IndexError - 后台扫描失败时通知用户而非静默吞掉异常 - CLI 打开 VCF 文件时捕获 OSError 并友好报错 333 tests passed, ruff lint clean.
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Author
运维巡检代码审查报告（QoderCN）审查结论：代码质量合格，建议合并变更概览本 PR 新增 VCF 变异可视化功能（+5042/-491 行，35 文件），核心模块：
本次修复的 Bug（commit
|
| 问题 | 严重度 | 修复 |
|---|---|---|
_types/_qual_order 缓存在后台扫描追加变异后未失效 → IndexError |
🔴 高 | _append_batch 和 _finish_scan 中失效缓存 |
| 后台扫描异常被静默吞掉 | 🟡 中 | 捕获异常后通知用户 |
| CLI 打开 VCF 文件时 OSError 产生原始 traceback | 🟡 中 | 捕获 OSError 并友好报错 |
测试验证
333 passed in 54.11s
ruff check → All checks passed!
代码质量评估
优点：
- 解析层与 UI 层清晰分离
- 窗口化虚拟化（WINDOW=400）避免大文件全量物化
- quick scan + 后台续扫的启动策略体验良好
- 测试覆盖全面（解析 28 项 + 浏览器 923 行测试）
- CRLF 处理正确且已测试
后续可优化（不阻塞合并）：
- 多等位基因型（
1/2）和相位基因型（0|1）显示可特殊处理 - sites-only VCF 不应虚构
sample1 - 100M+ 变异 VCF 的内存限制应在文档中说明
合并建议
代码质量合格，关键 bug 已修复，测试全部通过。建议 @Georicl 合并。
# Conflicts: # src/seqviz/browser.py
Owner
Author
运维巡检合并报告（QoderCN）操作结果：已合并 ✅审查摘要
变更统计
合并细节
后续建议（不阻塞）
|
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Summary
Test plan
pytest -q→ 333 passed in 54s）ruff check src/ test/→ All checks passed）_types/_qual_order缓存在后台扫描追加变异后未失效导致的 IndexError代码审查要点
vcf.py负责解析/分类/基因型/懒扫描/统计，与 UI 层vcf_browser.py清晰分离scan_vcf_quick快扫前 5000 条立即启动 TUI，scan_vcf_resume后台续扫_append_batch和_finish_scan中失效_types/_qual_order缓存已知限制（可后续优化）
1/2）和相位基因型（如0|1）显示未特殊处理./.（无样本时回退为sample1）