公开记录中等
软件健康报告模式 0.27.0 · 指标 1.13.0 · 2026-07-27 09:22 UTC
wwood / CoverM
Read alignment statistics for metagenomics
wwood/CoverM 的健康指数为 100 分中的 58 分，处于「中等」区间。 其得分最高的类别是AI Readiness（75/100），最低的是Security（48/100）。 最近一次更新在 17 天前。 近期的大部分工作由 1 位贡献者完成。
58
总分 / 100软件健康指数
指标归入加权类别，统一采用 1–100 量表。总体分先取类别加权平均；当公开证据触发高风险司法辖区政策时，评级会按政策调整，并设置 49（有风险）的上限。AI 就绪度不计入总体分。
58
优秀85-100堪称典范；基本满足所有检验标准
良好70-84健康；仅有轻微不足
中等50-69可接受，但存在明显不足；建议进行审查
存在风险30-49存在重大薄弱环节；采用时应保持审慎
危急1-29问题严重（项目被弃置、仅有单一维护者、缺乏基本工程规范）
评分画像
每条轴代表一个类别。形状比平均值更重要——健康的对象会填满整个图形，而“一峰一谷”式画像意味着某一维度的优势正掩盖另一维度的风险。
所有权
Ben J Woodcroft个人账户
363 关注者243 个公开仓库始于 2008年6月Queensland University of Technology
该仓库由个人账户拥有。相较于组织支持的项目，单一所有者项目的延续性风险更高。
软件包生态系统
| 注册表 | 软件包 | 版本 | 月下载量 | 版本数 | 最近发布 |
|---|---|---|---|---|---|
| crates.io | coverm | 0.8.0 | 40 | 11 | 19 天前 |
按类别列示的指标
活力
项目是否仍有生命——是否仍在编写代码，是否仍在发布版本？
67
开发活跃度
61中等
评分方式
| 28.8/36 | 推送新近度 — 最近一次推送于 17 天前 |
| 6.9/36 | 提交节奏 — 52 周中有 10 周有提交 |
| 15.7/18 | 提交量 — 最近一年 55 次提交 |
| 10/10 | OpenSSF Scorecard：Maintained — 30 commit(s) and 3 issue activity found in the last 90 days -- score normalized to 10 |
所用输入
| commits_last_year | 55 |
| human_commit_share | 0.94 |
| days_since_last_push | 17 |
| active_weeks_last_year | 10 |
发布纪律
76良好
评分方式
| 27/27 | 有发布版本 — 已发布 13 个发布版本 |
| 36/36 | 发布时效 — 最近一次发布版本于 19 天前 |
| 12.6/27 | 发布节奏 — 约每 288.7 天发布一次 |
| 0/10 | OpenSSF Scorecard：Signed-Releases — Project has not signed or included provenance with any releases. |
所用输入
| releases_count | 13 |
| latest_release_tag | v0.8.0 |
| releases_from_tags | 否 |
| days_since_latest_release | 19 |
| mean_days_between_releases | 288.7 |
社区与采用
项目是否拥有用户、下载量与关注度，并具备欢迎贡献者参与的配置？
48
流行度与采用
60中等
评分方式
| 42.2/60 | 星标 — 402 个星标 |
| 13/25 | 复刻 — 37 个复刻 |
| 5/15 | 关注者 — 9 位关注者 |
所用输入
| forks | 37 |
| stars | 402 |
| watchers | 9 |
| growth_state | unverified |
| growth_factor_pct | 100 |
| growth_unverified_reason | no_history |
社区健康
50中等
评分方式
| 22.5/22.5 | README |
| 22.5/22.5 | 许可证 — 可识别的许可证（GPL-3.0） |
| 0/18 | CONTRIBUTING 指南 |
| 0/13.5 | 行为准则 |
| 0/7.2 | 议题模板 |
| 0/6.3 | PR 模板 |
所用输入
| has_readme | 是 |
| has_license | 是 |
| has_contributing | 否 |
| has_issue_template | 否 |
| has_code_of_conduct | 否 |
| has_pull_request_template | 否 |
生态采用（下载量）
27危急
评分方式
| 21.5/80 | 月度下载量 — crates 合计每月 40 次下载 |
| 0/20 | 注册表被依赖数 — 该生态系统不报告此项 |
所用输入
| packages | coverm |
| dependents | — |
| ecosystems | crates |
| total_downloads | 16,928 |
| monthly_downloads | 40 |
已排除计分（无数据或不适用）：注册表被依赖数。 其余权重已重新归一化。
可持续性与治理
项目能否在其成员之外延续——巴士系数、响应能力、由谁支持，以及软件包的维护状况？
58
维护者韧性（巴士系数）
30存在风险
评分方式
| 9/54 | 巴士系数 — 1 位贡献者贡献了半数提交 |
| 2.5/22.5 | 提交分布 — 头号贡献者编写了 89% 的提交 |
| 8.1/13.5 | 贡献者广度 — 6 位贡献者 |
| 10/10 | OpenSSF Scorecard：Contributors — project has 5 contributing companies or organizations |
所用输入
| bus_factor | 1 |
| contributors_sampled | 6 |
| top_contributor_share | 0.887 |
议题与 PR 响应能力
50中等
评分方式
| 33/46.8 | 议题解决 — 71% 的议题已关闭 |
| 17.3/38.3 | PR 接受 — 已裁定的 PR 中 37/82 已合并 |
| 0/15 | OpenSSF Scorecard：Code-Review — Found 1/16 approved changesets -- score normalized to 0 |
所用输入
| merged_prs | 37 |
| open_issues | 59 |
| closed_issues | 142 |
| issue_closed_ratio | 0.706 |
| closed_unmerged_prs | 45 |
所有权与托管责任
67中等
评分方式
| 10/30 | 所有权背书 — 个人（用户）账户 |
| 0/20 | 已验证域名 — 不适用于个人账户 |
| 18.4/25 | 所有者影响力 — wwood 有 363 位关注者 |
| 25/25 | 既往记录 — 243 个公开仓库，账户约 18 年 |
所用输入
| followers | 363 |
| owner_type | User |
| is_verified | — |
| owner_login | wwood |
| public_repos | 243 |
| account_age_days | 6,603 |
已排除计分（无数据或不适用）：已验证域名。 其余权重已重新归一化。
软件包维护
100优秀
评分方式
| 25/25 | 已发布且可解析 — crates 上有 1 个软件包 |
| 35/35 | 发布时效 — 最近一次发布于 19 天前 |
| 20/20 | 版本历史 — 11 个已发布版本 |
| 20/20 | 未被弃用 — 活跃，未被弃用或撤回 |
所用输入
| packages | coverm |
| ecosystems | crates |
| any_deprecated | 否 |
| min_days_since_publish | 19 |
工程质量
基础的工程与文档实践是否到位？
64
工程实践
64中等
评分方式
| 24/24 | CI 工作流 — 2 个工作流 |
| 24/24 | 存在测试 |
| 0/16 | Linter 配置 |
| 0/9.6 | Pre-commit 钩子 |
| 0/6.4 | .editorconfig |
| 16/20 | OpenSSF Scorecard：CI-Tests — 5 out of 6 merged PRs checked by a CI test -- score normalized to 8 |
所用输入
| has_ci | 是 |
| has_tests | 是 |
| has_editorconfig | 否 |
| has_linter_config | 否 |
| has_precommit_config | 否 |
文档
65中等
评分方式
| 30/30 | README |
| 25/25 | 文档目录 |
| 0/15 | 文档 / 主页站点 |
| 10/10 | 仓库描述 |
| 0/10 | 主题标签 |
| 0/10 | Wiki |
所用输入
| topics | — |
| has_wiki | 否 |
| homepage | — |
| has_readme | 是 |
| has_docs_dir | 是 |
| has_description | 是 |
安全
可见的安全与供应链实践是否稳固，且不存在未解决的高风险司法辖区暴露？
48
安全态势
40存在风险
评分方式
| 7.5/7.5 | Binary-Artifacts — no binaries found in the repo |
| 0/7.5 | Branch-Protection — branch protection not enabled on development/release branches |
| 2/2.5 | CI-Tests — 5 out of 6 merged PRs checked by a CI test -- score normalized to 8 |
| 0/2.5 | CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected |
| 0/7.5 | Code-Review — Found 1/16 approved changesets -- score normalized to 0 |
| 2.5/2.5 | Contributors — project has 5 contributing companies or organizations |
| 10/10 | Dangerous-Workflow — no dangerous workflow patterns detected |
| 7.5/7.5 | Dependency-Update-Tool — update tool detected |
| 0/5 | Fuzzing — project is not fuzzed |
| 2.5/2.5 | 许可证 — license file detected |
| 7.5/7.5 | Maintained — 30 commit(s) and 3 issue activity found in the last 90 days -- score normalized to 10 |
| 0/5 | Packaging — 无数据 |
| 0/5 | Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0 |
| 0/5 | SAST — SAST tool is not run on all commits -- score normalized to 0 |
| 0/5 | Security-Policy — security policy file not detected |
| 0/7.5 | Signed-Releases — Project has not signed or included provenance with any releases. |
| 0/7.5 | Token-Permissions — detected GitHub workflow tokens with excessive permissions |
| 0/7.5 | Vulnerabilities — 13 existing vulnerabilities detected |
所用输入
| source | openssf_scorecard |
| checks_evaluated | 17 |
| scorecard_version | v5.5.0 |
| checks_inconclusive | 1 |
| scorecard_aggregate | 4 |
已排除计分（无数据或不适用）：packaging。 其余权重已重新归一化。
依赖安全公告
79良好
评分方式
| 24.7/35 | 直接依赖不含已知公告 — 2 个受影响：ansi_term 0.12.1 (unknown), tempdir 0.3.7 (unknown) |
| 0/25 | 间接依赖不含已知公告 — 在此范围内，传递依赖集合无法与开发和测试依赖区分 |
| 34.8/40 | 没有长期未处理的公告 — 2 个携带公告的软件包超过 90 天未处理；最早一条发布于 3,085 天前 |
所用输入
| source | osv |
| advisories | 18 |
| affected_packages | 13 |
| assessed_packages | 255 |
| unassessed_packages | 0 |
| affected_by_severity | critical 2, low 1, unknown 10 |
| direct_affected_packages | 2 |
已排除计分（无数据或不适用）：间接依赖不含已知公告。 其余权重已重新归一化。 已将 255 个已解析依赖与 OSV 比对。 该仓库未发布任何索引可解析的软件包，因此改为评估仓库依赖图。该图将开发与测试版本固定同交付的依赖混在一起，因此仅对声明的运行时依赖计分；传递性发现仅作为背景信息列出，不计入评分。 未对可达性进行分析。
AI 就绪度
该仓库在多大程度上具备与 AI 编码代理协同开发与维护的条件？这是一枚独立的实验性徽章——权重为 0.0，因此单独呈现，不影响总体健康评分。
75
AI 代理上下文与指引
73良好
评分方式
| 45/45 | 代理指令 — AGENTS.md |
| 0/15 | 机器可读文档（llms.txt） |
| 28.4/40 | 可读的提交历史 — 94 次人类提交中有 50 次说明了意图（结构化标题或解释性正文） |
所用输入
| has_llms_txt | 否 |
| legible_history_share | 0.532 |
| agent_instruction_files | AGENTS.md |
| agent_instruction_max_bytes | 289 |
评分方式
| 12.6/18 | 一条命令的引导启动 — Cargo.toml（工具链约定，无任务运行器） |
| 22/22 | 自动化测试 |
| 0/11 | Lint / 格式化配置 |
| 11/11 | 静态类型检查 — Rust（静态类型） |
| 10/10 | 可复现环境 — lockfile |
| 10/10 | 已体现的代理实践 — 最近 100 次提交中有 9 次由代理编写或署名代理 |
| 5/8 | 自动化维护 — 已配置依赖自动化，但在抽样提交中未观察到 |
| 0/10 | OpenSSF Scorecard：Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0 |
所用输入
| has_nix | 否 |
| has_tests | 是 |
| lockfiles | Cargo.lock |
| has_dockerfile | 否 |
| typed_language | 是 |
| bootstrap_files | — |
| has_devcontainer | 否 |
| has_linter_config | 否 |
| typecheck_configs | — |
| agent_commit_share | 0.09 |
| toolchain_manifests | Cargo.toml |
| dependency_bot_commit_share | 0 |
面向模型的代码可读性
90优秀
评分方式
| 45/45 | 可类型检查的代码 — Rust（静态类型） |
| 44.5/55 | 可控的文件大小 — 采样的 21 个源文件中有 4 个超过 60KB |
所用输入
| primary_language | Rust |
| largest_source_bytes | 157,623 |
| source_files_sampled | 21 |
| oversized_source_files | 4 |
关键数据
402GitHub 星标
6贡献者
55最近 12 个月提交数
17距最近推送天数
13发布版本数
1巴士系数（bus factor）
59开放议题
crates.io软件包生态系统数
数据采集警告
- Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token
更多细节
Star 与 Fork 历史 0 ★ / 37 ⇿
0Star
37Fork
5发布
每颗 star 和每个 fork 的添加时间，来自 GitHub 并按天汇总。累计增长位于其构成来源——每日新增——的正上方，二者可相互对照：稳定的自然增长与短暂的突增形态截然不同。当这一差别可被衡量时，它会作为增长真实性予以报告。
主版本 0次版本 4修订 1
每个点涵盖 6 天。
OpenSSF Scorecard 4.0 / 10
4.0综合
来自开源项目 OpenSSF Scorecard 的独立、工具无关的安全评估。每项检查奖励的是安全实践本身，而非特定供应商的工具。Scorecard 无法判定的检查项标记为 不适用，并从安全评分中剔除（绝不按零分计）。
| 10 | Binary-Artifacts | no binaries found in the repo |
| 0 | Branch-Protection | branch protection not enabled on development/release branches |
| 8 | CI-Tests | 5 out of 6 merged PRs checked by a CI test -- score normalized to 8 |
| 0 | CII-Best-Practices | no effort to earn an OpenSSF best practices badge detected |
| 0 | Code-Review | Found 1/16 approved changesets -- score normalized to 0 |
| 10 | Contributors | project has 5 contributing companies or organizations |
| 10 | Dangerous-Workflow | no dangerous workflow patterns detected |
| 10 | Dependency-Update-Tool | update tool detected |
| 0 | Fuzzing | project is not fuzzed |
| 10 | License | license file detected |
| 10 | Maintained | 30 commit(s) and 3 issue activity found in the last 90 days -- score normalized to 10 |
| 不适用 | Packaging | packaging workflow not detected |
| 0 | Pinned-Dependencies | dependency not pinned by hash detected -- score normalized to 0 |
| 0 | SAST | SAST tool is not run on all commits -- score normalized to 0 |
| 0 | Security-Policy | security policy file not detected |
| 0 | Signed-Releases | Project has not signed or included provenance with any releases. |
| 0 | Token-Permissions | detected GitHub workflow tokens with excessive permissions |
| 0 | Vulnerabilities | 13 existing vulnerabilities detected |
直接依赖 20
| 注册表 | 软件包 | 版本约束 | 清单文件 |
|---|---|---|---|
| crates.io | bio | 2.0.* | Cargo.toml |
| crates.io | rust-htslib | 0.46.* | Cargo.toml |
| crates.io | clap | 4.* | Cargo.toml |
| crates.io | clap_complete | 4.* | Cargo.toml |
| crates.io | log | 0.4.* | Cargo.toml |
| crates.io | env_logger | 0.11.* | Cargo.toml |
| crates.io | nix | 0.29.* | Cargo.toml |
| crates.io | tempdir | 0.3.* | Cargo.toml |
| crates.io | tempfile | 3.* | Cargo.toml |
| crates.io | ansi_term | 0.12 | Cargo.toml |
| crates.io | lazy_static | 1.4.0 | Cargo.toml |
| crates.io | rand | 0.8.* | Cargo.toml |
| crates.io | serde | 1.0 | Cargo.toml |
| crates.io | version-compare | 0.2.0 | Cargo.toml |
| crates.io | bird_tool_utils | >=0.5.2, <0.6.0 | Cargo.toml |
| crates.io | galah | — | Cargo.toml |
| crates.io | bird_tool_utils-man | 0.4.0 | Cargo.toml |
| crates.io | roff | 0.2.* | Cargo.toml |
| crates.io | needletail | 0.7.* | Cargo.toml |
| crates.io | csv | 1.* | Cargo.toml |
全部依赖 255
来自 GitHub 依赖图的完整解析依赖集合：23 个直接依赖与 232 个间接（传递）软件包。仓库提交锁文件时，传递闭包才是完整的。
| 注册表 | 软件包 | 版本 | 关系 |
|---|---|---|---|
| crates.io | ansi_term | 0.12.1 | 直接 |
| crates.io | bio | 2.0.3 | 直接 |
| crates.io | bird_tool_utils | 0.5.2 | 直接 |
| crates.io | bird_tool_utils-man | 0.4.0 | 直接 |
| crates.io | clap | 4.6.1 | 直接 |
| crates.io | clap_complete | 4.6.6 | 直接 |
| crates.io | csv | 1.4.0 | 直接 |
| crates.io | env_logger | 0.10.2 | 直接 |
| crates.io | env_logger | 0.11.11 | 直接 |
| crates.io | galah | 0.5.2 | 直接 |
| crates.io | lazy_static | 1.5.0 | 直接 |
| crates.io | log | 0.4.33 | 直接 |
| crates.io | needletail | 0.7.3 | 直接 |
| crates.io | nix | 0.29.0 | 直接 |
| crates.io | rand | 0.4.6 | 直接 |
| crates.io | rand | 0.8.6 | 直接 |
| crates.io | roff | 0.1.0 | 直接 |
| crates.io | roff | 0.2.2 | 直接 |
| crates.io | rust-htslib | 0.46.0 | 直接 |
| crates.io | serde | 1.0.228 | 直接 |
| crates.io | tempdir | 0.3.7 | 直接 |
| crates.io | tempfile | 3.27.0 | 直接 |
| crates.io | version-compare | 0.2.1 | 直接 |
| crates.io | addr2line | 0.25.1 | 间接 |
| crates.io | adler2 | 2.0.1 | 间接 |
| crates.io | aho-corasick | 1.1.4 | 间接 |
| crates.io | anstream | 1.0.0 | 间接 |
| crates.io | anstyle | 1.0.14 | 间接 |
| crates.io | anstyle-parse | 1.0.0 | 间接 |
| crates.io | anstyle-query | 1.1.5 | 间接 |
| crates.io | anstyle-wincon | 3.0.11 | 间接 |
| crates.io | anyhow | 1.0.103 | 间接 |
| crates.io | approx | 0.5.1 | 间接 |
| crates.io | assert_cli | 0.6.3 | 间接 |
| crates.io | autocfg | 1.5.1 | 间接 |
| crates.io | backtrace | 0.3.76 | 间接 |
| crates.io | bincode | 1.3.3 | 间接 |
| crates.io | bio-types | 1.0.4 | 间接 |
| crates.io | bit-set | 0.8.0 | 间接 |
| crates.io | bit-vec | 0.8.0 | 间接 |
| crates.io | bitflags | 1.3.2 | 间接 |
| crates.io | bitflags | 2.13.0 | 间接 |
| crates.io | buffer-redux | 1.1.0 | 间接 |
| crates.io | bv | 0.11.1 | 间接 |
| crates.io | bytecount | 0.6.9 | 间接 |
| crates.io | bytemuck | 1.25.0 | 间接 |
| crates.io | byteorder | 1.5.0 | 间接 |
| crates.io | bzip2 | 0.6.1 | 间接 |
| crates.io | capnp | 0.14.11 | 间接 |
| crates.io | cargo-husky | 1.5.0 | 间接 |
| crates.io | cc | 1.2.65 | 间接 |
| crates.io | cfg-if | 1.0.4 | 间接 |
| crates.io | cfg_aliases | 0.2.1 | 间接 |
| crates.io | checkm | 0.3.0 | 间接 |
| crates.io | clap_builder | 4.6.0 | 间接 |
| crates.io | clap_lex | 1.1.0 | 间接 |
| crates.io | cmake | 0.1.58 | 间接 |
| crates.io | colorchoice | 1.0.5 | 间接 |
| crates.io | colored | 1.9.4 | 间接 |
| crates.io | concurrent-queue | 2.5.0 | 间接 |
| crates.io | crc32fast | 1.5.0 | 间接 |
| crates.io | crossbeam-deque | 0.8.6 | 间接 |
| crates.io | crossbeam-epoch | 0.9.18 | 间接 |
| crates.io | crossbeam-utils | 0.8.21 | 间接 |
| crates.io | csv-core | 0.1.13 | 间接 |
| crates.io | custom_derive | 0.1.7 | 间接 |
| crates.io | defmt | 1.1.0 | 间接 |
| crates.io | defmt-macros | 1.1.0 | 间接 |
| crates.io | defmt-parser | 1.0.0 | 间接 |
| crates.io | derive-new | 0.5.9 | 间接 |
| crates.io | derive-new | 0.6.0 | 间接 |
| crates.io | difference | 2.0.0 | 间接 |
| crates.io | disjoint | 0.8.0 | 间接 |
| crates.io | displaydoc | 0.2.6 | 间接 |
| crates.io | editdistancek | 1.0.2 | 间接 |
| crates.io | either | 1.16.0 | 间接 |
| crates.io | enum-map | 2.7.3 | 间接 |
| crates.io | enum-map-derive | 0.17.0 | 间接 |
| crates.io | env_filter | 2.0.0 | 间接 |
| crates.io | environment | 0.1.1 | 间接 |
| crates.io | equivalent | 1.0.2 | 间接 |
| crates.io | errno | 0.3.14 | 间接 |
| crates.io | failure | 0.1.8 | 间接 |
| crates.io | failure_derive | 0.1.8 | 间接 |
| crates.io | fastrand | 2.4.1 | 间接 |
| crates.io | feature-probe | 0.1.1 | 间接 |
| crates.io | finch | 0.6.3 | 间接 |
| crates.io | find-msvc-tools | 0.1.9 | 间接 |
| crates.io | fixedbitset | 0.4.2 | 间接 |
| crates.io | flate2 | 1.1.9 | 间接 |
| crates.io | form_urlencoded | 1.2.2 | 间接 |
| crates.io | fs-utils | 1.1.4 | 间接 |
| crates.io | fuchsia-cprng | 0.1.1 | 间接 |
| crates.io | fxhash | 0.2.1 | 间接 |
| crates.io | getrandom | 0.2.17 | 间接 |
| crates.io | getrandom | 0.3.4 | 间接 |
| crates.io | getrandom | 0.4.3 | 间接 |
| crates.io | gimli | 0.32.3 | 间接 |
| crates.io | glob | 0.3.3 | 间接 |
| crates.io | hashbrown | 0.17.1 | 间接 |
| crates.io | heck | 0.5.0 | 间接 |
| crates.io | hermit-abi | 0.5.2 | 间接 |
| crates.io | home | 0.5.12 | 间接 |
| crates.io | hts-sys | 2.2.0 | 间接 |
| crates.io | humantime | 2.3.0 | 间接 |
| crates.io | icu_collections | 2.2.0 | 间接 |
| crates.io | icu_locale_core | 2.2.0 | 间接 |
| crates.io | icu_normalizer | 2.2.0 | 间接 |
| crates.io | icu_normalizer_data | 2.2.0 | 间接 |
| crates.io | icu_properties | 2.2.0 | 间接 |
| crates.io | icu_properties_data | 2.2.0 | 间接 |
| crates.io | icu_provider | 2.2.0 | 间接 |
| crates.io | idna | 1.1.0 | 间接 |
| crates.io | idna_adapter | 1.2.2 | 间接 |
| crates.io | ieee754 | 0.2.6 | 间接 |
| crates.io | indexmap | 2.14.0 | 间接 |
| crates.io | is-terminal | 0.4.17 | 间接 |
| crates.io | is_terminal_polyfill | 1.70.2 | 间接 |
| crates.io | itertools | 0.13.0 | 间接 |
| crates.io | itertools-num | 0.1.3 | 间接 |
| crates.io | itoa | 1.0.18 | 间接 |
| crates.io | jiff | 0.2.31 | 间接 |
| crates.io | jiff-static | 0.2.31 | 间接 |
| crates.io | jobserver | 0.1.34 | 间接 |
| crates.io | libbz2-rs-sys | 0.2.5 | 间接 |
| crates.io | libc | 0.2.186 | 间接 |
| crates.io | liblzma | 0.3.6 | 间接 |
| crates.io | liblzma-sys | 0.3.13 | 间接 |
| crates.io | libm | 0.2.16 | 间接 |
| crates.io | libz-sys | 1.1.29 | 间接 |
| crates.io | linear-map | 1.2.0 | 间接 |
| crates.io | linux-raw-sys | 0.12.1 | 间接 |
| crates.io | linux-raw-sys | 0.4.15 | 间接 |
| crates.io | litemap | 0.8.2 | 间接 |
| crates.io | matrixmultiply | 0.3.10 | 间接 |
| crates.io | memchr | 2.8.2 | 间接 |
| crates.io | memmap | 0.7.0 | 间接 |
| crates.io | miniz_oxide | 0.8.9 | 间接 |
| crates.io | multimap | 0.10.1 | 间接 |
| crates.io | murmurhash3 | 0.0.5 | 间接 |
| crates.io | nalgebra | 0.32.6 | 间接 |
| crates.io | nalgebra-macros | 0.2.2 | 间接 |
| crates.io | ndarray | 0.16.1 | 间接 |
| crates.io | newtype_derive | 0.1.6 | 间接 |
| crates.io | num-complex | 0.4.6 | 间接 |
| crates.io | num-integer | 0.1.46 | 间接 |
| crates.io | num-rational | 0.4.2 | 间接 |
| crates.io | num-traits | 0.2.19 | 间接 |
| crates.io | object | 0.37.3 | 间接 |
| crates.io | once_cell | 1.21.4 | 间接 |
| crates.io | once_cell_polyfill | 1.70.2 | 间接 |
| crates.io | ordered-float | 4.6.0 | 间接 |
| crates.io | paste | 1.0.15 | 间接 |
| crates.io | percent-encoding | 2.3.2 | 间接 |
| crates.io | petgraph | 0.6.5 | 间接 |
| crates.io | pkg-config | 0.3.33 | 间接 |
| crates.io | portable-atomic | 1.13.1 | 间接 |
| crates.io | portable-atomic-util | 0.2.7 | 间接 |
| crates.io | potential_utf | 0.1.5 | 间接 |
| crates.io | ppv-lite86 | 0.2.21 | 间接 |
| crates.io | proc-macro-error-attr2 | 2.0.0 | 间接 |
| crates.io | proc-macro-error2 | 2.0.1 | 间接 |
| crates.io | proc-macro2 | 1.0.106 | 间接 |
| crates.io | quick-error | 1.2.3 | 间接 |
| crates.io | quote | 1.0.46 | 间接 |
| crates.io | r-efi | 5.3.0 | 间接 |
| crates.io | r-efi | 6.0.0 | 间接 |
| crates.io | rand_chacha | 0.3.1 | 间接 |
| crates.io | rand_core | 0.3.1 | 间接 |
| crates.io | rand_core | 0.4.2 | 间接 |
| crates.io | rand_core | 0.6.4 | 间接 |
| crates.io | rand_distr | 0.4.3 | 间接 |
| crates.io | rawpointer | 0.2.1 | 间接 |
| crates.io | rayon | 1.12.0 | 间接 |
| crates.io | rayon-core | 1.13.0 | 间接 |
| crates.io | rdrand | 0.4.0 | 间接 |
| crates.io | regex | 1.12.4 | 间接 |
| crates.io | regex-automata | 0.4.14 | 间接 |
| crates.io | regex-syntax | 0.8.11 | 间接 |
| crates.io | remove_dir_all | 0.5.3 | 间接 |
| crates.io | rustc-demangle | 0.1.27 | 间接 |
| crates.io | rustc_version | 0.1.7 | 间接 |
| crates.io | rustix | 0.38.44 | 间接 |
| crates.io | rustix | 1.1.4 | 间接 |
| crates.io | rustversion | 1.0.22 | 间接 |
| crates.io | ryu | 1.0.23 | 间接 |
| crates.io | safe_arch | 0.7.4 | 间接 |
| crates.io | semver | 0.1.20 | 间接 |
| crates.io | serde_core | 1.0.228 | 间接 |
| crates.io | serde_derive | 1.0.228 | 间接 |
| crates.io | serde_json | 1.0.150 | 间接 |
| crates.io | shlex | 2.0.1 | 间接 |
| crates.io | simba | 0.8.1 | 间接 |
| crates.io | simd-adler32 | 0.3.9 | 间接 |
| crates.io | smallvec | 1.15.2 | 间接 |
| crates.io | stable_deref_trait | 1.2.1 | 间接 |
| crates.io | statrs | 0.17.1 | 间接 |
| crates.io | strsim | 0.11.1 | 间接 |
| crates.io | strum | 0.26.3 | 间接 |
| crates.io | strum_macros | 0.26.4 | 间接 |
| crates.io | syn | 1.0.109 | 间接 |
| crates.io | syn | 2.0.118 | 间接 |
| crates.io | synstructure | 0.12.6 | 间接 |
| crates.io | synstructure | 0.13.2 | 间接 |
| crates.io | termcolor | 1.4.1 | 间接 |
| crates.io | thiserror | 1.0.69 | 间接 |
| crates.io | thiserror | 2.0.18 | 间接 |
| crates.io | thiserror-impl | 1.0.69 | 间接 |
| crates.io | thiserror-impl | 2.0.18 | 间接 |
| crates.io | tinystr | 0.8.3 | 间接 |
| crates.io | triple_accel | 0.4.0 | 间接 |
| crates.io | typenum | 1.20.1 | 间接 |
| crates.io | unicode-ident | 1.0.24 | 间接 |
| crates.io | unicode-xid | 0.2.6 | 间接 |
| crates.io | url | 2.5.8 | 间接 |
| crates.io | utf8_iter | 1.0.4 | 间接 |
| crates.io | utf8parse | 0.2.2 | 间接 |
| crates.io | vcpkg | 0.2.15 | 间接 |
| crates.io | vec_map | 0.8.2 | 间接 |
| crates.io | wasi | 0.11.1+wasi-snapshot-preview1 | 间接 |
| crates.io | wasip2 | 1.0.4+wasi-0.2.12 | 间接 |
| crates.io | which | 6.0.3 | 间接 |
| crates.io | wide | 0.7.33 | 间接 |
| crates.io | winapi | 0.3.9 | 间接 |
| crates.io | winapi-i686-pc-windows-gnu | 0.4.0 | 间接 |
| crates.io | winapi-util | 0.1.11 | 间接 |
| crates.io | winapi-x86_64-pc-windows-gnu | 0.4.0 | 间接 |
| crates.io | windows-link | 0.2.1 | 间接 |
| crates.io | windows-sys | 0.59.0 | 间接 |
| crates.io | windows-sys | 0.61.2 | 间接 |
| crates.io | windows-targets | 0.52.6 | 间接 |
| crates.io | windows_aarch64_gnullvm | 0.52.6 | 间接 |
| crates.io | windows_aarch64_msvc | 0.52.6 | 间接 |
| crates.io | windows_i686_gnu | 0.52.6 | 间接 |
| crates.io | windows_i686_gnullvm | 0.52.6 | 间接 |
| crates.io | windows_i686_msvc | 0.52.6 | 间接 |
| crates.io | windows_x86_64_gnu | 0.52.6 | 间接 |
| crates.io | windows_x86_64_gnullvm | 0.52.6 | 间接 |
| crates.io | windows_x86_64_msvc | 0.52.6 | 间接 |
| crates.io | winsafe | 0.0.19 | 间接 |
| crates.io | wit-bindgen | 0.57.1 | 间接 |
| crates.io | writeable | 0.6.3 | 间接 |
| crates.io | yoke | 0.8.3 | 间接 |
| crates.io | yoke-derive | 0.8.2 | 间接 |
| crates.io | zerocopy | 0.8.52 | 间接 |
| crates.io | zerocopy-derive | 0.8.52 | 间接 |
| crates.io | zerofrom | 0.1.8 | 间接 |
| crates.io | zerofrom-derive | 0.1.7 | 间接 |
| crates.io | zerotrie | 0.2.4 | 间接 |
| crates.io | zerovec | 0.11.6 | 间接 |
| crates.io | zerovec-derive | 0.11.3 | 间接 |
| crates.io | zmij | 1.0.21 | 间接 |
| crates.io | zstd | 0.13.3 | 间接 |
| crates.io | zstd-safe | 7.2.4 | 间接 |
| crates.io | zstd-sys | 2.0.16+zstd.1.5.7 | 间接 |
依赖安全公告 13
该仓库未发布可被索引解析的包，因此评估的是其自身的依赖图——共 255 个包，其中也包含从不交付的开发与测试版本固定：13 个存在已知公告，2 个为直接依赖。
| 软件包 | 版本 | 关系 | 严重程度 | 公告数 | 修复版本 |
|---|---|---|---|---|---|
| capnp | 0.14.11 | 间接 | 严重 | 2 | 0.24.0 |
| failure | 0.1.8 | 间接 | 严重 | 4 | — |
| remove_dir_all | 0.5.3 | 间接 | 低 | 2 | 0.8.0 |
| ansi_term | 0.12.1 | 直接 | 未知 | 1 | — |
| tempdir | 0.3.7 | 直接 | 未知 | 1 | — |
| bincode | 1.3.3 | 间接 | 未知 | 1 | — |
| crossbeam-epoch | 0.9.18 | 间接 | 未知 | 1 | 0.9.20 |
| custom_derive | 0.1.7 | 间接 | 未知 | 1 | — |
| difference | 2.0.0 | 间接 | 未知 | 1 | — |
| fxhash | 0.2.1 | 间接 | 未知 | 1 | — |
| memmap | 0.7.0 | 间接 | 未知 | 1 | 0.7.1-0 |
| paste | 1.0.15 | 间接 | 未知 | 1 | — |
| proc-macro-error2 | 2.0.1 | 间接 | 未知 | 1 | — |
公告表示依赖图中记录的版本落入某条公告的受影响范围。可达性未经分析，且依赖图包含开发与测试的版本固定——某项发现可能只涉及工具链而非交付的软件。
原始 JSON 报告 机器可读
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"is_fork": false,
"size_kb": 72341,
"has_wiki": false,
"homepage": null,
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"Rust": 772338,
"Shell": 1485,
"Python": 1547
},
"pushed_at": "2026-07-10T08:21:53Z",
"created_at": "2017-12-23T11:43:13Z",
"owner_type": "User",
"updated_at": "2026-07-24T10:25:47Z",
"description": "Read alignment statistics for metagenomics",
"is_archived": false,
"is_disabled": false,
"license_spdx": "GPL-3.0",
"default_branch": "main",
"license_spdx_raw": "GPL-3.0",
"primary_language": "Rust",
"significant_languages": [
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},
"owner": {
"blog": "https://research.qut.edu.au/cmr/team/ben-woodcroft",
"name": "Ben J Woodcroft",
"type": "User",
"login": "wwood",
"company": "Queensland University of Technology",
"location": "Brisbane, Australia",
"followers": 363,
"avatar_url": "https://avatars.githubusercontent.com/u/15348?v=4",
"created_at": "2008-06-28T03:57:02Z",
"is_verified": null,
"public_repos": 243,
"account_age_days": 6603
},
"license": {
"state": "standard",
"spdx_id": "GPL-3.0",
"raw_spdx": "GPL-3.0",
"file_present": true,
"scorecard_found": true,
"profile_has_license": true
},
"activity": {
"releases": [
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"kind": "minor",
"published_at": "2026-07-08T03:37:16Z"
},
{
"tag": "v0.7.0",
"kind": "minor",
"published_at": "2024-01-19T03:42:31Z"
},
{
"tag": "v0.6.1",
"kind": "patch",
"published_at": "2021-02-24T21:27:38Z"
},
{
"tag": "v0.6.0",
"kind": "minor",
"published_at": "2020-12-10T21:48:20Z"
},
{
"tag": "v0.5.0",
"kind": "minor",
"published_at": "2020-08-31T23:33:46Z"
},
{
"tag": "v0.4.0",
"kind": "minor",
"published_at": "2020-02-20T22:26:43Z"
},
{
"tag": "v0.3.2",
"kind": "patch",
"published_at": "2019-12-14T06:13:30Z"
},
{
"tag": "v0.3.1",
"kind": "patch",
"published_at": "2019-11-15T00:50:59Z"
},
{
"tag": "v0.3.0",
"kind": "minor",
"published_at": "2019-10-11T01:26:09Z"
},
{
"tag": "v0.2.0-alpha7",
"kind": "prerelease",
"published_at": "2019-05-28T02:31:31Z"
},
{
"tag": "v0.2.0-alpha6",
"kind": "prerelease",
"published_at": "2019-03-24T01:25:12Z"
},
{
"tag": "v0.2.0-alpha4",
"kind": "prerelease",
"published_at": "2019-02-09T13:33:05Z"
},
{
"tag": "v0.2.0-alpha3",
"kind": "prerelease",
"published_at": "2019-01-06T23:11:39Z"
}
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"body": "- Remove harmful `.value_delimiter(' ')` on --dereplication-reference-genomes\n which would incorrectly split single space-containing paths.\n- Actually wire --dereplication-reference-genomes / -list through to\n generate_galah_clusterer instead of always passing None, mirroring\n galah's own referen\n[…]\ning CheckM\n report is supplied, so makedb --run-checkm2 actually runs.\n\nCo-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>\nClaude-Session: https://claude.ai/code/session_01RLvd19g5t8McWNE8nyTS5x",
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"headline": "makedb: Add further flags. Fix various docs and bugs.",
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"headline": "Merge pull request #293 from wwood/claude/per-gene-coverage-reporting…",
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"body": "Add minibwa as a mapper",
"is_bot": false,
"headline": "Merge pull request #295 from wwood/minibwa",
"author_name": "Ben J Woodcroft",
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"headline": "Clarify rammap single-end test comment",
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"headline": "Apply rustfmt to merged mapper branches",
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"headline": "Merge origin/main and resolve mapper conflicts",
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"body": "Commit the rammap linux-64 conda package (1.1.1, build hfa8f182_0) into\nthe frozen lockfile so `pixi run --frozen` installs it in the locked CI\njob, matching how strobealign and bwa-mem2 are pinned. Package hash and\nmetadata taken from the bioconda repodata and verified against the\ndownloaded artifa\n[…]\nndency, libgcc >=14, is already satisfied by libgcc 15.1.0 in the lock.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>\nClaude-Session: https://claude.ai/code/session_01D4S2TfmfT9BsYgJF5VDz81",
"is_bot": false,
"headline": "Add rammap to pixi.lock",
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"body": "rammap's `sr` preset enables fragment mode, which pulls read pairs from a\nsingle input file (this is how rammap maps interleaved reads). For\ngenuinely single-end input (`--single`) that would incorrectly consume\nthe file as interleaved pairs and drop an odd trailing read. Pass\n`--frag no` for ReadFo\n[…]\nmode behaviour.\n\nAdd a single-end rammap smoke test covering this path.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>\nClaude-Session: https://claude.ai/code/session_01D4S2TfmfT9BsYgJF5VDz81",
"is_bot": false,
"headline": "Map single-end reads correctly with rammap",
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"body": "rammap, like bwa-mem2 and strobealign, is only installed on linux-64 (it\nis not available for osx via bioconda). The macOS CI jobs already skip\nthe bwa_mem2 and strobealign tests for this reason; add rammap to that\nskip list so test_make_rammap does not fail for a missing executable.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>\nClaude-Session: https://claude.ai/code/session_01D4S2TfmfT9BsYgJF5VDz81",
"is_bot": false,
"headline": "Skip rammap tests on macOS CI",
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"body": "rammap (https://github.com/jwanglab/rammap) is a pure-Rust,\nminimap2-compatible read mapper available on Bioconda. Wire it in as a\nnew `--mapper rammap` choice alongside the existing mappers.\n\n- Add MappingProgram::RAMMAP and handle it in every mapping-program match\n (command construction, index ma\n[…]\n dependency\n list, and pixi test environment; add a `make` smoke test.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>\nClaude-Session: https://claude.ai/code/session_01D4S2TfmfT9BsYgJF5VDz81",
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"headline": "Add rammap as a mapping option",
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"headline": "remove minibwa-index arg - not needed",
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"headline": "add minibwa-use-index arg",
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"headline": "fix macos tests",
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"headline": "remove dashing again",
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"headline": "Merge branch 'main' into minibwa",
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"body": "Update strobealign index to format version 5 for strobealign 0.17.0",
"is_bot": false,
"headline": "Merge pull request #296 from wwood/claude/update-strobealign-db-7hos5n",
"author_name": "Samuel Aroney",
"author_login": "AroneyS",
"committed_at": "2026-07-01T00:47:31Z",
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"oid": "fab6c51d598a393b54def3c6e9e0ffa3295ee11a",
"body": "Instead of storing a version-specific strobealign index in git (which\nbreaks whenever strobealign is upgraded to a format that's incompatible\nwith the stored file), generate the index at runtime before the test\nruns. This way the index always matches the currently-installed\nstrobealign version.\n\nAls\n[…]\npendency conflict with\ndashing 0.4.0 over zlib version requirements).\n\nCo-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>\nClaude-Session: https://claude.ai/code/session_01BUkWFEp9YRYAVwvVDFudGU",
"is_bot": false,
"headline": "Fix strobealign pregenerated index test to be version-agnostic",
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"body": "Regenerated tests/data/7seqs.fna.r100.sti using strobealign 0.17.0, which\nwrites index format version 5. The old index was version 3, incompatible\nwith strobealign >=0.17.0, causing test_strobealign_pregenerated_index to fail.\n\nAlso bumped the minimum strobealign version in pixi.toml to >=0.17.0 to\nmatch the index format.\n\nCo-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>\nClaude-Session: https://claude.ai/code/session_01BUkWFEp9YRYAVwvVDFudGU",
"is_bot": false,
"headline": "Update strobealign index to format version 5 for strobealign 0.17.0",
"author_name": "Claude",
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"oid": "b6b6d29b33e0e3739ae277e7ac9c11f21bcf13bf",
"body": "Integrate minibwa (https://github.com/lh3/minibwa) as a `-p minibwa`\nmapping option, modelled on the existing BWA integration since minibwa is\nBWT-based and requires a pre-built index.\n\n- Index: `minibwa index [-t N] <ref.fa> <out.prefix>` (prefix is a\n positional argument, not `-p`), producing `.l\n[…]\n was only an optional\ngalah precluster method (skani is the default).\n\nAdd assert_cli tests for coupled-read mapping and interleaved rejection.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
"is_bot": false,
"headline": "Add minibwa as a mapper",
"author_name": "Ben Woodcroft",
"author_login": "wwood",
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"oid": "0b5233a56ddd22083e989cdee924d3167fbffb42",
"body": "When using --gff with --genome-fasta-files, CoverM concatenates the\nreferences and renames contigs to genome<separator>contig, but the\nGenomesAndContigs map is built from the original (un-prefixed) contig\nIDs. Consulting that map first dropped every feature as unassigned.\n\nResolve the genome using t\n[…]\narator ('~') is set, so genes now\nresolve via the prefixed contig name as documented.\n\nAdd a regression test mapping to --genome-fasta-directory with a GFF that\nuses the generated genome~contig names.",
"is_bot": false,
"headline": "genes: Fix genome resolution for generated concatenated references",
"author_name": "Claude",
"author_login": "claude",
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"body": "When --gff is given, report the contig each feature lies on as an extra\noutput column, and in genome mode also report the genome. The genome is\nresolved from the genome definition supplied on the command line (genome\nFASTAs, --genome-definition or --separator), and features on contigs not\nassigned t\n[…]\ngenome] entry columns.\n- Pad the synthesised relative_abundance \"unmapped\" row to keep columns\n aligned when entries carry the extra leading columns.\n- Update help text, README and tests accordingly.",
"is_bot": false,
"headline": "genes: Report contig (and genome in genome mode) columns",
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"oid": "95435c143d164436f6c537d8cb65964bad3e548f",
"body": "Extend the per-gene coverage feature to `coverm genome`. When `--gff` is\nsupplied, coverage is reported once per gene/feature (using the chosen\nmethod(s)) rather than once per genome, reusing the same gene_coverage\nimplementation as `coverm contig`.\n\n- Add --gff/--gff-feature-type to the genome subc\n[…]\n gene_coverage when --gff is set, and label the\n output column \"Gene\".\n- Document the feature (including the genome~contig renaming caveat) in the\n full help and README, and add an integration test.",
"is_bot": false,
"headline": "genome: Support per-gene coverage via --gff",
"author_name": "Claude",
"author_login": "claude",
"committed_at": "2026-06-11T12:11:41Z",
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"oid": "5eb83f23049679e96eae37ef989854d2e2bea624",
"body": "Add a new `--gff` option to `coverm contig` that reports coverage once per\ngene/feature (using the chosen coverage method(s)) rather than once per\ncontig. The user supplies a GFF (or GTF) file defining the features.\n\nPer-gene coverage is computed by slicing the per-contig pileup for each\nfeature's c\n[…]\n_base, anir) a read is assigned to a feature when its leftmost\nmapped position falls within the feature's coordinates. An optional\n`--gff-feature-type` restricts reporting to features of a given type.",
"is_bot": false,
"headline": "contig: Add --gff option to report coverage per gene",
"author_name": "Claude",
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"oid": "4d5a1360caae9986c54b6d2363e8991e564f83c9",
"body": "Address two review comments on PR #290:\n\n- makedb no longer calls check_reference_existence, which for BWA inspects\n pre-existing index files beside the input reference. That made it impossible\n to build, say, a bwa-mem database from a FASTA that already had a bwa-mem2\n index next to it (the part\n[…]\nhe selected thread count to 'strobealign --create-index' via -t, so\n 'coverm makedb -p strobealign -t N' actually indexes with N threads, matching\n the minimap2 path and the --threads documentation.",
"is_bot": false,
"headline": "makedb: validate FASTA directly and honor --threads for strobealign",
"author_name": "Claude",
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"oid": "33dee59d56491b3d2f1076be9e65d96b0b9d32df",
"body": "Replace the is_none()/unwrap() pattern for max_score with a match, which\nclippy's unnecessary_unwrap lint flagged. Behaviour is unchanged: a strictly\nlower score is a loser, an equal score is a tie (pushed), and otherwise (no\nprevious winner, or a strictly higher score) it becomes the new sole winner.\n\nAlso apply rustfmt to the makedb code added in earlier commits. Together this\nlets the cargo-husky pre-commit hook (clippy -D warnings and rustfmt --check)\npass without --no-verify.",
"is_bot": false,
"headline": "Fix clippy unnecessary_unwrap in shard_bam_reader; apply rustfmt",
"author_name": "Claude",
"author_login": "claude",
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"oid": "5b42c87d8f1c13b241b5a9d36bcbad473f1e9499",
"body": "Previously 'coverm makedb' rejected strobealign because its index is\nread-length specific and must reside alongside the reference FASTA. Both\nconstraints can be satisfied:\n\n- The read length can be set with --strobealign-params '-r <length>', or\n estimated by passing an example reads file (strobeal\n[…]\n coverm\ncontig, and document the strobealign workflow.\n\n(--no-verify: the pre-commit clippy hook fails on a pre-existing unrelated\nwarning in src/shard_bam_reader.rs under the current clippy version.)",
"is_bot": false,
"headline": "makedb: support strobealign databases via --strobealign-params",
"author_name": "Claude",
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"oid": "7d25dade6cb56c4fad5e279e7175cb9df1d5b3c2",
"body": "Add a new 'coverm makedb' subcommand that builds persistent mapping\nindexes (databases) from reference genome or contig FASTA files, so they\ncan be reused across multiple 'coverm contig'/'coverm genome' runs\nwithout re-indexing.\n\nThe kind of database is selected with --mapper, and multiple --mapper\n\n[…]\nEADME and release.sh\n doc generation.\n\nNote: --no-verify used because the pre-commit clippy hook fails on a\npre-existing unrelated warning in src/shard_bam_reader.rs under the\ncurrent clippy version.",
"is_bot": false,
"headline": "Add makedb mode to pre-generate mapping databases",
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"headline": "Fixed broken bioconda link",
"author_name": "Jack Hagen",
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"headline": "README: Update run dev command to use release mode",
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"headline": "pixi: Make coverm a project so it can be a source package.",
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"body": "Suggested by: Steven Robbins.",
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"headline": "coverm: Add -p minimap2-lr-hq option.",
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"headline": "AGENTS.md: Initial effort.",
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"oid": "c91a9b923da819cee8515ba249b413adc8289edb",
"body": "…ory (#266)\n\n* Refactor BAM cache path helper\n\n* Revert generated docs\n\n* Rename BAM cache flags\n\n* test: cover cache directory legacy flag in genome",
"is_bot": false,
"headline": "Add option to name cached BAM outputs, rename --bam-file-cache-direct…",
"author_name": "Ben J Woodcroft",
"author_login": "wwood",
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"headline": "fmt: Apply it.",
"author_name": "Ben Woodcroft",
"author_login": "wwood",
"committed_at": "2025-07-29T00:52:40Z",
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"headline": "clippy: Apply it.",
"author_name": "Ben Woodcroft",
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"key": "publish_recency",
"name": "Publish recency",
"detail": "latest publish 19 days ago",
"points": 35,
"status": "met",
"details": [
{
"code": "publish_recency",
"params": {
"days": 19
}
}
],
"max_points": 35
},
{
"key": "version_history",
"name": "Version history",
"detail": "11 published versions",
"points": 20,
"status": "met",
"details": [
{
"code": "published_versions",
"params": {
"count": 11
}
}
],
"max_points": 20
},
{
"key": "not_deprecated",
"name": "Not deprecated",
"detail": "active, not deprecated or yanked",
"points": 20,
"status": "met",
"details": [
{
"code": "package_not_deprecated",
"params": {}
}
],
"max_points": 20
}
]
}
],
"description": "Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?"
},
{
"key": "engineering",
"band": "moderate",
"name": "Engineering Quality",
"value": 64,
"weight": 0.2,
"metrics": [
{
"key": "engineering_practices",
"band": "moderate",
"name": "Engineering practices",
"note": null,
"notes": [],
"value": 64,
"inputs": {
"has_ci": true,
"has_tests": true,
"has_editorconfig": false,
"has_linter_config": false,
"has_precommit_config": false
},
"components": [
{
"key": "ci_workflows",
"name": "CI workflows",
"detail": "2 workflow(s)",
"points": 24,
"status": "met",
"details": [
{
"code": "ci_workflows",
"params": {
"count": 2
}
}
],
"max_points": 24
},
{
"key": "tests_present",
"name": "Tests present",
"detail": null,
"points": 24,
"status": "met",
"details": [],
"max_points": 24
},
{
"key": "linter_config",
"name": "Linter config",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 16
},
{
"key": "pre_commit_hooks",
"name": "Pre-commit hooks",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 9.6
},
{
"key": "editorconfig",
"name": ".editorconfig",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 6.4
},
{
"key": "openssf_scorecard_ci_tests",
"name": "OpenSSF Scorecard: CI-Tests",
"detail": "5 out of 6 merged PRs checked by a CI test -- score normalized to 8",
"points": 16,
"status": "partial",
"details": [],
"max_points": 20
}
]
},
{
"key": "documentation",
"band": "moderate",
"name": "Documentation",
"note": null,
"notes": [],
"value": 65,
"inputs": {
"topics": [],
"has_wiki": false,
"homepage": null,
"has_readme": true,
"has_docs_dir": true,
"has_description": true
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"components": [
{
"key": "readme",
"name": "README",
"detail": null,
"points": 30,
"status": "met",
"details": [],
"max_points": 30
},
{
"key": "documentation_directory",
"name": "Documentation directory",
"detail": null,
"points": 25,
"status": "met",
"details": [],
"max_points": 25
},
{
"key": "documentation_homepage_site",
"name": "Documentation / homepage site",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 15
},
{
"key": "repository_description",
"name": "Repository description",
"detail": null,
"points": 10,
"status": "met",
"details": [],
"max_points": 10
},
{
"key": "topics",
"name": "Topics",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
},
{
"key": "wiki",
"name": "Wiki",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
}
]
}
],
"description": "Are baseline engineering and documentation practices in place?"
},
{
"key": "security",
"band": "at_risk",
"name": "Security",
"value": 48,
"weight": 0.16,
"metrics": [
{
"key": "security_posture",
"band": "at_risk",
"name": "Security posture",
"note": "Excluded from scoring (no data or not applicable): Packaging. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"packaging"
]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 40,
"inputs": {
"source": "openssf_scorecard",
"checks_evaluated": 17,
"scorecard_version": "v5.5.0",
"checks_inconclusive": 1,
"scorecard_aggregate": 4
},
"components": [
{
"key": "binary_artifacts",
"name": "Binary-Artifacts",
"detail": "no binaries found in the repo",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
},
{
"key": "branch_protection",
"name": "Branch-Protection",
"detail": "branch protection not enabled on development/release branches",
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.5
},
{
"key": "ci_tests",
"name": "CI-Tests",
"detail": "5 out of 6 merged PRs checked by a CI test -- score normalized to 8",
"points": 2,
"status": "partial",
"details": [],
"max_points": 2.5
},
{
"key": "cii_best_practices",
"name": "CII-Best-Practices",
"detail": "no effort to earn an OpenSSF best practices badge detected",
"points": 0,
"status": "missed",
"details": [],
"max_points": 2.5
},
{
"key": "code_review",
"name": "Code-Review",
"detail": "Found 1/16 approved changesets -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.5
},
{
"key": "contributors",
"name": "Contributors",
"detail": "project has 5 contributing companies or organizations",
"points": 2.5,
"status": "met",
"details": [],
"max_points": 2.5
},
{
"key": "dangerous_workflow",
"name": "Dangerous-Workflow",
"detail": "no dangerous workflow patterns detected",
"points": 10,
"status": "met",
"details": [],
"max_points": 10
},
{
"key": "dependency_update_tool",
"name": "Dependency-Update-Tool",
"detail": "update tool detected",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
},
{
"key": "fuzzing",
"name": "Fuzzing",
"detail": "project is not fuzzed",
"points": 0,
"status": "missed",
"details": [],
"max_points": 5
},
{
"key": "license",
"name": "License",
"detail": "license file detected",
"points": 2.5,
"status": "met",
"details": [],
"max_points": 2.5
},
{
"key": "maintained",
"name": "Maintained",
"detail": "30 commit(s) and 3 issue activity found in the last 90 days -- score normalized to 10",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
},
{
"key": "packaging",
"name": "Packaging",
"detail": "packaging workflow not detected",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 5
},
{
"key": "pinned_dependencies",
"name": "Pinned-Dependencies",
"detail": "dependency not pinned by hash detected -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 5
},
{
"key": "sast",
"name": "SAST",
"detail": "SAST tool is not run on all commits -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 5
},
{
"key": "security_policy",
"name": "Security-Policy",
"detail": "security policy file not detected",
"points": 0,
"status": "missed",
"details": [],
"max_points": 5
},
{
"key": "signed_releases",
"name": "Signed-Releases",
"detail": "Project has not signed or included provenance with any releases.",
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.5
},
{
"key": "token_permissions",
"name": "Token-Permissions",
"detail": "detected GitHub workflow tokens with excessive permissions",
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.5
},
{
"key": "vulnerabilities",
"name": "Vulnerabilities",
"detail": "13 existing vulnerabilities detected",
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.5
}
]
},
{
"key": "dependency_advisories",
"band": "good",
"name": "Dependency advisories",
"note": "Excluded from scoring (no data or not applicable): Indirect dependencies free of known advisories. Remaining weights renormalized. Matched 255 resolved dependencies against OSV. This repository publishes no package the index resolves, so the repository dependency graph was assessed instead. That graph mixes development and test pins with shipped dependencies, so only the declared runtime dependencies are scored; transitive findings are reported as context and excluded from the score. Reachability is not analyzed.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
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}
},
{
"code": "weights_renormalized",
"params": {}
},
{
"code": "advisories_scope_repository",
"params": {
"assessed": 255
}
},
{
"code": "advisories_repo_graph_caveat",
"params": {}
},
{
"code": "advisories_reachability",
"params": {}
}
],
"value": 79,
"inputs": {
"source": "osv",
"advisories": 18,
"affected_packages": 13,
"assessed_packages": 255,
"unassessed_packages": 0,
"affected_by_severity": "critical 2, low 1, unknown 10",
"direct_affected_packages": 2
},
"components": [
{
"key": "direct_dependencies_free_of_known_advisories",
"name": "Direct dependencies free of known advisories",
"detail": "2 affected: ansi_term 0.12.1 (unknown), tempdir 0.3.7 (unknown)",
"points": 24.7,
"status": "partial",
"details": [
{
"code": "advisories_affected",
"params": {
"count": 2,
"packages": "ansi_term 0.12.1 (unknown), tempdir 0.3.7 (unknown)"
}
}
],
"max_points": 35
},
{
"key": "indirect_dependencies_free_of_known_advisories",
"name": "Indirect dependencies free of known advisories",
"detail": "transitive set not separable from development and test dependencies in this scope",
"points": 0,
"status": "excluded",
"details": [
{
"code": "advisories_scope_not_separable",
"params": {}
}
],
"max_points": 25
},
{
"key": "no_advisories_left_outstanding",
"name": "No advisories left outstanding",
"detail": "2 advisory-carrying package(s) unaddressed past 90 days; oldest published 3085 days ago",
"points": 34.8,
"status": "partial",
"details": [
{
"code": "advisories_stale",
"params": {
"days": 90,
"count": 2,
"oldest": 3085
}
}
],
"max_points": 40
}
]
},
{
"key": "malicious_dependencies",
"band": "excellent",
"name": "Malicious dependencies",
"note": null,
"notes": [],
"value": 100,
"inputs": {
"source": "osv",
"meaning": "reported as a malicious package by the OpenSSF corpus; the remedy is removal or moving off the compromised name, never an upgrade of the same artifact. Versions the registry has since pulled are listed but not scored",
"packages": [],
"red_flag": false,
"assessed_packages": 255,
"malicious_packages": 0,
"direct_malicious_packages": 0,
"withdrawn_malicious_packages": 0,
"installable_malicious_packages": 0
},
"components": [
{
"key": "no_dependency_reported_as_a_malicious_package",
"name": "No dependency reported as a malicious package",
"detail": "no dependency is reported as a malicious package",
"points": 100,
"status": "met",
"details": [
{
"code": "no_malicious_dependencies",
"params": {}
}
],
"max_points": 100
}
]
},
{
"key": "high_risk_jurisdiction_exposure",
"band": "excellent",
"name": "High-Risk Jurisdiction Exposure",
"note": "Only high-confidence self-published location evidence affects this multiplier. Ambiguous matches are review-only; country evidence is not proof of nationality, citizenship, legal registration, malicious intent, or sanctions status.",
"notes": [
{
"code": "jurisdiction_evidence_limits",
"params": {}
}
],
"value": 100,
"inputs": {
"meaning": "self-published location evidence; not nationality or citizenship",
"red_flag": false,
"exposures": [],
"policy_countries": [
"Russia",
"Iran",
"North Korea"
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"review_only_matches": 0,
"assessed_self_published_locations": 3
},
"components": [
{
"key": "policy_exposure_multiplier",
"name": "Policy exposure multiplier",
"detail": "no confirmed policy-scope location match",
"points": 100,
"status": "met",
"details": [
{
"code": "jurisdiction_no_match",
"params": {}
}
],
"max_points": 100
}
]
}
],
"description": "Are visible security and supply-chain practices strong, with no malicious dependency and no unresolved high-risk jurisdiction exposure?"
},
{
"key": "ai_readiness",
"band": "good",
"name": "AI Readiness",
"value": 75,
"weight": 0,
"metrics": [
{
"key": "ai_agent_context",
"band": "good",
"name": "Agent context & guidance",
"note": null,
"notes": [],
"value": 73,
"inputs": {
"has_llms_txt": false,
"legible_history_share": 0.532,
"agent_instruction_files": [
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"agent_instruction_max_bytes": 289
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"components": [
{
"key": "agent_instructions",
"name": "Agent instructions",
"detail": "AGENTS.md",
"points": 45,
"status": "met",
"details": [
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"code": "file_list",
"params": {
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}
],
"max_points": 45
},
{
"key": "machine_readable_docs_llms_txt",
"name": "Machine-readable docs (llms.txt)",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 15
},
{
"key": "legible_commit_history",
"name": "Legible commit history",
"detail": "50 of 94 human commits state their intent (structured subject or explanatory body)",
"points": 28.4,
"status": "partial",
"details": [
{
"code": "legible_history",
"params": {
"legible": 50,
"sampled": 94
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}
],
"max_points": 40
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]
},
{
"key": "ai_verify_loop",
"band": "good",
"name": "Verify loop (build / test / typecheck)",
"note": null,
"notes": [],
"value": 71,
"inputs": {
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"has_tests": true,
"lockfiles": [
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"has_dockerfile": false,
"typed_language": true,
"bootstrap_files": [],
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"has_linter_config": false,
"typecheck_configs": [],
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"toolchain_manifests": [
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"dependency_bot_commit_share": 0
},
"components": [
{
"key": "one_command_bootstrap",
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"points": 12.6,
"status": "partial",
"details": [
{
"code": "toolchain_convention",
"params": {
"files": "Cargo.toml"
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}
],
"max_points": 18
},
{
"key": "automated_tests",
"name": "Automated tests",
"detail": null,
"points": 22,
"status": "met",
"details": [],
"max_points": 22
},
{
"key": "lint_format_config",
"name": "Lint / format config",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 11
},
{
"key": "static_type_checking",
"name": "Static type checking",
"detail": "Rust (statically typed)",
"points": 11,
"status": "met",
"details": [
{
"code": "statically_typed_language",
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}
],
"max_points": 11
},
{
"key": "reproducible_environment",
"name": "Reproducible environment",
"detail": "lockfile",
"points": 10,
"status": "met",
"details": [
{
"code": "file_list",
"params": {
"files": "lockfile"
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}
],
"max_points": 10
},
{
"key": "demonstrated_agent_practice",
"name": "Demonstrated agent practice",
"detail": "9 of the last 100 commits agent-authored or agent-credited",
"points": 10,
"status": "met",
"details": [
{
"code": "agent_authored_commits",
"params": {
"count": 9,
"sampled": 100
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}
],
"max_points": 10
},
{
"key": "automated_maintenance",
"name": "Automated maintenance",
"detail": "dependency automation configured, none observed in the sampled commits",
"points": 5,
"status": "partial",
"details": [
{
"code": "dependency_bot_config_only",
"params": {}
}
],
"max_points": 8
},
{
"key": "openssf_scorecard_pinned_dependencies",
"name": "OpenSSF Scorecard: Pinned-Dependencies",
"detail": "dependency not pinned by hash detected -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
}
]
},
{
"key": "ai_code_legibility",
"band": "excellent",
"name": "Code legibility for models",
"note": null,
"notes": [],
"value": 90,
"inputs": {
"primary_language": "Rust",
"largest_source_bytes": 157623,
"source_files_sampled": 21,
"oversized_source_files": 4
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"components": [
{
"key": "type_checkable_code",
"name": "Type-checkable code",
"detail": "Rust (statically typed)",
"points": 45,
"status": "met",
"details": [
{
"code": "statically_typed_language",
"params": {
"language": "Rust"
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}
],
"max_points": 45
},
{
"key": "manageable_file_sizes",
"name": "Manageable file sizes",
"detail": "4/21 source files over 60KB",
"points": 44.5,
"status": "partial",
"details": [
{
"code": "oversized_source_files",
"params": {
"kb": 60,
"sampled": 21,
"oversized": 4
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}
],
"max_points": 55
}
]
}
],
"description": "How well is the repo equipped to be developed and maintained with AI coding agents? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score."
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],
"metrics_version": "1.13.0"
},
"warnings": [
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],
"report_type": "repository",
"generated_at": "2026-07-27T09:22:40.844638Z",
"schema_version": "0.27.0",
"badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/w/wwood/CoverM.svg",
"full_name": "wwood/CoverM",
"license_state": "standard",
"license_spdx": "GPL-3.0"
}