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VirologyCharite/iterated-consensus

Iteratively build a consensus sequence from a BAM/FASTQ by remapping against each new consensus until convergence

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  • Python
  • ★ 0
  • commit 24047fe090a6
  • scored 2026-11-14
  • scoring prov-5+qual-2+sec-2

AI provenance

0%

possible

Confidence
43%
Coverage
100%

Estimated share of AI-generated code. Explicit attribution is a lower bound.

Code quality

63/100

weak

Confidence
90%
Coverage
100%

Complexity, duplication, lint density, tests, CI, docs and review process.

Security

74/100

adequate

Confidence
85%
Coverage
100%

Secrets, static analysis, vulnerable dependencies, CI and supply-chain posture.

AI provenance

0% possible

Weak signals consistent with AI-assisted development.

How the score is built

  • Explicitly attributed share0%
  • Unattributed share in AI-pace bursts29%
  • Estimated AI-generated share0%
  • AI tool configuration files0
  • Work sessions at AI pace1
  • Releases at AI pacenot measured
  • Coding-style index (1.0+ means possible)0.00

Lines added per month all AI-attributed share

  1. 2026-087,757 · 0% AI
  2. 2026-10228 · 0% AI

Evidence by analyzer

Explicit AI attributionok
attributed_commit_share
0.0%
attributed_commits
0
attributed_loc
0
attributed_loc_share
0.0%
commits
13
effective_loc
7,985
tools_detected
0
AI tool configurationok
artifacts
0
tools_configured
0
workflow_agents
0
Commit velocityok1 item
excluded_import_loc
3,220
flagged_loc
2,338
flagged_loc_share
49.1%
flagged_units
1
max_loc_per_hour
695.86
measured_loc
4,765
median_loc_per_hour
105.92
pr_timed_units
0
pre_ai_era_burst_loc
0
pre_ai_era_bursts
0
pre_ai_era_measured_loc
0
work_units
8
Release velocityskipped
Coding styleok
count:assistant_voice
0
count:emoji_in_code
0
count:narrated_steps
0
count:placeholder
0
files:assistant_voice
0
files:emoji_in_code
0
files:narrated_steps
0
files:placeholder
0
index
0
lines_scanned
3,269
per_kloc:assistant_voice
0
per_kloc:emoji_in_code
0
per_kloc:narrated_steps
0
per_kloc:placeholder
0

Code quality

63 weak

Code quality is weak: test-to-source ratio 1.33, no CI test run detected; 17% of function code in complex or long functions; 0% duplicated lines. Weakest area: lint.

How the score is built

  • Complexity60
  • Duplication100
  • Lint and smells37
  • Tests and CI55
  • Documentation85
  • Type safety40
  • Review processnot measured

Evidence by analyzer

Complexity (lizard)ok2 items
complex_functions
2
function_nloc
1,784
functions
115
long_functions
2
many_param_functions
3
mean_ccn
4.34
p90_ccn
9
risky_nloc_share
16.8%
Duplication (jscpd)ok
compared_lines
2,514
duplicated_lines
0
duplicated_share
0.0%
files
16
Lintok
category:best-practice
1
category:correctness
5
category:maintainability
7
findings
13
scanned_lines
3,269
weighted_findings
13
Tests and CIok
check:ci_present
no
check:ci_runs_lint
no
check:ci_runs_tests
no
check:has_tests
yes
check:test_ratio
yes
check:tests_cochange
yes
ci_files
0
cochange_commits
11
cochange_share
90.9%
source_lines
3,269
test_lines
4,338
test_ratio
1.33
Documentationok3 items
  • README.md README.md
  • LICENSE LICENSE
  • CHANGELOG.md CHANGELOG.md
check:changelog
yes
check:contributing
no
check:license
yes
check:readme
yes
readme_lines
629
Type safetyok
check:low_escape_density
yes
check:strict_config
no
escapes
2
escapes_per_kloc
0.62

Security

74 adequate

Security posture is adequate: 31 known vulnerabilities in 2 dependencies; 3 high-severity SAST findings. Weakest area: posture.

How the score is built

  • Secrets100
  • Static analysis (SAST)76
  • Vulnerable dependencies77
  • CI workflowsnot measured
  • Security posture0
  • OpenSSF Scorecardnot measured

Evidence by analyzer

OpenSSF Scorecardskipped

no published OpenSSF Scorecard result for this repo

Package registriesok
checked
8
declared
8
lookup_errors
0
missing
0
recent
0
Secrets (gitleaks)ok
secrets_current
0
secrets_history
0
secrets_low_confidence
0
secrets_nonprod
0
Static analysis (opengrep)ok
findings
4
findings_high
3
findings_low
0
findings_medium
1
parse_errors
0
scanned_lines
3,269
weighted_findings
2.50
Dependencies (osv-scanner)ok
penalty
16
vulnerabilities
31
vulnerable_packages
2
vulns_critical
0
vulns_high
11
vulns_low
5
vulns_medium
15
vulns_unknown
0
CI workflows (zizmor)skipped
Security postureok
check:dependency_updates
no
check:lockfiles
yes
check:security_policy
no
check:signed_commits
no
signed_commit_share
0.0%
unpinned_manifests
0
Release downloadsok
binary_assets
0
signals
0
suspicious
0

Findings

14 high29 medium5 low

SeverityRuleLocationMessageTool
high opengrep/python.lang.security.audit.dangerous-subprocess-use-audit src/iterated_consensus/commands.py:106 Detected subprocess function 'run' without a static string. If this data can be controlled by a malicious actor, it may be an instance of command injection. Audit the use of this call to ensure it is not controllable by an external... Static analysis (opengrep)
high opengrep/python.lang.security.audit.dangerous-subprocess-use-audit src/iterated_consensus/commands.py:53 Detected subprocess function 'run' without a static string. If this data can be controlled by a malicious actor, it may be an instance of command injection. Audit the use of this call to ensure it is not controllable by an external... Static analysis (opengrep)
high opengrep/python.lang.security.audit.dangerous-subprocess-use-audit src/iterated_consensus/commands.py:59 Detected subprocess function 'run' without a static string. If this data can be controlled by a malicious actor, it may be an instance of command injection. Audit the use of this call to ensure it is not controllable by an external... Static analysis (opengrep)
high osv/GHSA-394h-qwmc-48pf uv.lock [email protected] (PyPI) is affected by GHSA-394h-qwmc-48pf Dependencies (osv-scanner)
high osv/GHSA-5vjq-rrrf-7h2q uv.lock [email protected] (PyPI) is affected by GHSA-5vjq-rrrf-7h2q Dependencies (osv-scanner)
high osv/GHSA-6w3r-xr62-4xcp uv.lock [email protected] (PyPI) is affected by GHSA-6w3r-xr62-4xcp Dependencies (osv-scanner)
high osv/GHSA-8rjx-v5ww-45pp uv.lock [email protected] (PyPI) is affected by GHSA-8rjx-v5ww-45pp Dependencies (osv-scanner)
high osv/GHSA-94p9-xgh2-xp45 uv.lock [email protected] (PyPI) is affected by PYSEC-2026-4011, GHSA-94p9-xgh2-xp45 Dependencies (osv-scanner)
high osv/GHSA-c947-3pg5-gm8q uv.lock [email protected] (PyPI) is affected by GHSA-c947-3pg5-gm8q Dependencies (osv-scanner)
high osv/GHSA-c978-59m8-c77v uv.lock [email protected] (PyPI) is affected by GHSA-c978-59m8-c77v Dependencies (osv-scanner)
high osv/GHSA-p58f-9548-mpm2 uv.lock [email protected] (PyPI) is affected by PYSEC-2026-4013, GHSA-p58f-9548-mpm2 Dependencies (osv-scanner)
high osv/GHSA-v4x8-3wr5-3wq8 uv.lock [email protected] (PyPI) is affected by GHSA-v4x8-3wr5-3wq8 Dependencies (osv-scanner)
high osv/GHSA-vxj4-q4g9-crj7 uv.lock [email protected] (PyPI) is affected by GHSA-vxj4-q4g9-crj7 Dependencies (osv-scanner)
high osv/GHSA-x78j-v8h9-3j2q uv.lock [email protected] (PyPI) is affected by PYSEC-2026-4014, GHSA-x78j-v8h9-3j2q Dependencies (osv-scanner)
medium opengrep/python.lang.maintainability.is-function-without-parentheses src/iterated_consensus/bam.py:148 Is "is_unmapped" a function or an attribute? If it is a function, you may have meant read.is_unmapped() because read.is_unmapped is always true. Lint
medium opengrep/python.lang.maintainability.is-function-without-parentheses src/iterated_consensus/bam.py:148 Is "is_secondary" a function or an attribute? If it is a function, you may have meant read.is_secondary() because read.is_secondary is always true. Lint
medium opengrep/python.lang.maintainability.is-function-without-parentheses src/iterated_consensus/bam.py:149 Is "is_supplementary" a function or an attribute? If it is a function, you may have meant read.is_supplementary() because read.is_supplementary is always true. Lint
medium opengrep/python.lang.maintainability.is-function-without-parentheses src/iterated_consensus/commands.py:107 Is "is_shell" a function or an attribute? If it is a function, you may have meant rendered.is_shell() because rendered.is_shell is always true. Lint
medium opengrep/python.lang.maintainability.is-function-without-parentheses src/iterated_consensus/commands.py:53 Is "is_shell" a function or an attribute? If it is a function, you may have meant cmd.is_shell() because cmd.is_shell is always true. Lint
medium opengrep/python.lang.maintainability.is-function-without-parentheses src/iterated_consensus/commands.py:61 Is "is_shell" a function or an attribute? If it is a function, you may have meant cmd.is_shell() because cmd.is_shell is always true. Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list src/iterated_consensus/report.py:111 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list src/iterated_consensus/report.py:118 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list src/iterated_consensus/report.py:210 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.best-practice.manual-defaultdict-list-create src/iterated_consensus/report.py:233 manually creating a defaultdict - use collections.defaultdict(list) Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list src/iterated_consensus/report.py:97 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.maintainability.is-function-without-parentheses src/iterated_consensus/runner.py:253 Is "is_whole_file" a function or an attribute? If it is a function, you may have meant resolved.is_whole_file() because resolved.is_whole_file is always true. Lint
medium opengrep/python.lang.correctness.common-mistakes.string-concat-in-list src/iterated_consensus/runner.py:485 Detected strings that are implicitly concatenated inside a list. Python will implicitly concatenate strings when not explicitly delimited. Was this supposed to be individual elements of the list? Lint
medium opengrep/python.lang.security.audit.dynamic-urllib-use-detected src/iterated_consensus/reference.py:121 Detected a dynamic value being used with urllib. urllib supports 'file://' schemes, so a dynamic value controlled by a malicious actor may allow them to read arbitrary files. Audit uses of urllib calls to ensure user data cannot control... Static analysis (opengrep)
medium osv/GHSA-43mp-35q3-x3fq uv.lock [email protected] (PyPI) is affected by GHSA-43mp-35q3-x3fq Dependencies (osv-scanner)
medium osv/GHSA-558c-9hv2-4prj uv.lock [email protected] (PyPI) is affected by GHSA-558c-9hv2-4prj Dependencies (osv-scanner)
medium osv/GHSA-6627-m3xw-93mp uv.lock [email protected] (PyPI) is affected by GHSA-6627-m3xw-93mp Dependencies (osv-scanner)
medium osv/GHSA-69hj-f68j-2879 uv.lock [email protected] (PyPI) is affected by GHSA-69hj-f68j-2879 Dependencies (osv-scanner)
medium osv/GHSA-8mx5-7m5m-r77g uv.lock [email protected] (PyPI) is affected by GHSA-8mx5-7m5m-r77g Dependencies (osv-scanner)
medium osv/GHSA-9c4x-gm8v-wgc4 uv.lock [email protected] (PyPI) is affected by GHSA-9c4x-gm8v-wgc4 Dependencies (osv-scanner)
medium osv/GHSA-9h9j-4vrj-gf7g uv.lock [email protected] (PyPI) is affected by PYSEC-2026-4012, GHSA-9h9j-4vrj-gf7g Dependencies (osv-scanner)
medium osv/GHSA-cw65-gx24-rc82 uv.lock [email protected] (PyPI) is affected by GHSA-cw65-gx24-rc82 Dependencies (osv-scanner)
medium osv/GHSA-cwqr-hh33-gh44 uv.lock [email protected] (PyPI) is affected by GHSA-cwqr-hh33-gh44 Dependencies (osv-scanner)
medium osv/GHSA-fc2g-4w5p-6whm uv.lock [email protected] (PyPI) is affected by GHSA-fc2g-4w5p-6whm Dependencies (osv-scanner)
medium osv/GHSA-fq56-3cx3-fjxp uv.lock [email protected] (PyPI) is affected by GHSA-fq56-3cx3-fjxp Dependencies (osv-scanner)
medium osv/GHSA-hhxq-47xx-j5xx uv.lock [email protected] (PyPI) is affected by GHSA-hhxq-47xx-j5xx Dependencies (osv-scanner)
medium osv/GHSA-j8f7-rjxc-mr56 uv.lock [email protected] (PyPI) is affected by GHSA-j8f7-rjxc-mr56 Dependencies (osv-scanner)
medium osv/GHSA-m462-7rxw-wvpg uv.lock [email protected] (PyPI) is affected by GHSA-m462-7rxw-wvpg Dependencies (osv-scanner)
medium osv/GHSA-rfpc-qcw5-3pc4 uv.lock [email protected] (PyPI) is affected by GHSA-rfpc-qcw5-3pc4 Dependencies (osv-scanner)
low osv/GHSA-494p-63j8-28p3 uv.lock [email protected] (PyPI) is affected by GHSA-494p-63j8-28p3 Dependencies (osv-scanner)
low osv/GHSA-567q-5qvw-pf92 uv.lock [email protected] (PyPI) is affected by GHSA-567q-5qvw-pf92 Dependencies (osv-scanner)
low osv/GHSA-9vhv-jxww-xfm5 uv.lock [email protected] (PyPI) is affected by GHSA-9vhv-jxww-xfm5 Dependencies (osv-scanner)
low osv/GHSA-cx28-75q4-x26q uv.lock [email protected] (PyPI) is affected by GHSA-cx28-75q4-x26q Dependencies (osv-scanner)
low osv/GHSA-qmx5-4p3x-wvqf uv.lock [email protected] (PyPI) is affected by GHSA-qmx5-4p3x-wvqf Dependencies (osv-scanner)

Tools and coverage

Every analyzer that ran on this commit. A failed or skipped tool is a coverage gap: its share of the score is left out and the coverage figure drops.

AnalyzerPillarStatusVersionFindingsNote
AI tool configurationAI provenanceoksignatures-v10
Explicit AI attributionAI provenanceoksignatures-v10
Release velocityAI provenanceskipped—0
Coding styleAI provenanceok—0
Commit velocityAI provenanceokprov-40
Complexity (lizard)Code qualityoklizard 1.25.10
DocumentationCode qualityok—0
Duplication (jscpd)Code qualityokrepotrust-dup-w60
LintCode qualityokopengrep 1.33.1; rules f1d2b562b41413
Tests and CICode qualityok—0
Type safetyCode qualityok—0
CI workflows (zizmor)Securityskipped—0
Dependencies (osv-scanner)Securityokosv-scanner version: 2.7.131
Release downloadsSecurityok—0
Security postureSecurityok—0
Package registriesSecurityok—0
Static analysis (opengrep)Securityokopengrep 1.33.1; rules f1d2b562b4144
OpenSSF ScorecardSecurityskipped—0no published OpenSSF Scorecard result for this repo
Secrets (gitleaks)Securityokgitleaks 8.30.10

Score history

Scores from different scoring versions aren't directly comparable.

ScoredCommitScoringAI provenanceQualitySecurity
2026-11-1424047fe090a6prov-5+qual-2+sec-20%6374
2026-11-1424047fe090a6prov-4+qual-2+sec-20%6374

Embed a badge

Maintainers can show these in a README. Badges update when the repository is re-scored.

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[![RepoTrust quality](https://repotrust.synapticcyber.com/badge/github.com/VirologyCharite/iterated-consensus/quality.svg)](https://repotrust.synapticcyber.com/r/github.com/VirologyCharite/iterated-consensus/)
[![RepoTrust security](https://repotrust.synapticcyber.com/badge/github.com/VirologyCharite/iterated-consensus/security.svg)](https://repotrust.synapticcyber.com/r/github.com/VirologyCharite/iterated-consensus/)
Full text report

Scores

Pillar Score Signal Confidence Coverage
AI provenance (estimated AI-generated share) 0 possible 43% 100%
Code quality 63 weak 90% 100%
Security 74 adequate 85% 100%

AI provenance

Weak signals consistent with AI-assisted development.

  • Explicitly attributed share (lower bound): 0.0%
  • Unattributed share in AI-consistent velocity bursts: 29.3%
  • Estimated AI-generated share: 0.0%
Month Lines added Attributed to AI
2026-08 7,757 0%
2026-10 228 0%

Evidence

  • 2,338 lines of first-party code in ~4.0h (584 lines/hour, 1 commit session) (cbe7133b9a2d)

AI provenance describes how code was produced; it is not a quality judgment. Unless attribution is explicit, these are signals consistent with AI generation, not proof. Squash/rebase workflows, imported code, and rewritten history reduce accuracy.

Code quality

Code quality is weak: test-to-source ratio 1.33, no CI test run detected; 17% of function code in complex or long functions; 0% duplicated lines. Weakest area: lint.

Area Score
Complexity (lizard) 60
Duplication 100
Code smells (Opengrep) 37
Tests and CI 55
Documentation 85
Type safety 40
Process (Scorecard review/maintenance) n/a
  • Functions: 115; mean complexity 4.3, 90th percentile 9; 2 complex and 2 long functions
  • Duplicated lines: 0.0% of 2,514 compared
  • Tests: 4,338 test lines for 3,269 source lines (ratio 1.33); CI test commands: none detected; 91% of recent source commits also change tests
  • Docs missing or thin: contributing

Most complex functions:

Security

Security posture is adequate: 31 known vulnerabilities in 2 dependencies; 3 high-severity SAST findings. Weakest area: posture.

Area Score
Secrets (gitleaks, tree + history) 100
Static analysis (Opengrep) 76
Vulnerable dependencies (OSV) 77
CI workflows (zizmor) n/a
Posture (policy, updates, signing, lockfiles) 0
OpenSSF Scorecard n/a
  • Known vulnerabilities: 31 in 2 packages (critical 0, high 11, medium 15, low 5)

  • Posture checks passed: lockfiles; missing: security policy, dependency updates, signed commits

Top findings

Severity Finding Location
high opengrep/python.lang.security.audit.dangerous-subprocess-use-audit: Detected subprocess function 'run' without a static string. If this data can be controlled by a malicious actor, it may be an instance of command injection. Audit the use of this call to ensure it is not controllable by an external resource. You may consider using 'shlex.escape()'. [confidence low] src/iterated_consensus/commands.py:53
high opengrep/python.lang.security.audit.dangerous-subprocess-use-audit: Detected subprocess function 'run' without a static string. If this data can be controlled by a malicious actor, it may be an instance of command injection. Audit the use of this call to ensure it is not controllable by an external resource. You may consider using 'shlex.escape()'. [confidence low] src/iterated_consensus/commands.py:59
high opengrep/python.lang.security.audit.dangerous-subprocess-use-audit: Detected subprocess function 'run' without a static string. If this data can be controlled by a malicious actor, it may be an instance of command injection. Audit the use of this call to ensure it is not controllable by an external resource. You may consider using 'shlex.escape()'. [confidence low] src/iterated_consensus/commands.py:106
high osv/GHSA-v4x8-3wr5-3wq8: [email protected] (PyPI) is affected by GHSA-v4x8-3wr5-3wq8 uv.lock
high osv/GHSA-94p9-xgh2-xp45: [email protected] (PyPI) is affected by PYSEC-2026-4011, GHSA-94p9-xgh2-xp45 uv.lock
high osv/GHSA-p58f-9548-mpm2: [email protected] (PyPI) is affected by PYSEC-2026-4013, GHSA-p58f-9548-mpm2 uv.lock
high osv/GHSA-x78j-v8h9-3j2q: [email protected] (PyPI) is affected by PYSEC-2026-4014, GHSA-x78j-v8h9-3j2q uv.lock
high osv/GHSA-394h-qwmc-48pf: [email protected] (PyPI) is affected by GHSA-394h-qwmc-48pf uv.lock
high osv/GHSA-5vjq-rrrf-7h2q: [email protected] (PyPI) is affected by GHSA-5vjq-rrrf-7h2q uv.lock
high osv/GHSA-6w3r-xr62-4xcp: [email protected] (PyPI) is affected by GHSA-6w3r-xr62-4xcp uv.lock
high osv/GHSA-8rjx-v5ww-45pp: [email protected] (PyPI) is affected by GHSA-8rjx-v5ww-45pp uv.lock
high osv/GHSA-c947-3pg5-gm8q: [email protected] (PyPI) is affected by GHSA-c947-3pg5-gm8q uv.lock
high osv/GHSA-c978-59m8-c77v: [email protected] (PyPI) is affected by GHSA-c978-59m8-c77v uv.lock
high osv/GHSA-vxj4-q4g9-crj7: [email protected] (PyPI) is affected by GHSA-vxj4-q4g9-crj7 uv.lock
medium opengrep/python.lang.security.audit.dynamic-urllib-use-detected: Detected a dynamic value being used with urllib. urllib supports 'file://' schemes, so a dynamic value controlled by a malicious actor may allow them to read arbitrary files. Audit uses of urllib calls to ensure user data cannot control the URLs, or consider using the 'requests' library instead. [confidence low] src/iterated_consensus/reference.py:121
medium osv/GHSA-6627-m3xw-93mp: [email protected] (PyPI) is affected by GHSA-6627-m3xw-93mp uv.lock
medium osv/GHSA-69hj-f68j-2879: [email protected] (PyPI) is affected by GHSA-69hj-f68j-2879 uv.lock
medium osv/GHSA-8mx5-7m5m-r77g: [email protected] (PyPI) is affected by GHSA-8mx5-7m5m-r77g uv.lock
medium osv/GHSA-9c4x-gm8v-wgc4: [email protected] (PyPI) is affected by GHSA-9c4x-gm8v-wgc4 uv.lock
medium osv/GHSA-cwqr-hh33-gh44: [email protected] (PyPI) is affected by GHSA-cwqr-hh33-gh44 uv.lock
medium osv/GHSA-fq56-3cx3-fjxp: [email protected] (PyPI) is affected by GHSA-fq56-3cx3-fjxp uv.lock
medium osv/GHSA-j8f7-rjxc-mr56: [email protected] (PyPI) is affected by GHSA-j8f7-rjxc-mr56 uv.lock
medium osv/GHSA-m462-7rxw-wvpg: [email protected] (PyPI) is affected by GHSA-m462-7rxw-wvpg uv.lock
medium osv/GHSA-rfpc-qcw5-3pc4: [email protected] (PyPI) is affected by GHSA-rfpc-qcw5-3pc4 uv.lock
medium osv/GHSA-9h9j-4vrj-gf7g: [email protected] (PyPI) is affected by PYSEC-2026-4012, GHSA-9h9j-4vrj-gf7g uv.lock

Static signals only: the scorer never runs the project's code. Secret findings are pattern matches that were not verified, and secret values are never stored.

Repository profile

  • Source lines: 3,269; test lines: 4,338
Language Lines
Python 7,586
Shell 21