Data Analysis
pysam
86100Total Score
Core Capability
85 / 100
Functional Suitability
11 / 12
Reliability
9 / 12
Performance & Context
7 / 8
Agent Usability
14 / 16
Human Usability
8 / 8
Security
11 / 12
Maintainability
9 / 12
Agent-Specific
16 / 20
Medical Task
20 / 20 Passed
91Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, extracting regions, calculating coverage, suitable for NGS data processing pipelines
4/4
87Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, extracting regions, calculating coverage, suitable for NGS data processing pipelines
4/4
85Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, extracting regions, calculating coverage, suitable for NGS data processing pipelines
4/4
85Documentation-first workflow with no packaged script requirement
4/4
85End-to-end case for Scope-focused workflow aligned to: Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, extracting regions, calculating coverage, suitable for NGS data processing pipelines
4/4
Veto GatesRequired pass for any deployment consideration
Skill Veto✓ All 4 gates passed
✓
Operational Stability
System remains stable across varied inputs and edge cases
PASS✓
Structural Consistency
Output structure conforms to expected skill contract format
PASS✓
Result Determinism
Equivalent inputs produce semantically equivalent outputs
PASS✓
System Security
No prompt injection, data leakage, or unsafe tool use detected
PASSResearch Veto✅ PASS — Applicable
| Dimension | Result | Detail |
|---|---|---|
| Scientific Integrity | PASS | The archived review kept this workflow anchored to supplied data fields and observable execution behavior, not fabricated results. |
| Practice Boundaries | PASS | Practice boundaries held because the package remained focused on Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant... rather than overclaiming what the records supported. |
| Methodological Ground | PASS | The legacy review kept the package aligned with its named analysis library, data structure, or processing workflow. |
| Code Usability | PASS | Code usability passed because the package still exposed a reviewable execution surface for its documented workflow. |
Core Capability85 / 100 — 8 Categories
Functional Suitability
Related legacy finding for pysam: Improve stress-case output rigor. Stress and boundary scenarios show weaker consistency
11 / 12
92%
Reliability
Related legacy finding for pysam: Improve stress-case output rigor. Stress and boundary scenarios show weaker consistency
9 / 12
75%
Performance & Context
The archived review left minor headroom in how this analysis workflow scales across heavier contexts.
7 / 8
88%
Agent Usability
The packaged analysis path is understandable, though the archived score suggests slightly clearer routing would help.
14 / 16
88%
Human Usability
Human usability reached full score in the archived evaluation.
8 / 8
100%
Security
A modest security gap remained in the archived evaluation despite otherwise controlled workflow behavior.
11 / 12
92%
Maintainability
The analysis package is maintainable overall, though the archived score suggests modest cleanup headroom.
9 / 12
75%
Agent-Specific
Agent specific was softened by the legacy issue 'Improve stress-case output rigor'. Stress and boundary scenarios show weaker consistency
16 / 20
80%
Core Capability Total85 / 100
Medical TaskExecution Average: 86.6 / 100 — Assertions: 20/20 Passed
91
Canonical
Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, extracting regions, calculating coverage, suitable for NGS data processing pipelines
4/4 ✓
87
Variant A
Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, extracting regions, calculating coverage, suitable for NGS data processing pipelines
4/4 ✓
85
Edge
Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, extracting regions, calculating coverage, suitable for NGS data processing pipelines
4/4 ✓
85
Variant B
Documentation-first workflow with no packaged script requirement
4/4 ✓
85
Stress
End-to-end case for Scope-focused workflow aligned to: Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, extracting regions, calculating coverage, suitable for NGS data processing pipelines
4/4 ✓
91
Canonical✅ Pass
Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, extracting regions, calculating coverage, suitable for NGS data processing pipelines
This canonical case stayed focused on extracting and normalizing evidence from the provided records instead of drifting into unsupported interpretation.
Basic 36/40|Specialized 55/60|Total 91/100
✅A1The pysam output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
87
Variant A✅ Pass
Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, extracting regions, calculating coverage, suitable for NGS data processing pipelines
This variant a case stayed focused on extracting and normalizing evidence from the provided records instead of drifting into unsupported interpretation.
Basic 34/40|Specialized 53/60|Total 87/100
✅A1The pysam output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
85
Edge✅ Pass
Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, extracting regions, calculating coverage, suitable for NGS data processing pipelines
The archived run treated Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment... as a bounded extraction workflow, keeping attention on source fields, fallback logic, and output shape.
Basic 33/40|Specialized 52/60|Total 85/100
✅A1The pysam output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
85
Variant B✅ Pass
Documentation-first workflow with no packaged script requirement
The archived run treated Documentation-first workflow with no packaged script requirement as a bounded analysis workflow rather than a purely narrative instruction path.
Basic 32/40|Specialized 53/60|Total 85/100
✅A1The pysam output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
85
Stress✅ Pass
End-to-end case for Scope-focused workflow aligned to: Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, extracting regions, calculating coverage, suitable for NGS data processing pipelines
Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant... remained an analysis-style extraction path whose value came from structured data capture rather than a freeform narrative response.
Basic 29/40|Specialized 56/60|Total 85/100
✅A1The pysam output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
Medical Task Total86.6 / 100
Key Strengths
- Primary routing is Data Analysis with execution mode A
- Static quality score is 85/100 and dynamic average is 78.6/100
- Assertions and command execution outcomes are recorded per input for human review
- Execution verification summary: No script verification was applicable