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rhshah/vFlank

https://github.com/rhshah/vFlank · scanned 2026-06-15 23:50 UTC (2 months, 3 weeks ago)

16 raw signals (0 security + 16 graph)

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UNIFIED Repobility · multi-layer engine · AI coders

Complete repo analysis

Last scanned 2 months, 3 weeks ago · v1 · 12 actionable findings from 1 signal source. 4 repeated signals grouped for readability. Security checks, system graph analysis, and verified AI-agent feedback are merged into one review queue.

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Combined
75.0
/100
Security checks
75
0 findings
System graph
75
77.8% cov · 12 findings
Critical
0
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Agents
10
0 votes
Crowd
0
reported
Severity distribution — click a segment to filter
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Severity: Critical 0 High 0 Medium 4 Low 4 9-Layer: Software Security Quality Integrity Frontend Hardware Data Network Cicd Source: Security checks 0 System graph 12 Crowd 0 Layer: Api 1 Hardware 3 Frontend 1 Cicd 3 Quality 4

All 413 nodes from the latest scan, grouped by kind. Each node is a unit the engine identified (file, function, endpoint, table…). Most users won't need this view — it's primarily for debugging the engine's graph extraction or for AI agents that want to enumerate the project structure.

LabelLayerStatusPath
_template software healthy tests/integration/test_consensus_bam.py:20
_make_bam software healthy tests/integration/test_consensus_bam.py:24
_genomic_to_read_idx software healthy tests/integration/test_consensus_bam.py:47
test_consensus_homozygous_matches_reads software healthy tests/integration/test_consensus_bam.py:51
test_heterozygous_becomes_N software healthy tests/integration/test_consensus_bam.py:59
test_heterozygous_iupac software healthy tests/integration/test_consensus_bam.py:66
test_window_depth software healthy tests/integration/test_consensus_bam.py:72
test_consensus_flank_source software healthy tests/integration/test_consensus_bam.py:80
test_small_run_with_bam_consensus software healthy tests/integration/test_consensus_bam.py:125
test_consensus_handles_deletion_reads_reference_length software healthy tests/integration/test_consensus_bam.py:180
test_consensus_flags_insertion_site software healthy tests/integration/test_consensus_bam.py:218
test_fusion_run_deletion_like software healthy tests/integration/test_fusion_pipeline.py:16
test_fusion_run_minus_strand_revcomp software healthy tests/integration/test_fusion_pipeline.py:45
test_fusion_run_with_bam_consensus software healthy tests/integration/test_fusion_pipeline.py:66
_write_reference software healthy tests/integration/test_small_pipeline.py:15
_write_maf software healthy tests/integration/test_small_pipeline.py:24
test_version_flag_and_subcommand_agree software healthy tests/integration/test_small_pipeline.py:36
test_emit_primer3_writes_boulder_io software healthy tests/integration/test_small_pipeline.py:45
test_run_produces_expected_fasta software healthy tests/integration/test_small_pipeline.py:65
test_dedup_collapses_same_variant_across_samples software healthy tests/integration/test_small_pipeline.py:107
test_truncated_flank_is_emitted_not_dropped software healthy tests/integration/test_small_pipeline.py:138
test_bare_named_single_contig_fasta_resolves software healthy tests/integration/test_small_pipeline.py:163
test_float_typed_chromosome_column_is_processed software healthy tests/integration/test_small_pipeline.py:189
test_pop_source_api_masks_via_monkeypatched_transport software healthy tests/integration/test_small_pipeline.py:219
fake_transport software healthy tests/integration/test_small_pipeline.py:272
test_ref_source_api_fetches_flanks_via_monkeypatched_transp… software healthy tests/integration/test_small_pipeline.py:256
test_ref_source_file_without_ref_genome_errors software healthy tests/integration/test_small_pipeline.py:292
test_pop_data_exome_without_files_errors software healthy tests/integration/test_small_pipeline.py:300
test_missing_required_column_errors software healthy tests/integration/test_small_pipeline.py:323
_reference software healthy tests/integration/test_run_api.py:21
test_run_small_from_buffer software healthy tests/integration/test_run_api.py:37
test_run_small_emit_primer3 software healthy tests/integration/test_run_api.py:53
test_run_fusion_from_buffer software healthy tests/integration/test_run_api.py:63
test_run_small_validates_options_before_io software healthy tests/integration/test_run_api.py:73
test_run_small_file_backend_requires_reference software healthy tests/integration/test_run_api.py:79
test_resolve_template_fills_N_from_reference software healthy tests/unit/test_emit_primer3.py:10
test_n_runs_coalesces_and_offsets software healthy tests/unit/test_emit_primer3.py:15
test_small_variant_record_target_and_excluded software healthy tests/unit/test_emit_primer3.py:21
test_junction_record_target_straddles_junction software healthy tests/unit/test_emit_primer3.py:31
test_write_primer3_boulder_io_structure software healthy tests/unit/test_emit_primer3.py:38
test_write_report software healthy tests/unit/test_report.py:4
test_parse_consensus_fasta software healthy tests/unit/test_consensus.py:8
test_overlay_keeps_adequate_depth software healthy tests/unit/test_consensus.py:13
test_overlay_lowcov_n software healthy tests/unit/test_consensus.py:19
test_overlay_lowcov_reference software healthy tests/unit/test_consensus.py:25
test_overlay_lowcov_gnomad software healthy tests/unit/test_consensus.py:31
test_genome_for_build software healthy tests/unit/test_reference_api.py:16
test_ucsc_contig_prefix_and_mito software healthy tests/unit/test_reference_api.py:23
test_build_url_contains_genome_and_coords software healthy tests/unit/test_reference_api.py:30
test_parse_returns_dna software healthy tests/unit/test_reference_api.py:39

Showing first 50 of this kind. Full payload available via the JSON button at the top of the page.

LabelLayerStatusPath
mkdocs.yml software healthy mkdocs.yml
README.md software healthy README.md
CLAUDE.md software healthy CLAUDE.md
CONTRIBUTING.md software healthy CONTRIBUTING.md
Dockerfile software healthy Dockerfile
.pre-commit-config.yaml software healthy .pre-commit-config.yaml
pyproject.toml software healthy pyproject.toml
LICENSE software healthy LICENSE
CHANGELOG.md software healthy CHANGELOG.md
test_consensus_bam.py software healthy tests/integration/test_consensus_bam.py
test_fusion_pipeline.py software healthy tests/integration/test_fusion_pipeline.py
test_small_pipeline.py software healthy tests/integration/test_small_pipeline.py
test_run_api.py software healthy tests/integration/test_run_api.py
test_emit_primer3.py software healthy tests/unit/test_emit_primer3.py
test_report.py software healthy tests/unit/test_report.py
test_consensus.py software healthy tests/unit/test_consensus.py
test_reference_api.py software healthy tests/unit/test_reference_api.py
test_breakpoints.py software healthy tests/unit/test_breakpoints.py
test_skips.py software healthy tests/unit/test_skips.py
test_variant.py software healthy tests/unit/test_variant.py
test_popfreq.py software healthy tests/unit/test_popfreq.py
test_fusion.py software healthy tests/unit/test_fusion.py
test_popfreq_api.py software healthy tests/unit/test_popfreq_api.py
test_flanks.py software healthy tests/unit/test_flanks.py
test_pipeline.py software healthy tests/unit/test_pipeline.py
test_chrom.py software healthy tests/unit/test_chrom.py
ARCHITECTURE.md software healthy docs/ARCHITECTURE.md
index.md software healthy docs/index.md
DEVELOPER.md software healthy docs/DEVELOPER.md
changelog.md software healthy docs/changelog.md
cli.md software healthy docs/reference/cli.md
api.md software healthy docs/reference/api.md
glossary.md software healthy docs/reference/glossary.md
extra.css software healthy docs/stylesheets/extra.css
indel-aware-consensus.md software healthy docs/research/indel-aware-consensus.md
gnomad-api.md software healthy docs/research/gnomad-api.md
bam-consensus.md software healthy docs/research/bam-consensus.md
genome-api.md software healthy docs/research/genome-api.md
emit-formats.md software healthy docs/research/emit-formats.md
webapp-repo-structure.md software healthy docs/research/webapp-repo-structure.md
orchestration-extraction.md software healthy docs/research/orchestration-extraction.md
web-app-and-hosting.md software healthy docs/research/web-app-and-hosting.md
sv-vcf-input.md software healthy docs/research/sv-vcf-input.md
small-variants.md software healthy docs/user-guide/small-variants.md
consensus.md software healthy docs/user-guide/consensus.md
masking.md software healthy docs/user-guide/masking.md
fusions.md software healthy docs/user-guide/fusions.md
recommended-usage.md software healthy docs/getting-started/recommended-usage.md
quickstart.md software healthy docs/getting-started/quickstart.md
installation.md software healthy docs/getting-started/installation.md

Showing first 50 of this kind. Full payload available via the JSON button at the top of the page.

LabelLayerStatusPath
FakeTransport software healthy tests/unit/test_reference_api.py:60
_FakeRef software healthy tests/unit/test_fusion.py:9
_FakeGnomad software healthy tests/unit/test_fusion.py:70
FakeTransport software healthy tests/unit/test_popfreq_api.py:58
_FakeRef software healthy tests/unit/test_flanks.py:17
FakeReference software healthy tests/unit/test_pipeline.py:19
Processed software healthy src/vflank/pipeline.py:56
Skipped software healthy src/vflank/pipeline.py:70
Duplicate software healthy src/vflank/pipeline.py:77
RunResult software healthy src/vflank/pipeline.py:87
VflankError software healthy src/vflank/errors.py:10
ReferenceError software healthy src/vflank/errors.py:14
MafError software healthy src/vflank/errors.py:18
PopFreqError software healthy src/vflank/errors.py:22
SvError software healthy src/vflank/errors.py:26
ConsensusError software healthy src/vflank/errors.py:30
ReferenceFasta software healthy src/vflank/io/reference.py:22
SvColumns software healthy src/vflank/io/breakpoints.py:23
Primer3Record software healthy src/vflank/io/emit_primer3.py:39
MafColumns software healthy src/vflank/io/maf.py:32
GnomadStore software healthy src/vflank/core/popfreq.py:126
FlankResult software healthy src/vflank/core/flanks.py:33
FlankSource software healthy src/vflank/core/flanks.py:70
ReferenceFlankSource software healthy src/vflank/core/flanks.py:76
_TransientApiError software healthy src/vflank/core/reference_api.py:88
ReferenceApiSource software healthy src/vflank/core/reference_api.py:108
_TransientApiError software healthy src/vflank/core/popfreq_api.py:95
GnomadApiSource software healthy src/vflank/core/popfreq_api.py:118
ConsensusPolicy software healthy src/vflank/core/consensus.py:24
BamConsensusSource software healthy src/vflank/core/consensus.py:187
ConsensusFlankSource software healthy src/vflank/core/consensus.py:253
Breakpoint software healthy src/vflank/core/fusion.py:26
Fusion software healthy src/vflank/core/fusion.py:35
JunctionResult software healthy src/vflank/core/fusion.py:45
Variant software healthy src/vflank/core/variant.py:15

LabelLayerStatusPath
tests software healthy tests
integration software healthy tests/integration
unit software healthy tests/unit
docs software healthy docs
reference software healthy docs/reference
stylesheets software healthy docs/stylesheets
research software healthy docs/research
user-guide software healthy docs/user-guide
getting-started software healthy docs/getting-started
includes software healthy docs/includes
.claude software healthy .claude
skills software healthy .claude/skills
ddpcr-conventions software healthy .claude/skills/ddpcr-conventions
.github software healthy .github
workflows software healthy .github/workflows
src software healthy src
vflank software healthy src/vflank
cli software healthy src/vflank/cli
io software healthy src/vflank/io
core software healthy src/vflank/core

LabelLayerStatusPath
lint cicd healthy .github/workflows/ci.yml
test cicd healthy .github/workflows/ci.yml
docs cicd healthy .github/workflows/ci.yml
deploy cicd healthy .github/workflows/docs.yml
pypi cicd healthy .github/workflows/release.yml
docker cicd healthy .github/workflows/release.yml

LabelLayerStatusPath
gha::ci cicd healthy .github/workflows/ci.yml
gha::docs cicd healthy .github/workflows/docs.yml
gha::release cicd healthy .github/workflows/release.yml

LabelLayerStatusPath
repobility-clone-qruqupmm software healthy /tmp/repobility-clone-qruqupmm

LabelLayerStatusPath
image::Dockerfile hardware healthy Dockerfile

LabelLayerStatusPath
vps::droplet hardware healthy .claude/skills/ddpcr-conventions/SKILL.md

LabelLayerStatusPath
auth::.github/workflows/release.yml security healthy .github/workflows/release.yml

LabelLayerStatusPath
GITHUB_TOKEN cicd healthy —
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