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openvax / isovar
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Repo Added 05 Jan 2018 08:34PM UTC
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  • add-agents-md
  • add-columns-to-output-args
  • add-slice-method-to-protein-sequence
  • add-varcode-assembly-provider
  • agent/replace-pkg-resources
  • audit/core-api-and-docs
  • audit/osteosarc-all-vaccine-rna
  • audit/sid-vaxrank-followup
  • bump-1.6.0
  • chore/399-retire-three-fusions-builder
  • chore/524-python-311-minimum
  • chore/osteosarc-0.1.2
  • chore/osteosarc-0.11
  • chore/osteosarc-0.12
  • chore/osteosarc-0.13
  • chore/osteosarc-0.14
  • chore/osteosarc-0.9
  • chore/update-actions-node24
  • cli/help-text
  • cli/input-errors
  • codex/docs-cleanup-129-133-135
  • codex/explicit-phase-groups
  • codex/fix-allele-counts-cli-output
  • codex/fix-filter-flag-doc-example
  • codex/fix-position-1-fetch-start
  • codex/fix-read-level-cli-output
  • codex/merge-overlapping-fragments
  • codex/mutant-transcript-source
  • codex/phase-group-assembly-support
  • codex/phase-group-transcript-edits
  • codex/speed-up-read-collector-lookups
  • deps/386-osteosarc-0.7
  • deps/osteosarc-optional
  • deslop/dead-helpers
  • deslop/protein-selection-docs
  • docs-library-responsibilities
  • docs/human-friendly-audit
  • docs/human-friendly-pass
  • docs/osteosarc-sample-audit
  • edit-distance-from-reference-protein-sequence
  • exit-early-if-no-reference-contexts
  • explicit-phasing-of-somatic-variants
  • feat/226-cell-umi-allele-evidence
  • feat/297-germline-edit-attribution
  • feat/306-allele-interpretations
  • feat/324-protein-hypothesis-export
  • feat/350-linked-splice-paths
  • feat/350-orf-start-evidence
  • feat/364-shared-rna-path-schema
  • feat/387-germline-trans
  • feat/395-openvax-v1
  • feat/bundled-sid-reads
  • feat/extended-rna-footprints
  • feat/fusion-and-phasing-figures
  • feat/gene-anchored-sv-rna
  • feat/mutation-evidence-figures
  • feat/ont-read-lineage
  • feat/osteosarc-locus-fixtures
  • feat/protein-context-comparisons
  • feat/protein-prediction-gallery
  • feat/read-end-annotation
  • feat/read-phasing-in-cis
  • feat/shared-osteosarc-data
  • feat/subcommands-clean-figures
  • feat/supplied-fusion-transcripts
  • feat/sv-orf-read-evidence
  • feat/sv-orf-sequence-export
  • feat/sv-rna-prediction-comparison
  • feat/uniform-rna-support
  • feature/226-pooled-cell-attribution
  • feature/26-partial-read-support
  • feature/395-full-sid-panel
  • feature/411-control-phasing-calibration
  • feature/428-flanking-indel-matching
  • feature/437-dense-sv-support
  • feature/8-optional-base-quality
  • feature/archive-experiments-569
  • feature/archive-performance-246
  • feature/buffer-json-tokens
  • feature/clear-evidence-funnels
  • feature/colo829-original-rna-audit
  • feature/colo829-polished-allele-audit
  • feature/colo829-sv3-orf-audit
  • feature/colo829-whole-run-atlas
  • feature/cta-isoforms
  • feature/ddx17-splice-and-deletion-report
  • feature/dense-evidence-groups
  • feature/dense-exon-anchor-559
  • feature/dense-group-execution
  • feature/exon-anchored-sv-assembly
  • feature/exon-anchored-sv-rna-evidence
  • feature/exon-path-bridges-555
  • feature/exonic-funnel-evidence-report
  • feature/finish-ont-igkc-recovery
  • feature/gdc-viral-reconstruction
  • feature/multicategory-evidence-reports
  • feature/ncorf-rna-reconstruction
  • feature/orf-reference-context
  • feature/portable-audit-bundles
  • feature/proteome-adapter-542
  • feature/shared-uorf-catalog
  • feature/sid-neoorf-read-subsets
  • feature/sid-remaining-dense-recovery
  • feature/sid-sv-catalogue-audit
  • feature/source-backed-benchmark-examples
  • feature/stream-audit-decoding
  • feature/stream-audit-json
  • feature/stream-cli-resume
  • feature/stream-complete-sv-support
  • feature/sv-evidence-groups-464
  • feature/sv-high-coverage-audit-553
  • feature/sv-junction-evidence
  • feature/sv3-dense-template-stream-562
  • feature/sv3-frame-anchor-evidence-563
  • feature/sv3-rna-path-563
  • feature/unified-sv-rna-audit-305
  • feature/uorf-evidence-catalog
  • feature/uorf-initiation-context
  • feature/viral-orf-annotation
  • feature/viral-reference-objects
  • fix-126-self-subtraction-insertion
  • fix-127-mapq-none-typeerror-v2
  • fix-130-collapse-substrings-break
  • fix-131-n-reads-not-skipped
  • fix-132-max-protein-sequences-cap
  • fix-134-cli-soft-clipped-flag
  • fix-136-mutable-defaults
  • fix-137-logger-warn-deprecated
  • fix-149-cache-coverage
  • fix-150-document-assembly-assumptions
  • fix-151-max-sequences-circuit-breaker
  • fix-152-subclonal-allele-crash
  • fix-153-deterministic-merge
  • fix-docs-128-129-133-135
  • fix-left-align-indels
  • fix-mismatch-count-after-variant
  • fix-read-evidence-boundaries
  • fix/122-ensembl-release
  • fix/205-spdx-license
  • fix/237-pin-collection-benchmark-genome
  • fix/256-cli-input-errors
  • fix/258-csv-consistency
  • fix/301-gallery-readme
  • fix/345-version-guard
  • fix/353-orientation-flags
  • fix/358-coveralls-python
  • fix/361-inclusion-mapq
  • fix/361-mapq-255-unique-default
  • fix/362-orf-start-status
  • fix/363-sv-rna-provenance
  • fix/364-sv-helpers
  • fix/393-nested-subclone-trans
  • fix/399-fixture-record-references
  • fix/415-compatible-context-candidates
  • fix/454-clean-wheel-build
  • fix/505-close-test-sqlite
  • fix/522-splice-outcome-coding
  • fix/526-ensembl-cache-key
  • fix/align-variant-sequence-assembly-default
  • fix/aligned-reading-frame
  • fix/audit-bundle-clones
  • fix/audit-provenance-validation
  • fix/cache-ensembl-ci-downloads
  • fix/cli-api-defaults
  • fix/compatible-placement-phasing
  • fix/cross-platform-read-evidence
  • fix/declare-osteosarc-mitochondrial-code
  • fix/dense-splice-ambiguous-priority
  • fix/deploy-version-bump
  • fix/directional-phasing
  • fix/explicit-orf-genetic-codes
  • fix/fusion-paired-mate-identity
  • fix/germline-unmerged-mates
  • fix/insertion-boundary-reference
  • fix/intergenic-sv-orfs
  • fix/length-filter-respects-read-support
  • fix/library-scoped-umi-evidence
  • fix/observed-fusion-footprints
  • fix/phasing-other-allele-conflicts
  • fix/preserve-contained-assemblies
  • fix/read-group-phasing
  • fix/read-observation-identity
  • fix/reference-dataset-identity
  • fix/reject-symbolic-sv-inputs
  • fix/release-interpreter-consistency
  • fix/resumable-release-artifacts
  • fix/retain-required-reference-context
  • fix/sdist-release-tooling
  • fix/shared-fixture-mechanics
  • fix/sid-record-identity-cleanup
  • fix/skip-nonexonic-reference-contexts
  • fix/splice-compatible-overlap-assembly
  • fix/splice-outcome-filter
  • fix/supplementary-path-phasing
  • fix/sv-breakpoint-acquisition
  • fix/sv-insertion-ending-orfs
  • fix/sv-original-record-identity
  • fix/sv-preserve-direct-orfs
  • fix/sv-rna-long-read-evidence
  • fix/translation-intervals-and-assembly-support
  • fix/varcode-10.5.2
  • fix/verify-release-artifact-digests
  • fix/viral-sdist-evidence
  • handle-intergenic-effects
  • hcc1395-whole-run-atlas
  • hcc1395_colo829_evidence_pdfs
  • improve-assembly-scaling
  • master
  • more-rna-filtering-options
  • multiple-phasing-types
  • no-more-py27-on-travis
  • perf/compact-internal-read-coordinates
  • perf/coordinate-sharing-dict
  • perf/high-depth-read-support
  • perf/high-depth-rna-support
  • perf/read-collection-memory
  • read-phasing-adapter
  • refactor-cli
  • refactor/401-bundle-file
  • release/fusion-paired-mate-1-16-2
  • release/three-fusion-fixtures-1.21.11
  • run-integration-tests
  • speed-up-LocusRead-construction
  • test/osteosarc-three-fusion-orfs
  • test/real-rnaseq-platform-fixtures
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27 Oct 2026 02:15AM UTC coverage: 94.897% (-0.04%) from 94.941%
40437355131

push

github

web-flow
Reconstruct mutation-supporting RNA in supplied ncORF frames (#586)

* Reconstruct mutation-supporting RNA in supplied ncORF frames

* Include the pinned HCC1395 alignment receipt

* Show observed stops and clarify the resolved fusion report scope

148 of 162 new or added lines in 2 files covered. (91.36%)

12626 of 13305 relevant lines covered (94.9%)

0.95 hits per line

Relevant lines Covered
Build:
Build:
13305 RELEVANT LINES 12626 COVERED LINES
0.95 HITS PER LINE
Source Files on master
  • Tree
  • List 136
  • Changed 1
  • Source Changed 0
  • Coverage Changed 1
Coverage ∆ File Lines Relevant Covered Missed Hits/Line

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
40437355131 master Reconstruct mutation-supporting RNA in supplied ncORF frames (#586) * Reconstruct mutation-supporting RNA in supplied ncORF frames * Include the pinned HCC1395 alignment receipt * Show observed stops and clarify the resolved fusion report scope push 27 Oct 2026 02:36AM UTC web-flow github
94.9
40433637742 feature/ncorf-rna-reconstruction Merge d412be96c into 554ce45d4 Pull #586 27 Oct 2026 02:12AM UTC web-flow github
94.9
40427379491 master Audit DDX17 intronic RNA and mark verified protein deletions (#584) push 27 Oct 2026 01:08AM UTC web-flow github
94.94
40411933185 feature/ddx17-splice-and-deletion-report Merge 6f7717b22 into e660205f3 Pull #584 26 Oct 2026 10:48PM UTC web-flow github
94.94
40392072392 master Unify all-path SV RNA assessment and COLO829 audits (#580) * Unify all-path SV RNA assessment and source-separated cohort audits * Publish complete COLO829 audit and three-sample evidence funnels * Add sample landscapes, source-qualified protei... push 26 Oct 2026 08:35PM UTC web-flow github
94.94
40387175059 feature/unified-sv-rna-audit-305 Merge 7e1a291b1 into 62178f873 Pull #580 26 Oct 2026 07:50PM UTC web-flow github
94.94
40374873545 master Preserve explicit genetic codes in RNA translation and export (#578) * Preserve explicit genetic codes through RNA translation and export * Include native genetic-code fixtures in source distributions push 26 Oct 2026 06:35PM UTC web-flow github
95.29
40368072214 fix/explicit-orf-genetic-codes Merge e0cc6b7f0 into 4ea652933 Pull #578 26 Oct 2026 06:06PM UTC web-flow github
95.29
40255068307 master Merge pull request #573 from openvax/feature/sv3-frame-anchor-evidence-563 Audit all pinned CNIH3 RNA evidence for an SV3 frame anchor push 26 Oct 2026 02:13AM UTC web-flow github
95.28
40252056555 feature/sv3-frame-anchor-evidence-563 Merge 0d0d09277 into 0450cc032 Pull #573 26 Oct 2026 01:33AM UTC web-flow github
95.28
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