openvax / isovar

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LAST BUILD ON BRANCH refactor-cli

branch: refactor-cli

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• refactor-cli
• add-agents-md
• add-columns-to-output-args
• add-slice-method-to-protein-sequence
• add-varcode-assembly-provider
• agent/replace-pkg-resources
• audit/osteosarc-all-vaccine-rna
• bump-1.6.0
• 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
• deslop/dead-helpers
• deslop/protein-selection-docs
• docs/osteosarc-sample-audit
• edit-distance-from-reference-protein-sequence
• exit-early-if-no-reference-contexts
• explicit-phasing-of-somatic-variants
• feat/fusion-and-phasing-figures
• feat/mutation-evidence-figures
• feat/protein-context-comparisons
• feat/protein-prediction-gallery
• feat/subcommands-clean-figures
• feat/supplied-fusion-transcripts
• 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/align-variant-sequence-assembly-default
• fix/aligned-reading-frame
• fix/cache-ensembl-ci-downloads
• fix/cli-api-defaults
• fix/deploy-version-bump
• fix/fusion-paired-mate-identity
• fix/length-filter-respects-read-support
• fix/preserve-contained-assemblies
• fix/read-observation-identity
• fix/reject-symbolic-sv-inputs
• fix/release-interpreter-consistency
• fix/resumable-release-artifacts
• fix/retain-required-reference-context
• fix/sdist-release-tooling
• fix/splice-compatible-overlap-assembly
• fix/translation-intervals-and-assembly-support
• fix/verify-release-artifact-digests
• handle-intergenic-effects
• 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-rna-support
• perf/read-collection-memory
• read-phasing-adapter
• release/fusion-paired-mate-1-16-2
• run-integration-tests
• speed-up-LocusRead-construction
• test/real-rnaseq-platform-fixtures
• v1.10.0
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• v1.14.1
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• v1.16.1
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• v1.9.0

Build # 516

Build Type

push

travis-ci

Committed by iskandr

Commit Message

forgot to add new logging module

Coverage Stats

7 of 7 new or added lines in 1 file covered. (100.0%)

1289 of 1406 relevant lines covered (91.68%)

1.83 hits per line