LICENSE
MANIFEST.in
README.md
mkdocs.yml
pyproject.toml
docs/changelog.md
docs/command-line.md
docs/concepts.md
docs/corrections.md
docs/index.md
docs/map2.md
docs/openvax.md
docs/partner-recovery-spec.md
docs/python-api.md
docs/reads.md
docs/samples.md
docs/snapshots.md
docs/sv-candidates.md
docs/test-data.md
docs/testing.md
docs/timeline.md
docs/variants.md
osteosarc/__init__.py
osteosarc/__main__.py
osteosarc/alleles.py
osteosarc/bundles.py
osteosarc/cache.py
osteosarc/catalog.py
osteosarc/cli.py
osteosarc/cohort_bundle.py
osteosarc/corpus.py
osteosarc/curation.py
osteosarc/dataset.py
osteosarc/discovery.py
osteosarc/display.py
osteosarc/errors.py
osteosarc/fixture_assets.py
osteosarc/fixtures.py
osteosarc/models.py
osteosarc/parsing.py
osteosarc/provenance.py
osteosarc/reads.py
osteosarc/records.py
osteosarc/recovery.py
osteosarc/reference.py
osteosarc/retrieval.py
osteosarc/saved.py
osteosarc/shared.py
osteosarc/sv_candidates.py
osteosarc/timeline.py
osteosarc/urls.py
osteosarc/views.py
osteosarc.egg-info/PKG-INFO
osteosarc.egg-info/SOURCES.txt
osteosarc.egg-info/dependency_links.txt
osteosarc.egg-info/entry_points.txt
osteosarc.egg-info/requires.txt
osteosarc.egg-info/top_level.txt
osteosarc/data/allele_resolutions.json
osteosarc/data/evidence-overlaps.json
osteosarc/data/panels.json
osteosarc/data/retrieval-cases.json
osteosarc/data/sv_candidates.json
osteosarc/data/bundles/openvax-v1.release.json
osteosarc/data/bundles/openvax-v1.spec.json
osteosarc/data/bundles/openvax-v2.release.json
osteosarc/data/bundles/openvax-v2.spec.json
scripts/build_test_fixtures.py
scripts/check_allele_sources.py
scripts/check_docs.py
scripts/shared_test_data/audit_comprehensive.py
scripts/shared_test_data/build.py
scripts/shared_test_data/build_comprehensive.py
scripts/shared_test_data/catalog_comprehensive.py
scripts/shared_test_data/controls_comprehensive.py
scripts/shared_test_data/package_comprehensive.py
scripts/shared_test_data/required_isovar.py
scripts/shared_test_data/required_topiary.py
scripts/shared_test_data/required_varcode.py
scripts/shared_test_data/required_vaxrank.py
scripts/shared_test_data/verify_evidence_comprehensive.py
tests/conftest.py
tests/test_allele_resolution.py
tests/test_alleles.py
tests/test_bundles.py
tests/test_cache.py
tests/test_cohort_bundle.py
tests/test_comprehensive_audit.py
tests/test_consumer_usage.py
tests/test_corpus.py
tests/test_curation.py
tests/test_curation_revisions.py
tests/test_dataset.py
tests/test_discovery.py
tests/test_fixtures.py
tests/test_parsing.py
tests/test_provenance.py
tests/test_reads.py
tests/test_recovery.py
tests/test_retrieval.py
tests/test_saved.py
tests/test_shared.py
tests/test_sv_candidates.py
tests/test_timeline.py
tests/data/bam-metadata.tsv
tests/data/bams.json
tests/data/bucket_listing.json
tests/data/curation_snapshots.json
tests/data/cytometry.tsv
tests/data/data.html
tests/data/dicom-studies.json
tests/data/events.json
tests/data/fastqs-consolidated.tsv
tests/data/flow-manifest.json
tests/data/lab_results.tsv
tests/data/mrd.json
tests/data/pathology-slides.json
tests/data/provenance.json
tests/data/samples-consolidated.tsv
tests/data/samples.json
tests/data/source-variants.json
tests/data/timeline.csv
tests/data/vaccine_overlap.json
tests/data/vafs-columns.tsv
tests/data/vafs.tsv
tests/data/variants.html
tests/data/additional_svs/README.md
tests/data/additional_svs/T1-ONT-tagged.bam
tests/data/additional_svs/T1-ONT-tagged.bam.bai
tests/data/additional_svs/T1-PacBio.bam
tests/data/additional_svs/T1-PacBio.bam.bai
tests/data/additional_svs/T1-short.bam
tests/data/additional_svs/T1-short.bam.bai
tests/data/additional_svs/T2-ONT-tagged.bam
tests/data/additional_svs/T2-ONT-tagged.bam.bai
tests/data/additional_svs/candidate-hypotheses.json
tests/data/additional_svs/events.json
tests/data/additional_svs/receipts.json
tests/data/additional_svs/recipe.json
tests/data/allele_resolution/FAM157A-ncbi.txt
tests/data/allele_resolution/NC_000001.10.fasta
tests/data/allele_resolution/NC_000001.11.fasta
tests/data/allele_resolution/NC_000002.11.fasta
tests/data/allele_resolution/NC_000002.12.fasta
tests/data/allele_resolution/NC_000003.11.fasta
tests/data/allele_resolution/NC_000003.12.fasta
tests/data/allele_resolution/NC_000007.13.fasta
tests/data/allele_resolution/NC_000007.14.fasta
tests/data/allele_resolution/README.md
tests/data/allele_resolution/natera-catalogue.tsv
tests/data/allele_resolution/provenance.json
tests/data/allele_resolution/source-variants.json
tests/data/allele_resolution/tempus.freebayes.vcf
tests/data/allele_resolution/tempus.pindel.vcf
tests/data/allele_resolution/vafs.tsv
tests/data/allele_resolution/variant-index.json
tests/data/comprehensive/README.md
tests/data/comprehensive/catalog.json.gz
tests/data/comprehensive/checksums.json
tests/data/comprehensive/count-source-aliases.json
tests/data/comprehensive/historical-rna.json
tests/data/comprehensive/inputs.json.gz
tests/data/comprehensive/spec.json
tests/data/comprehensive/summary.json
tests/data/evidence-overlap/README.md
tests/data/evidence-overlap/c75479dce2b07bbf.bam
tests/data/evidence-overlap/e5c28abdbf307d55.bam
tests/data/evidence-overlap/fastqs-consolidated.tsv
tests/data/evidence-overlap/receipts.json
tests/data/retrieval/00-ABCF2-chr7-151218156-f30f618fb76a0e49.bam
tests/data/retrieval/00-ABCF2-chr7-151218156-f30f618fb76a0e49.bam.bai
tests/data/retrieval/44-MT_ND5-chrM-12994-238f917202dd9997.bam
tests/data/retrieval/44-MT_ND5-chrM-12994-238f917202dd9997.bam.bai
tests/data/retrieval/45-MT_ND5-chrM-12994-fbeb5d8a415e4d18.bam
tests/data/retrieval/45-MT_ND5-chrM-12994-fbeb5d8a415e4d18.bam.bai
tests/data/retrieval/48-NR2F2-chr15-96332299-fbeb5d8a415e4d18.bam
tests/data/retrieval/48-NR2F2-chr15-96332299-fbeb5d8a415e4d18.bam.bai
tests/data/retrieval/README.md
tests/data/retrieval/historical-manifest.json