.clang-format
.gitignore
CHANGELOG.md
CONTRIBUTING.md
LICENSE
MANIFEST.in
Makefile
README.md
dev.py
prek.toml
pyproject.toml
setup.py
uv.lock
.github/workflows/cd.yml
.github/workflows/ci.yml
.github/workflows/docs.yml
docs/.gitignore
docs/Makefile
docs/_config.yml
docs/_toc.yml
docs/api_reference.md
docs/bcftools_emulation.md
docs/bgen.md
docs/bgen_conversion.md
docs/build.sh
docs/cli_ref.md
docs/format_conversion.md
docs/installation.md
docs/intro.md
docs/plink.md
docs/plink_conversion.md
docs/reading_vcz.md
docs/storage_backends.md
docs/vcf.md
docs/_ext/sphinx_click_groups.py
docs/data/make_sample_vcz.py
docs/data/sample.vcz.zip
lib/compute.c
lib/formats.c
lib/meson.build
lib/test_compute.c
lib/test_formats.c
lib/test_zlib.c
lib/vcztools.h
performance/README.md
performance/bench_padding.py
performance/benchmarks.md
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performance/compare.py
performance/encoding_microbench.py
tests/__init__.py
tests/conftest.py
tests/test_azure.py
tests/test_bcftools_validation.py
tests/test_bgen.py
tests/test_bgen_validation.py
tests/test_calculate.py
tests/test_cli.py
tests/test_cpython_interface.py
tests/test_dtype_matrix.py
tests/test_filter.py
tests/test_float_dtypes.py
tests/test_format_encoder.py
tests/test_plink.py
tests/test_plink_validation.py
tests/test_public_api.py
tests/test_query.py
tests/test_regions.py
tests/test_retrieval.py
tests/test_stats.py
tests/test_tskit_data.py
tests/test_utils.py
tests/test_variant_filter.py
tests/test_vcf_roundtrip.py
tests/test_vcf_writer.py
tests/test_vcz_builder.py
tests/utils.py
tests/vcz_builder.py
tests/data/txt/regions-3col.tsv
tests/data/txt/samples.txt
tests/data/txt/samples_empty.txt
tests/data/vcf/1kg_2020_chr20_annotations.bcf
tests/data/vcf/1kg_2020_chr20_annotations.bcf.csi
tests/data/vcf/1kg_2020_chr20_annotations.vcz.zip
tests/data/vcf/1kg_2020_chrM.vcf.gz
tests/data/vcf/1kg_2020_chrM.vcf.gz.csi
tests/data/vcf/1kg_2020_chrM.vcz.zip
tests/data/vcf/chr22.vcf.gz
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tests/data/vcf/chr22.vcz.zip
tests/data/vcf/field_type_combos.vcf.gz
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tests/data/vcf/field_type_combos.vcz.zip
tests/data/vcf/msprime_diploid.vcf.gz
tests/data/vcf/msprime_diploid.vcf.gz.csi
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tests/data/vcf/regenerate_vcz_fixtures.py
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tests/data/vcf/sample-split-alleles.vcf.gz.csi
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tests/data/vcf/sample.vcz.zip
tests/data/vcf/sample.vcz3.zip
validation/.gitignore
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validation/README.md
validation/__init__.py
validation/conftest.py
validation/generate_data.py
validation/helpers.py
validation/reference.py
validation/test_bgenix.py
validation/test_bolt_lmm.py
validation/test_plink19.py
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vcztools/__init__.py
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vcztools/_version.py
vcztools/bcftools_filter.py
vcztools/bgen.py
vcztools/calculate.py
vcztools/cli.py
vcztools/constants.py
vcztools/format_encoder.py
vcztools/plink.py
vcztools/provenance.py
vcztools/query.py
vcztools/regions.py
vcztools/retrieval.py
vcztools/stats.py
vcztools/utils.py
vcztools/variant_filter.py
vcztools/vcf_writer.py
vcztools/virtual_fields.py
vcztools.egg-info/PKG-INFO
vcztools.egg-info/SOURCES.txt
vcztools.egg-info/dependency_links.txt
vcztools.egg-info/entry_points.txt
vcztools.egg-info/requires.txt
vcztools.egg-info/top_level.txt