VCF reader unit tests#3

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amd-pdebski:vcf_unit_tests

Commits on May 9, 2025

Create ci.yml
amd-pdebski
authored

Commits on Jun 7, 2025

WIP: VCF

mwiewior
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Piotr Dębski
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Refactor

mwiewior
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Piotr Dębski
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Parsing info draft

mwiewior
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Working parser

mwiewior
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Refactoring infos

mwiewior
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async-trait downgrade

mwiewior
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Reverting to 0-based

mwiewior
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Renamed columns

mwiewior
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Piotr Dębski
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Add retry go operator

mwiewior
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Piotr Dębski
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Add IOTimeout

mwiewior
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Piotr Dębski
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Fixing streams

mwiewior
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Piotr Dębski
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Adding s3

mwiewior
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fix: Basic fields

mwiewior
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Adding support for remote reading of uncompressed VCFs

mwiewior
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Fix header

mwiewior
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Optimize variant_end

mwiewior
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Enabling projection

mwiewior
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Fixing local vcf without compression and gcs reads optimization

mwiewior
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Piotr Dębski
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Fixing local vcf reading with no compression

mwiewior
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Describe VCF

mwiewior
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fix: Tag case sensitive

mwiewior
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add unit tests for storage

Piotr Dębski
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Piotr Dębski
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add performance/time measurement for batch processing vcf with noodles

amd-pdebski
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Piotr Dębski
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add retry mechanism and adjust chunk size along with minimal concurrent fetches

amd-pdebski
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Piotr Dębski
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Refactor scan to separate projected schema computation and use Field::nullable flag

amd-pdebski
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propagate builders errors

amd-pdebski
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Piotr Dębski
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Optimize OptionalField::new() to use with_capacity

amd-pdebski
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Piotr Dębski
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Improve info_to_arrow_type logic

amd-pdebski
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Piotr Dębski
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refactor format fields and cleanup code

amd-pdebski
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complete bgzf compressed files format ingestion tests

amd-pdebski
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add bgzf test in similar format to test_noodles.rs

amd-pdebski
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add docker-compose for testing iceberg

amd-pdebski
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Cleanup a few warnings

mwiewior
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Bump runner image

mwiewior
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Update storage.rs

amd-pdebski
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Update storage.rs

amd-pdebski
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Update storage.rs

amd-pdebski
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Update storage.rs

amd-pdebski
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