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Fix indexing issues #44

Merged
merged 21 commits into from
Feb 28, 2024
Merged

Fix indexing issues #44

merged 21 commits into from
Feb 28, 2024

Commits on Feb 26, 2024

  1. Disable extra empty regions

    @jeromekelleher
    jeromekelleher committed Feb 26, 2024
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  2. Mostly working parallel explode

    @jeromekelleher
    jeromekelleher committed Feb 26, 2024
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Commits on Feb 27, 2024

  1. Some notes on problems and workarounds

    @jeromekelleher
    jeromekelleher committed Feb 27, 2024
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  2. Factor needlessly slow Path/string double check

    @jeromekelleher
    jeromekelleher committed Feb 27, 2024
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  3. Refactored index tests into vcf_utils class

    @jeromekelleher
    jeromekelleher committed Feb 27, 2024
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  4. Refactor vcf partition tests into test_vcf_utils

    @jeromekelleher
    jeromekelleher committed Feb 27, 2024
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  5. Rename some test files and start move into vcf utils

    @jeromekelleher
    jeromekelleher committed Feb 27, 2024
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  6. Move CSI and Tabix code into vcf_utils module

    @jeromekelleher
    jeromekelleher committed Feb 27, 2024
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  7. Add tabix index for example with extra contigs in header

    @jeromekelleher
    jeromekelleher committed Feb 27, 2024
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  8. Move around data files

    @jeromekelleher
    jeromekelleher committed Feb 27, 2024
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  9. Fix various issues with indexing, partial refactor

    @jeromekelleher
    jeromekelleher committed Feb 27, 2024
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Commits on Feb 28, 2024

  1. Minimal changes to get things working again

    @jeromekelleher
    jeromekelleher committed Feb 28, 2024
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  2. Add vcf-partition command and isolate Tabix issue

    @jeromekelleher
    jeromekelleher committed Feb 28, 2024
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  3. Fix bug in Tabix handling

    @jeromekelleher
    jeromekelleher committed Feb 28, 2024
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  4. Fix region sorting problem

    @jeromekelleher
    jeromekelleher committed Feb 28, 2024
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  5. Add test example for ordering issue

    @jeromekelleher
    jeromekelleher committed Feb 28, 2024
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  6. Port code into vcf_utils file

    @jeromekelleher
    jeromekelleher committed Feb 28, 2024
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  7. Factor out fsspec calls

    @jeromekelleher
    jeromekelleher committed Feb 28, 2024
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  8. Pad out tests

    @jeromekelleher
    jeromekelleher committed Feb 28, 2024
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  9. Remove unused utilities

    @jeromekelleher
    jeromekelleher committed Feb 28, 2024
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  10. Added format_version to JSON config files

    @jeromekelleher
    jeromekelleher committed Feb 28, 2024
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