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Demultiplexed FASTQ support #23

Merged
merged 16 commits into from
Sep 6, 2023
Merged

Demultiplexed FASTQ support #23

merged 16 commits into from
Sep 6, 2023

Commits on Aug 30, 2023

  1. Set version to 3.7.0-SNAPSHOT

    @mtomko
    mtomko committed Aug 30, 2023
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  2. Close all iterators 

    This is a minor bugfix
    @mtomko
    mtomko committed Aug 30, 2023
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Commits on Aug 31, 2023

  1. Optional column barcode policy 

    For demultiplexed FASTQs, there is no column barcode policy
    @mtomko
    mtomko committed Aug 31, 2023
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Commits on Sep 5, 2023

  1. DmuxedIterable

    @mtomko
    mtomko committed Sep 5, 2023
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  2. Demultiplexed reads sources

    @mtomko
    mtomko committed Sep 5, 2023
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  3. Add stub implementation of CloseableIterator

    @mtomko
    mtomko committed Sep 5, 2023
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  4. Demultiplexed barcode sources

    @mtomko
    mtomko committed Sep 5, 2023
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  5. barcodeSource supports demultiplexed inputs

    @mtomko
    mtomko committed Sep 5, 2023
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  6. Command-line support 

    Add `--demultiplexed` flag
    @mtomko
    mtomko committed Sep 5, 2023
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  7. Basic integration test

    @mtomko
    mtomko committed Sep 5, 2023
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  8. Add some unmatched constructs

    @mtomko
    mtomko committed Sep 5, 2023
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  9. Add paired-end integration test

    @mtomko
    mtomko committed Sep 5, 2023
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  10. Update CHANGELOG

    @mtomko
    mtomko committed Sep 5, 2023
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  11. Update manual

    @mtomko
    mtomko committed Sep 5, 2023
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Commits on Sep 6, 2023

  1. Add new integration tests to all target

    @mtomko
    mtomko committed Sep 6, 2023
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  2. Move computation of FoundBarcode up one level

    @mtomko
    mtomko committed Sep 6, 2023
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