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Restore lost functionality post-streaming #170

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willbradshaw opened this issue Jan 30, 2025 · 0 comments

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enhancement priority_1

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willbradshaw commented Jan 30, 2025

As part of moving the pipeline over to streaming, some important functionality was lost:

Grouping for deduplication
Deduplication with Clumpify
Duplicate annotation with Bowtie2
Addition of duplicate information to output TSV
Clade counting

Some or all of this should be restored in a future version. Duplicate marking in particular is high priority.

willbradshaw added enhancement priority_1 labels

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