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pre-alignment collate options#268

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Commits on Mar 4, 2020

• add selection of pre-alignment collate methods (simple collation not enough for realignment of coordinate-sorted input)

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• move initial collate step upstream (allows subssampling to be retained in realignment)

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• extend port extraction in command arrays to recursively check inside elements which are themselves arrays

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• extend samtool -F filter to remove supplementary reads before subsampling (for realignment)

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Commits on Dec 4, 2021

• Merge branch 'devel' into pa_collate_options

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