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GroupReadsByUmi may fail when marking duplicates including secondary/supplementary reads #964

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Commits on Jan 31, 2024

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  3. fix: properly template-coordinate sort and duplicate mark secondary a…

    …nd supplementary reads
    
    Secondary and supplementary reads must use the coordinates of the
    primary alignments within the template, otherwise they will not
    guaranteed to be next the primary alignments in the file.  Therefore,
    we've added the "rp" and "mp" tags to store the SA-tag equivalent
    information for the primary alignment.  This keeps information about the
    primary alignments with the secondary and supplementary alignments.
    nh13 committed Jan 31, 2024
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