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Mark Duplicate Bitflag & include secondary & Supplimentary Reads #934

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wants to merge 17 commits into from
Closed

Mark Duplicate Bitflag & include secondary & Supplimentary Reads #934

wants to merge 17 commits into from

Commits on Aug 29, 2023

  1. consolodate imports

    @JoeVieira
    JoeVieira committed Aug 29, 2023
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  2. consolodate imports

    @JoeVieira
    JoeVieira committed Aug 29, 2023
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  3. Logic to calculate scores duplicate scores using htslib duplication d… 

    …etection strategies.

Set duplicate flag as needed on all reads inside Template which are not the top scoring read set.
    @JoeVieira
    JoeVieira committed Aug 29, 2023
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  4. basic test for duplicate marking

    @JoeVieira
    JoeVieira committed Aug 29, 2023
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  5. use mark dup flag to gate functionality, reorganize comments

    @JoeVieira
    JoeVieira committed Aug 29, 2023
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  6. single ended tests

    @JoeVieira
    JoeVieira committed Aug 29, 2023
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Commits on Aug 30, 2023

  1. simplify comparison and score calculation into one method, using sort… 

    …With.
    @JoeVieira
    JoeVieira committed Aug 30, 2023
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  2. comments

    @JoeVieira
    JoeVieira committed Aug 30, 2023
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  3. adjustments to tests for more explicit tie breaking.

    @JoeVieira
    JoeVieira committed Aug 30, 2023
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  4. ensure dups are not marked if flag not passed

    @JoeVieira
    JoeVieira committed Aug 30, 2023
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Commits on Aug 31, 2023

  1. remove extra linebreak

    @JoeVieira
    JoeVieira committed Aug 31, 2023
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  2. optionally include secondary & supplementary reads.

    @JoeVieira
    JoeVieira committed Aug 31, 2023
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Commits on Sep 1, 2023

  1. doc strings / usage docs

    @JoeVieira
    JoeVieira committed Sep 1, 2023
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  2. remove extra line break

    @JoeVieira
    JoeVieira committed Sep 1, 2023
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  3. formatting

    @JoeVieira
    JoeVieira committed Sep 1, 2023
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  4. formatting

    @JoeVieira
    JoeVieira committed Sep 1, 2023
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Commits on Sep 12, 2023

  1. clarify duplicate comments

    @JoeVieira
    JoeVieira authored Sep 12, 2023
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