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Tool to consensus call overlapping bases in paired end reads. Adds direct support in the consensus calling tools too. #805

Merged
merged 25 commits into from
Apr 4, 2022
Merged

Tool to consensus call overlapping bases in paired end reads. Adds direct support in the consensus calling tools too. #805

merged 25 commits into from
Apr 4, 2022

Commits on Mar 21, 2022

  1. Personal tool to correct overlapping bases

    @nh13
    nh13 committed Mar 21, 2022
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  2. fixups

    @nh13
    nh13 committed Mar 21, 2022
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  3. add a few options

    @nh13
    nh13 committed Mar 21, 2022
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  4. doc

    @nh13
    nh13 committed Mar 21, 2022
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  5. fix

    @nh13
    nh13 committed Mar 21, 2022
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  6. fixups

    @nh13
    nh13 committed Mar 21, 2022
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  7. move out of personal

    @nh13
    nh13 committed Mar 21, 2022
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  8. quick and dirty wiring

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    nh13 committed Mar 21, 2022
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  9. unit tests

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    nh13 committed Mar 21, 2022
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Commits on Mar 22, 2022

  1. one more test

    @nh13
    nh13 committed Mar 22, 2022
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Commits on Mar 25, 2022

  1. Apply suggestions from code review 

    Co-authored-by: Tim Fennell <[email protected]>
    @nh13 @tfenne
    nh13 and tfenne authored Mar 25, 2022
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  2. Update src/main/scala/com/fulcrumgenomics/bam/CallOverlappingConsensu… 

    …sBases.scala
    @nh13
    nh13 authored Mar 25, 2022
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  3. Apply suggestions from code review 

    Co-authored-by: Tim Fennell <[email protected]>
    @nh13 @tfenne
    nh13 and tfenne authored Mar 25, 2022
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  4. Apply suggestions from code review 

    Co-authored-by: Tim Fennell <[email protected]>
    @nh13 @tfenne
    nh13 and tfenne authored Mar 25, 2022
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  5. review fixups

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    nh13 committed Mar 25, 2022
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Commits on Mar 26, 2022

  1. some review fixups

    @nh13
    nh13 committed Mar 26, 2022
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  2. fix tests

    @nh13
    nh13 committed Mar 26, 2022
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  3. Apply suggestions from code review 

    Co-authored-by: Tim Fennell <[email protected]>
    @nh13 @tfenne
    nh13 and tfenne authored Mar 26, 2022
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  4. revert sumBy, not in scala 2.13

    @nh13
    nh13 committed Mar 26, 2022
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  5. simplify OverlappingBasesConsensusCaller.call

    @nh13
    nh13 committed Mar 26, 2022
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  6. fixups

    @nh13
    nh13 committed Mar 26, 2022
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  7. remove options

    @nh13
    nh13 committed Mar 26, 2022
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  8. add agreement and disagreement strategies to tests

    @nh13
    nh13 committed Mar 26, 2022
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Commits on Apr 4, 2022

  1. revert sort message

    @nh13
    nh13 committed Apr 4, 2022
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  2. review fixups

    @nh13
    nh13 committed Apr 4, 2022
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