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Upgrade to using ska2 #383

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wants to merge 30 commits into from
Closed

Upgrade to using ska2 #383

wants to merge 30 commits into from

Commits on Jun 22, 2023

  1. Mask repeats with ska2

    @nickjcroucher
    nickjcroucher committed Jun 22, 2023
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Commits on Sep 7, 2023

  1. Add R plotting script

    @nickjcroucher
    nickjcroucher committed Sep 7, 2023
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  2. Update R dependencies for plotting

    @nickjcroucher
    nickjcroucher committed Sep 7, 2023
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  3. Add plotting test

    @nickjcroucher
    nickjcroucher committed Sep 7, 2023
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  4. Remove jellyfish deletion command

    @nickjcroucher
    nickjcroucher committed Sep 7, 2023
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  5. Update obsolete macro

    @nickjcroucher
    nickjcroucher committed Sep 7, 2023
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  6. Update from setup.py to pip

    @nickjcroucher
    nickjcroucher committed Sep 7, 2023
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  7. Correct interpreter path

    @nickjcroucher
    nickjcroucher committed Sep 7, 2023
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  8. Remove obsolete deletion command

    @nickjcroucher
    nickjcroucher committed Sep 7, 2023
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  9. Add unique sequences for ska test

    @nickjcroucher
    nickjcroucher committed Sep 7, 2023
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  10. Define prototype for main

    @nickjcroucher
    nickjcroucher committed Sep 7, 2023
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  11. Add sequences to test

    @nickjcroucher
    nickjcroucher committed Sep 7, 2023
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  12. Fix kmer length

    @nickjcroucher
    nickjcroucher committed Sep 7, 2023
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Commits on Sep 8, 2023

  1. Fix annotation

    @nickjcroucher
    nickjcroucher committed Sep 8, 2023
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  2. Ensure latest llvm

    @nickjcroucher
    nickjcroucher committed Sep 8, 2023
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  3. Remove coverage flag from OSX compilation

    @nickjcroucher
    nickjcroucher committed Sep 8, 2023
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  4. Distribute libclang across clang versions

    @nickjcroucher
    nickjcroucher committed Sep 8, 2023
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  5. Remove sudo to prevent cache permissions problems

    @nickjcroucher
    nickjcroucher committed Sep 8, 2023
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  6. Enable taxon label size adjustment

    @nickjcroucher
    nickjcroucher committed Sep 8, 2023
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  7. Enable direct annotation of the tree

    @nickjcroucher
    nickjcroucher committed Sep 8, 2023
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  8. Add clade annotation to plotting test

    @nickjcroucher
    nickjcroucher committed Sep 8, 2023
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  9. Add input validation

    @nickjcroucher
    nickjcroucher committed Sep 8, 2023
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  10. Annotate main function

    @nickjcroucher
    nickjcroucher committed Sep 8, 2023
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Commits on Sep 9, 2023

  1. Ensure compatibility with different inputs

    @nickjcroucher
    nickjcroucher committed Sep 9, 2023
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  2. Add comprehensive plotting tests

    @nickjcroucher
    nickjcroucher committed Sep 9, 2023
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Commits on Sep 10, 2023

  1. Fix type in commands

    @nickjcroucher
    nickjcroucher committed Sep 10, 2023
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  2. Update with links to plotting advice

    @nickjcroucher
    nickjcroucher committed Sep 10, 2023
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Commits on Sep 11, 2023

  1. Add plotting documentation

    @nickjcroucher
    nickjcroucher committed Sep 11, 2023
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  2. Add necessary plotting commands

    @nickjcroucher
    nickjcroucher committed Sep 11, 2023
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  3. Fix broken link

    @nickjcroucher
    nickjcroucher committed Sep 11, 2023
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