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Moving ORF as an AbstractGenomicInterval{T} #34

Merged
merged 40 commits into from
Jul 1, 2024
Merged

Moving ORF as an AbstractGenomicInterval{T} #34

merged 40 commits into from
Jul 1, 2024

Commits on May 18, 2024

  1. First steps towards ORFs as GenomicIntervals

    @camilogarciabotero
    camilogarciabotero committed May 18, 2024
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  2. Some io fixes, and tests

    @camilogarciabotero
    camilogarciabotero committed May 18, 2024
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Commits on May 21, 2024

  1. Some attempts to correct tests

    @camilogarciabotero
    camilogarciabotero committed May 21, 2024
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Commits on May 23, 2024

  1. refactor: Remove unused code in runtests.jl

    @camilogarciabotero
    camilogarciabotero committed May 23, 2024
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  2. Relax some tests

    @camilogarciabotero
    camilogarciabotero committed May 23, 2024
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Commits on May 25, 2024

  1. Move get_variable_name outside loop

    @camilogarciabotero
    camilogarciabotero committed May 25, 2024
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Commits on Jun 3, 2024

  1. Major refactor of the ORF type and also add some groundwork for RBS

    @camilogarciabotero
    camilogarciabotero committed Jun 3, 2024
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  2. Update deps

    @camilogarciabotero
    camilogarciabotero committed Jun 3, 2024
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  3. Improve getindex with some types

    @camilogarciabotero
    camilogarciabotero committed Jun 3, 2024
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  4. Up translate and other utils are now more stable

    @camilogarciabotero
    camilogarciabotero committed Jun 3, 2024
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  5. Update the min_len into minlen

    @camilogarciabotero
    camilogarciabotero committed Jun 3, 2024
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  6. Remove unused function

    @camilogarciabotero
    camilogarciabotero committed Jun 3, 2024
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  7. Update deps

    @camilogarciabotero
    camilogarciabotero committed Jun 3, 2024
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Commits on Jun 5, 2024

  1. Refactor finders with correct score calculation

    @camilogarciabotero
    camilogarciabotero committed Jun 5, 2024
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  2. chore: Update Julia version to 1.10.4

    @camilogarciabotero
    camilogarciabotero committed Jun 5, 2024
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Commits on Jun 8, 2024

  1. Update README

    @camilogarciabotero
    camilogarciabotero committed Jun 8, 2024
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  2. Manifest update

    @camilogarciabotero
    camilogarciabotero committed Jun 8, 2024
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  3. Create Features struct and include it in the ORF as the NamedTuple field

    @camilogarciabotero
    camilogarciabotero committed Jun 8, 2024
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  4. Refactor code to improve precompile file size and loading speed

    @camilogarciabotero
    camilogarciabotero committed Jun 8, 2024
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  5. Update io methods

    @camilogarciabotero
    camilogarciabotero committed Jun 8, 2024
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  6. Remove getorfs.jl

    @camilogarciabotero
    camilogarciabotero committed Jun 8, 2024
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  7. Update finder methods with the Feature struct

    @camilogarciabotero
    camilogarciabotero committed Jun 8, 2024
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  8. Update lors from BMC taking only one argument

    @camilogarciabotero
    camilogarciabotero committed Jun 8, 2024
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  9. Update naivecolletor.jl to new BMC losr

    @camilogarciabotero
    camilogarciabotero committed Jun 8, 2024
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Commits on Jun 9, 2024

  1. Update iscoding method, so that it takes an ORF directly

    @camilogarciabotero
    camilogarciabotero committed Jun 9, 2024
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  2. Update score method to handle directly the score field

    @camilogarciabotero
    camilogarciabotero committed Jun 9, 2024
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  3. Update finder methods kwargs to only use the scheme kwargs

    @camilogarciabotero
    camilogarciabotero committed Jun 9, 2024
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  4. After fixing the lors from BMC package the lordr is also updated, req… 

    …uires a new version of BMC.
    @camilogarciabotero
    camilogarciabotero committed Jun 9, 2024
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  5. Update to BMC v0.10.1

    @camilogarciabotero
    camilogarciabotero committed Jun 9, 2024
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  6. Update some docstring in lordr

    @camilogarciabotero
    camilogarciabotero committed Jun 9, 2024
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Commits on Jul 1, 2024

  1. Update deps

    @camilogarciabotero
    camilogarciabotero committed Jul 1, 2024
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  2. Update getindex of ORFs

    @camilogarciabotero
    camilogarciabotero committed Jul 1, 2024
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  3. reduce ORF type fields: get rid of seq

    @camilogarciabotero
    camilogarciabotero committed Jul 1, 2024
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  4. Add new internal methods for calling var names and symbol

    @camilogarciabotero
    camilogarciabotero committed Jul 1, 2024
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  5. Update docs simple coding rule

    @camilogarciabotero
    camilogarciabotero committed Jul 1, 2024
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  6. Up deps and extras

    @camilogarciabotero
    camilogarciabotero committed Jul 1, 2024
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  7. Add YAML extra

    @camilogarciabotero
    camilogarciabotero committed Jul 1, 2024
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  8. Update gitignore and delete Manifest

    @camilogarciabotero
    camilogarciabotero committed Jul 1, 2024
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  9. Update actions cache and cov

    @camilogarciabotero
    camilogarciabotero committed Jul 1, 2024
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  10. refactor: Simplify NaiveCollector createorfs function

    @camilogarciabotero
    camilogarciabotero committed Jul 1, 2024
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