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refactor!: clean up app #474

Merged
merged 120 commits into from
Aug 7, 2023
Merged

refactor!: clean up app #474

merged 120 commits into from
Aug 7, 2023

Commits on May 10, 2023

  1. refactor: update TokenType + remove protein termination classifier

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    korikuzma committed May 10, 2023
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  2. refactor: Remove TokenMatchType (not necessary)

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    korikuzma committed May 10, 2023
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  3. forgot to remove additional match_type

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    korikuzma committed May 10, 2023
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  4. refactor: clean up handling unknown tokens

    @korikuzma
    korikuzma committed May 10, 2023
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  5. refactor: Rename GeneMatchToken to GeneToken

    @korikuzma
    korikuzma committed May 10, 2023
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  6. refactor: create AltType str enum

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    korikuzma committed May 10, 2023
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  7. refactor: update TokenType type

    @korikuzma
    korikuzma committed May 10, 2023
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  8. refactor: remove LookupType enum (not used)

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    korikuzma committed May 10, 2023
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Commits on May 22, 2023

  1. wip: add work for tokenizers

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    korikuzma committed May 22, 2023
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Commits on May 26, 2023

  1. wip: storing progress

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Commits on Jun 6, 2023

  1. wip: store progress for delins

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    korikuzma committed Jun 6, 2023
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Commits on Jun 12, 2023

  1. wip: store progress for cdna insertion

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    korikuzma committed Jun 12, 2023
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  2. wip: store progress for ref agree

    @korikuzma
    korikuzma committed Jun 12, 2023
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  3. wip: minor cleanup of validators

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    korikuzma committed Jun 12, 2023
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Commits on Jun 13, 2023

  1. wip: store progress for protein stop gain

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    korikuzma committed Jun 13, 2023
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  2. wip: store initial work for genomic dup

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    korikuzma committed Jun 13, 2023
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Commits on Jun 20, 2023

  1. wip: store progress for genomic ambiguous dups

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  2. wip: progress for genomic del

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    korikuzma committed Jun 20, 2023
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Commits on Jun 22, 2023

  1. wip: remove canonical variation work

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    korikuzma committed Jun 22, 2023
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  2. wip: fix classifiers

    @korikuzma
    korikuzma committed Jun 22, 2023
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  3. wip: handle if mane none in translators

    @korikuzma
    korikuzma committed Jun 22, 2023
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  4. wip: tmp stop running gh actions

    @korikuzma
    korikuzma committed Jun 22, 2023
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Commits on Jun 26, 2023

  1. wip: more progress for normalize

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Commits on Jun 27, 2023

  1. wip: store more progress

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  2. wip: add genomic del ambiguous

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    korikuzma committed Jun 27, 2023
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Commits on Jun 28, 2023

  1. iMerge branch 'main' into issue-332-kori-merge-main

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    korikuzma committed Jun 28, 2023
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  2. wip: fix tokenizers

    @korikuzma
    korikuzma committed Jun 28, 2023
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  3. wip: clean up classifier tests

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    korikuzma committed Jun 28, 2023
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  4. wip: rename coding dna --> cdna

    @korikuzma
    korikuzma committed Jun 28, 2023
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  5. wip: storing progress for dup1

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    korikuzma committed Jun 28, 2023
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Commits on Jun 29, 2023

  1. wip: dup/del progress

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    korikuzma committed Jun 29, 2023
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Commits on Jun 30, 2023

  1. wip: more progress for dup del

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    korikuzma committed Jun 30, 2023
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  2. wip: get hgvs dup del mode tests to pass

    @korikuzma
    korikuzma committed Jun 30, 2023
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  3. wip: fix bug in to_vrs

    @korikuzma
    korikuzma committed Jun 30, 2023
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Commits on Jul 5, 2023

  1. wip: rm unused fixture + fix normalize test

    @korikuzma
    korikuzma committed Jul 5, 2023
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Commits on Jul 13, 2023

  1. Merge branch 'main' into issue-332-kori

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    korikuzma committed Jul 13, 2023
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  2. wip: use local cool-seq-tool

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    korikuzma committed Jul 13, 2023
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  3. wip: classification.gene --> classification.gene_token

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    korikuzma committed Jul 13, 2023
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  4. wip: fixes to gene -> gene_token in classifiers

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    korikuzma committed Jul 13, 2023
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Commits on Jul 14, 2023

  1. wip: fix cool-seq-tool imports

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    korikuzma committed Jul 14, 2023
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  2. wip: fix setting gene in genomic translators 

    sometimes gene token does not exist
    @korikuzma
    korikuzma committed Jul 14, 2023
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  3. wip: fix case for BRAF V512E test in normalize

    @korikuzma
    korikuzma committed Jul 14, 2023
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  4. wip: update genomic sub for normalize

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    korikuzma committed Jul 14, 2023
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  5. wip: rm support for some acs

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    korikuzma committed Jul 14, 2023
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Commits on Jul 16, 2023

  1. wip: more progress for genomic

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    korikuzma committed Jul 16, 2023
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Commits on Jul 17, 2023

  1. wip: initial work for to_copy_number

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    korikuzma committed Jul 17, 2023
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  2. wip: sort translation results 

    mane select -> mane plus clinical -> longest compatible remaining ->
grch38 -> na
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  3. wip: rm get_mane_valid_result

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    korikuzma committed Jul 17, 2023
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  4. wip: sort translation result

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    korikuzma committed Jul 17, 2023
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  5. wip: fix gnomad vcf / genomic insertion

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    korikuzma committed Jul 17, 2023
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Commits on Jul 18, 2023

  1. wip: fix classifier test

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    korikuzma committed Jul 18, 2023
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  2. wip: more fixes

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    korikuzma committed Jul 18, 2023
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Commits on Jul 19, 2023

  1. wip: fix gnomad vcf to protein

    @korikuzma
    korikuzma committed Jul 19, 2023
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  2. wip: fix cnv tests

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    korikuzma committed Jul 19, 2023
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Commits on Jul 20, 2023

  1. wip: make mappings an instance var

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  2. wip: update initializing cst

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    korikuzma committed Jul 20, 2023
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  3. wip: rm gene_tokens

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    korikuzma committed Jul 20, 2023
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  4. wip: clean up some todos

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  5. wip: more cleanup

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  6. wip: clean up some flake8 errors

    @korikuzma
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Commits on Jul 21, 2023

  1. wip: clean up del/dup ambiguous translate method

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  2. wip: clean up genomic del/dup translator

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    korikuzma committed Jul 21, 2023
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  3. wip: flake8 + fix gnomad vcf to protein

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  4. wip: more flake8

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Commits on Jul 24, 2023

  1. wip: rm todos for issues 

    Placed these inside the issues on GH
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  2. wip: fix gnomad vcf deletions

    @korikuzma
    korikuzma committed Jul 24, 2023
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  3. wip: update cool-seq-tool version

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  4. wip: transcripts --> accessions

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  5. wip: rm todos (made new issues / commented on existing)

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  6. wip: coding dna --> cdna

    @korikuzma
    korikuzma committed Jul 24, 2023
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  7. wip: validate gene pos

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    korikuzma committed Jul 24, 2023
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  8. wip: update validation checks

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    korikuzma committed Jul 24, 2023
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  9. wip: rm todo check liftover note

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Commits on Jul 25, 2023

  1. wip: remove unused code

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  2. wip: rename instance vars + imports for vrs-python

    @korikuzma
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  3. wip: clean up class instance vars

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  4. wip: rm CodonTable class, create function in gnomad vcf to protein

    @korikuzma
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  5. wip: more flake8

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  6. wip: HGVSDupDelModeEnum -> HGVSDupDelModeOption + fix CopyChange import

    @korikuzma
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  7. wip: clean up validator tests

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Commits on Jul 26, 2023

  1. wip: move validator fixtures

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  2. wip: rm duplications from to_vrs

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  3. wip: add amplification import + allow parentheses in hgvs

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  4. wip: accidentally used wrong var name

    @korikuzma
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  5. wip: update translator tests + fix translator bugs

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  6. wip: add amplification validator test

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  7. wip: move classifier tests back to yaml

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  8. wip: move validator tests back to yaml

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  9. wip: refactor tokenizer tests

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Commits on Jul 27, 2023

  1. wip: cleanup schemas (flake8/enum changes)

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  2. wip: cleanup classifiers (flake8)

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  3. wip: flake8 for normalize + utils 

    moved get_hgvs_dup_del_mode to normalize since it was only being called
there
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  4. wip: cleanup tests (flake8/vulture)

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  5. wip: resolve flake8 errors

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  6. wip: update gh actions

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    korikuzma committed Jul 27, 2023
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  7. add more comments

    @korikuzma
    korikuzma committed Jul 27, 2023
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  8. bump version

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Commits on Jul 29, 2023

  1. cleanup: replace flake8 with ruff

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  2. Merge branch 'main' into issue-332-kori

    @korikuzma
    korikuzma committed Jul 29, 2023
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  3. cleanup: add black

    @korikuzma
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  4. style: add isort to ruff select

    @korikuzma
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  5. fix: hgvs_to_copy_number_count requires baseline_copies

    @korikuzma
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  6. cicd: combine black + ruff into one job

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  7. style: remove old noqa

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Commits on Jul 30, 2023

  1. refactor: create methods for validating pos

    @korikuzma
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  2. refactor: add method for validating protein hgvs classification

    @korikuzma
    korikuzma committed Jul 30, 2023
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  3. refactor: cdna + protein translators

    @korikuzma
    korikuzma committed Jul 30, 2023
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Commits on Jul 31, 2023

  1. style: ignore ANN003 - missing-type-kwargs

    @korikuzma
    korikuzma committed Jul 31, 2023
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  2. fix: classifier import

    @korikuzma
    korikuzma committed Jul 31, 2023
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Commits on Aug 1, 2023

  1. docs: cleanup readme

    @korikuzma
    korikuzma committed Aug 1, 2023
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  2. refactor: ensure unique list of warnings in service response

    @korikuzma
    korikuzma committed Aug 1, 2023
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  3. fix: validate Allele in to_vrs_allele

    @korikuzma
    korikuzma committed Aug 1, 2023
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  4. pr review changes 

    - update docstrings / return types
- update license dates
- add metadata to setup.cfg
- ignore E501 in ruff since it will be handled by black
- update get_translations to accept valid results rather than validation
  summary
- update enum in main.py to Tag + add Main tag for /normalize and
  /to_vrs
    @korikuzma
    korikuzma committed Aug 1, 2023
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  5. fix: forgot to update return in to copy number variation

    @korikuzma
    korikuzma committed Aug 1, 2023
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  6. update readme on why we return cdna when given gene genomic change

    @korikuzma
    korikuzma committed Aug 1, 2023
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  7. pr review changes 

    - Remove unused classification_type method
- Update type hints / return types
- Remove del_or_dup and use AltType
    @korikuzma
    korikuzma committed Aug 1, 2023
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  8. update invalid tests for normalize + put in todo reminder

    @korikuzma
    korikuzma committed Aug 1, 2023
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Commits on Aug 2, 2023

  1. tests: add test for genomic delins change w gene

    @korikuzma
    korikuzma committed Aug 2, 2023
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  2. tests: stop checking exact gene normalizer response 

    - Assumes gene normalizer works correctly. Only checks that gene_context
  is present if given in the test fixture
    @korikuzma
    korikuzma committed Aug 2, 2023
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  3. pr review changes: update type hints + docstrings

    @korikuzma
    korikuzma committed Aug 2, 2023
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