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Merge pull request #21 from uab-cgds-worthey/dev
DITTO using Neural Networks and SHAP
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‎.editorconfig‎

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# top-most EditorConfig file
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root = true
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# global definitions
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[*]
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end_of_line = lf
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insert_final_newline = true
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trim_trailing_whitespace = true
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indent_size = 4
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indent_style = space
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# override indents for specific filetypes
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[*.{md,yml,yaml,html,css,scss,js,cff}]
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indent_size = 2

‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: Bug report
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about: Create a report to help us improve
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title: ''
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labels: bug
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assignees: ''
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---
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**Describe the bug**
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A clear and concise description of what the bug is.
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**To Reproduce**
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Steps to reproduce the behavior:
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**Expected behavior**
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A clear and concise description of what you expected to happen.
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**Screenshots**
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If applicable, add screenshots to help explain your problem.
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**Environment used**
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OS, relevant tool versions, etc.
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**Additional context**
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Add any other context about the problem here.

‎.github/ISSUE_TEMPLATE/feature_request.md‎

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---
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name: Feature request
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about: Suggest an idea for this project
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title: ''
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labels: enhancement
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assignees: ''
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---
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**Is your feature request related to a problem? Please describe.**
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A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
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**Describe the solution you'd like**
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A clear and concise description of what you want to happen.
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**Describe alternatives you've considered**
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A clear and concise description of any alternative solutions or features you've considered.
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**Additional context**
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Add any other context or screenshots about the feature request here.

‎.github/pull_request_template.md‎

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* **Please check if the PR fulfills these requirements**
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- [ ] Tested as per the documentation and they passed
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- [ ] Docs have been added / updated (for bug fixes / features)
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* **What kind of change does this PR introduce?** (Bug fix, feature, docs update, ...)
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* **What is the current behavior?** (You can also link to an open issue here)
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* **What is the new behavior (if this is a feature change)?**
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* **Does this PR introduce a breaking change?** (What changes might users need to make in their application due to this PR?)
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* **Other information**:

‎.github/workflows/linting.yml‎

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name: Linting- Markdown,Shell
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on:
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push:
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workflow_dispatch:
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jobs:
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markdown-linting:
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name: Markdown lint
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runs-on: ubuntu-22.04
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steps:
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- name: Checkout Code
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uses: actions/checkout@v3
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- name: markdownlint-cli
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uses: nosborn/[email protected]
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with:
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files: .
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config_file: ".markdownlint.json"
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# dot: false
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# ignore_files: '".git*/**"'
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markdown-check-links:
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name: Markdown - checking links
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runs-on: ubuntu-22.04
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steps:
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- uses: actions/checkout@v3
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- uses: gaurav-nelson/github-action-markdown-link-check@v1
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with:
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config-file: ".markdownlint.json"
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shellcheck:
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name: Shellcheck
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runs-on: ubuntu-22.04
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steps:
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- uses: actions/checkout@v3
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- name: Run ShellCheck
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uses: ludeeus/action-shellcheck@master

‎.gitignore‎

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*.egg
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*.err
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*.out
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*.db
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*.py*.sh
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*.tsv
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*.csv
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*.gz*
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.DS_Store
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# PyInstaller
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# Usually these files are written by a python script from a template
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nosetests.xml
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coverage.xml
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*,cover
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*.pdf
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# Translations
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*.mo
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# conda
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.conda
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# Database
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*.db
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*.rdb
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# Pycharm
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.idea
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.ipynb_checkpoints/
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# exclude data from source control by default
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/data/
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cagi*/
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work
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#snakemake
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#snakemake or nextflow
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.snakemake/
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# data/
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variant_annotation/data/
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# exclude test data used for development
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to_be_deleted/test_data/data/ref
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to_be_deleted/test_data/data/reads
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.nextflow/
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.nextflow*
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report*
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#logs
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# .java/fonts dir get created when creating fastqc conda env
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/.vscode/settings.json

‎.markdownlint.json‎

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{
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"default": true,
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"MD007": {
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"indent": 2
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},
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"MD013": {
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"line_length": 120,
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"tables": false
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}
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}

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