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lingminhaolingminhao
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Merge pull request #557 from GoekeLab/devel_pre
add github issue and pull request template to the main repository
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‎.github/ISSUE_TEMPLATE/bambu-bug-report.yml‎

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name: "Bug report"
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description: "Report a problem with bambu (include a minimal reproducible example and session info)."
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title: "[Bug]: "
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labels: ["bug"]
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body:
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- type: markdown
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attributes:
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value: |
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Thanks for reporting an issue! To help us fix it quickly, please provide as much detail as possible.
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**Do not include any sensitive/private data**.
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- type: dropdown
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id: bug_area
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attributes:
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label: Affected Area
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description: Which part of bambu is having issues?
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options:
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- "Installation"
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- "Transcript Discovery"
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- "Transcript Quantification"
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- "Annotation"
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- "Bambu Output / Visualization"
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- "Performance (CPU, Memory, Storage)"
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- "Others"
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validations:
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required: true
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- type: textarea
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id: description
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attributes:
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label: Issue Description
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description: |
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A clear description of what happened, what you expected to happen, and any troubleshooting you've already tried.
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placeholder: "I ran bambu with X parameters and got Y error, but I expected Z..."
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validations:
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required: true
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- type: textarea
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id: repro_code
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attributes:
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label: Minimal Reproducible Example (R Code)
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description: |
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Provide the smallest possible R code snippet that reproduces the issue.
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render: r
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placeholder: |
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library(bambu)
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# Your code here...
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validations:
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required: true
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- type: textarea
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id: input_data
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attributes:
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label: Input Data Details
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description: |
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Describe the inputs needed to reproduce (e.g., sequencing platform, reference used, approx. dataset size).
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placeholder: |
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- Sequencing Platform (e.g. ONT / PacBio):
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- Reference Genome (name & version):
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- Reference Annotation (name & version):
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- Approx. dataset size / number of reads:
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validations:
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required: true
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- type: dropdown
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id: reproducibility
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attributes:
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label: Reproducibility
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description: How often does this bug occur?
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options:
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- "Always (every time I run this)"
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- "Intermittently (only sometimes)"
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- "Once (haven't been able to repeat it)"
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validations:
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required: true
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- type: textarea
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id: environment
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attributes:
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label: Session Info
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description: |
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Paste the output of `sessionInfo()`.
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placeholder: |
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```r
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sessionInfo()
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```
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validations:
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required: true
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- type: checkboxes
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id: pr_interest
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attributes:
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label: Contribution
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options:
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- label: "I can provide a small public dataset/toy example for reproduction."
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validations:
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required: false
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- type: checkboxes
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id: checklist
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attributes:
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label: Checklist
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options:
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- label: "I searched existing issues to avoid duplicates."
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required: true
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- label: "I included a minimal reproducible code snippet."
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required: true
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- label: "I included session/environment information."
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required: true
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- type: markdown
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attributes:
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value: |
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---
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*This form is for bug reports. For feature enhancements, please use the **Feature Request** template. For general questions or discussions, please visit the [**Discussions**](https://github.com/GoekeLab/bambu/discussions) tab.*

‎.github/ISSUE_TEMPLATE/bambu-feature-request.yml‎

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name: "Feature request"
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description: "Suggest an improvement or new feature for bambu."
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title: "[Feature]: "
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labels: ["enhancement"]
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body:
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- type: markdown
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attributes:
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value: |
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Have an idea for a new feature or improvement? We'd love to hear it!
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Please check if a similar request already exists before opening a new one.
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- type: dropdown
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id: feature_area
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attributes:
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label: Feature Area
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description: Which part of bambu would this feature affect?
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options:
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- "Transcript Discovery"
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- "Transcript Quantification"
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- "Output / Visualization"
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- "Performance / Memory Optimization"
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- "New Functionality"
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- "Others"
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validations:
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required: true
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- type: textarea
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id: goal
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attributes:
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label: The Goal or Problem
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description: |
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What is the goal you are trying to achieve, or what problem are you trying to solve?
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Why is this important for your workflow?
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placeholder: "I want to be able to X because currently I have to Y manually..."
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validations:
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required: true
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- type: textarea
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id: proposal
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attributes:
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label: The Proposal & Example Usage (Optional)
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description: |
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Describe the feature you'd like to see.
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If possible, include a code example or pseudo-code showing how you imagine it working.
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render: r
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placeholder: |
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# Example of how I'd like to use it:
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bambu(reads, annotations, new_param = TRUE)
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validations:
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required: false
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- type: textarea
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id: alternatives
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attributes:
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label: Alternatives Considered (Optional)
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description: Have you tried any other ways to achieve this? Any existing workarounds?
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placeholder: "I tried using package Z, but it doesn't handle X well..."
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validations:
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required: false
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- type: checkboxes
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id: checklist
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attributes:
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label: Checklist
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options:
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- label: "I searched existing issues to avoid duplicates."
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required: true
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- label: "I described a concrete use case and success criteria."
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required: true
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- type: markdown
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attributes:
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value: |
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---
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*This form is for feature enhancements. For bug reports, please use the **Bug Report** template. For general questions or discussions, please visit the [**Discussions**](https://github.com/GoekeLab/bambu/discussions) tab.*

‎.github/pull_request_template.md‎

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## Related Issue
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Fixes # (issue number)
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## Type of Change
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- [ ] **Bug fix** (non-breaking change which fixes an issue)
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- [ ] **New feature** (please specify if the change breaks existing functionality)
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- [ ] **Non breaking change** (the feature doesn't change existing functionality)
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- [ ] **Breaking change** (the feature that would cause existing functionality to not work as expected)
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- [ ] **Documentation update**
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- [ ] **Performance optimization**
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## Description
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Please provide a summary and the motivation for the changes. Why is this change necessary? What problem does it solve?
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## Implementation Details
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Briefly describe how the changes were implemented. Which specific code segments or logic paths within the primary functional arguments (e.g., `demultiplexed`, `discovery`, `quant`) are affected? Include relevant technical details for any algorithmic changes or data structure modifications specific to Bambu.
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## Impact of Changes
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Briefly describe the impact of the implemented changes. For example:
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- Results are identical to the previous version.
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- Bug fix only (no changes to output).
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- Adds one column to the SE object.
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- Transcript quantification results show minimal differences.
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## Checklist
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- [ ] My code follows the style guidelines of this project.
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- [ ] I have performed a self-review of my own code.
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- [ ] I have commented my code, particularly in hard-to-understand areas.
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- [ ] I have made corresponding changes to the documentation (vignettes, man pages).
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- [ ] I have tested the code on a full dataset, and any differences have been described in the Impact of Changes section.

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