Merge branch 'master' into enhanced-patterns

---

name: Bug report

about: Create a report to help us improve

title: ''

labels: bug

assignees: ''

---

**Describe the bug**

A clear and concise description of what the bug is.

**To Reproduce**

Steps to reproduce the behavior:

1. Go to '...'

2. Click on '....'

3. Scroll down to '....'

4. See error

**Expected behavior**

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**Screenshots**

If applicable, add screenshots to help explain your problem.

**Desktop (please complete the following information):**

 - OS: [e.g. macOS Mojave, Windows 10, etc]

 - Version [e.g. 1.6]

**Additional context**

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---

name: Custom issue template

about: Describe this issue template's purpose here.

title: ''

labels: ''

assignees: ''

---

---

name: Feature request

about: Suggest an idea for this project

title: ''

labels: ''

assignees: ''

---

**Is your feature request related to a problem? Please describe.**

A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]

**Describe the solution you'd like**

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**Describe alternatives you've considered**

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**Additional context**

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# Contributor Covenant Code of Conduct

## Our Pledge

In the interest of fostering an open and welcoming environment, we as

contributors and maintainers pledge to making participation in our project and

our community a harassment-free experience for everyone, regardless of age, body

size, disability, ethnicity, sex characteristics, gender identity and expression,

level of experience, education, socio-economic status, nationality, personal

appearance, race, religion, or sexual identity and orientation.

## Our Standards

Examples of behavior that contributes to creating a positive environment

include:

* Using welcoming and inclusive language

* Being respectful of differing viewpoints and experiences

* Gracefully accepting constructive criticism

* Focusing on what is best for the community

* Showing empathy towards other community members

Examples of unacceptable behavior by participants include:

* The use of sexualized language or imagery and unwelcome sexual attention or

 advances

* Trolling, insulting/derogatory comments, and personal or political attacks

* Public or private harassment

* Publishing others' private information, such as a physical or electronic

 address, without explicit permission

* Other conduct which could reasonably be considered inappropriate in a

 professional setting

## Our Responsibilities

Project maintainers are responsible for clarifying the standards of acceptable

behavior and are expected to take appropriate and fair corrective action in

response to any instances of unacceptable behavior.

Project maintainers have the right and responsibility to remove, edit, or

reject comments, commits, code, wiki edits, issues, and other contributions

that are not aligned to this Code of Conduct, or to ban temporarily or

permanently any contributor for other behaviors that they deem inappropriate,

threatening, offensive, or harmful.

## Scope

This Code of Conduct applies both within project spaces and in public spaces

when an individual is representing the project or its community. Examples of

representing a project or community include using an official project e-mail

address, posting via an official social media account, or acting as an appointed

representative at an online or offline event. Representation of a project may be

further defined and clarified by project maintainers.

## Enforcement

Instances of abusive, harassing, or otherwise unacceptable behavior may be

reported by contacting the project team at aidenlab@bcm.edu. All

complaints will be reviewed and investigated and will result in a response that

is deemed necessary and appropriate to the circumstances. The project team is

obligated to maintain confidentiality with regard to the reporter of an incident.

Further details of specific enforcement policies may be posted separately.

Project maintainers who do not follow or enforce the Code of Conduct in good

faith may face temporary or permanent repercussions as determined by other

members of the project's leadership.

## Attribution

This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,

available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html

[homepage]: https://www.contributor-covenant.org

For answers to common questions about this code of conduct, see

https://www.contributor-covenant.org/faq

# Contributing to Juicer

:+1::tada: First off, thanks for taking the time to contribute! :tada::+1:

The following is a set of guidelines for contributing to Juicer, which is hosted in the [Aiden Lab Repositories](https://github.com/aidenlab) on GitHub. These are mostly guidelines, not rules. Use your best judgment, and feel free to propose changes to this document in a pull request.

## Code of Conduct

This project and everyone participating in it is governed by the [Code of Conduct](CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to [aidenlab@bcm.edu](mailto:aidenlab@bcm.edu).

## I don't want to read this whole thing I just have a question!!!

> **Note:** Please don't file an issue to ask a question. You'll get faster results by using our [3D-Genomics Official Forum](https://aidenlab.org/forum.html). We have an official message board where the community chimes in with helpful advice if you have questions.

While we strongly suggest using the public forum so that the community at large benefits from the discussion, you can also send us an email at [aidenlab@bcm.edu](mailto:aidenlab@bcm.edu) for questions related to sensitive datasets.

## **Did you find a bug?**

* **Ensure the bug was not already reported** by searching on GitHub under [Issues](https://github.com/aidenlab/juicer/issues).

* If you're unable to find an open issue addressing the problem, [open a new one](https://github.com/aidenlab/juicer/issues/new). Be sure to include a **title and clear description**, as much relevant information as possible, and a **code sample, executable test case, or clear set of instructions** demonstrating the expected behavior that is not occurring.

## **Did you write a patch that fixes a bug?**

* Open a new GitHub pull request with the patch.

* Ensure the Pull Request description clearly describes the problem and solution. Include the relevant issue number if applicable.

## **Did you fix whitespace, format code, or make a purely cosmetic patch?**

Changes that are cosmetic in nature and do not add anything to the stability, functionality, or testability of Juicer are still welcome!

## **Do you intend to add a new feature or change an existing one?**

* Suggest your change by creating a Github issue! Reach out to us at [aidenlab@bcm.edu](mailto:aidenlab@bcm.edu) for advice and start writing code!

## **Do you have questions about the source code?**

* Ask any question about how to use Juicer in the [3D Genomics Official Forum](https://aidenlab.org/forum.html).

## **Do you want to contribute to the Juicer documentation?**

* Reach out to us at [aidenlab@bcm.edu](mailto:aidenlab@bcm.edu).

Juicer is a volunteer effort. We encourage you to pitch in and join the team!

Thanks! :heart: :heart: :heart:

The Center for Genome Architecture,

Baylor College of Medicine & Rice University