New upstream version 2.7.2b+dfsg

STAR 2.7.2b 2019/08/29

======================

Bug fixes in chimeric detection, contributed by Meng Xiao He (@mengxiao)

* Fix memory leak in handling chimeric multimappers: #721

* Ensure chimeric alignment score requirements are consistently checked: #722,#723.

STAR 2.7.2a 2019/08/13

======================

* Chimeric read reporting now requires that the chimeric read alignment score higher than the alternative non-chimeric alignment to the reference genome.  The Chimeric.out.junction file now includes the scores of the chimeric alignments and non-chimeric alternative alignments, in addition to the PEmerged bool attribute. (bhaas, Aug 2019)

* Fixed the problem with ALT=* in STAR-WASP.

* Implemented extras/scripts/soloBasicCellFilter.awk script to perform basic filtering of the STARsolo count matrices.

STAR 2.7.1a 2019/05/15

======================

**This version requires re-generation of the genome indexes**

# 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 dobin@cshl.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 STAR

The following is a set of guidelines for contributing to STAR hosted in the GitHub: https://github.com/alexdobin/STAR/. 

These are mostly guidelines, not rules. 

Use your best judgment, and feel free to propose changes to this document in a pull request.

#### Table Of Contents

[Code of Conduct](#code-of-conduct)

[How Can I Contribute?](#how-can-i-contribute)

  * [Ask a question](#ask-a-question)

  * [Reporting Bugs](#reporting-bugs)

  * [Suggesting Enhancements](#suggesting-enhancements)

  * [Pull Requests](#pull-requests)

## 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.

## How Can I Contribute?

### Ask a question

Please do not file an issue to ask a question.

The GitHub issue tracker is intended for bug reports and feature requests.

We have an official discussion forum where the community chimes in with helpful advice if you have questions.

* [STAR discussion forum](https://groups.google.com/forum/#!forum/rna-star)

### Reporting Bugs

This section guides you through submitting a bug report for STAR. 

Following these guidelines helps maintainers and the community understand your report, 

reproduce the behavior, and find related reports.

If you find a **Closed** issue that seems like it is the same thing that you're experiencing, 

open a new issue and include a link to the original issue in the body of your new one.

#### Before Submitting A Bug Report

* You might be able to find the cause of the problem and fix things yourself. 

Most importantly, check if you can reproduce the problem in the latest version of STAR

and if the problem happens when you run with mostly default parameters.

* Check the Log.out file for ERROR/WARNING/SOLUTION messages.

* Perform a through STAR GitHub issues to see if the problem has already been reported. 

If it has **and the issue is still open**, add a comment to the existing issue instead of opening a new one.

#### How Do I Submit A (Good) Bug Report?

Bugs are tracked as [GitHub issues](https://guides.github.com/features/issues/) on https://github.com/alexdobin/STAR/issues.

Explain the problem and include additional details to help maintainers reproduce the problem:

* **Use a clear and descriptive title** for the issue to identify the problem.

* **Describe the exact steps which reproduce the problem** in as many details as possible. For example, start by explaining how you run STAR, e.g. which command exactly you used in the terminal. When listing steps, **don't just say what you did, but explain how you did it.

* **Log.out**. Attach the Log.out file generated in the failed run. This file contains a lot of useful debugging information and is a starting point

* **Provide specific examples to demonstrate the steps**. Include links to files or GitHub projects, or copy/pasteable snippets, which you use in those examples. If you're providing snippets in the issue, use [Markdown code blocks](https://help.github.com/articles/markdown-basics/#multiple-lines).

* **Describe the behavior you observed after following the steps** and point out what exactly is the problem with that behavior.

* **Explain which behavior you expected to see instead and why.**

* **System information**. In many cases, the problems are associated with the hardware configurations. Provide a brief description of the CPU(s), RAM, storage. 

* **Can you reliably reproduce the issue?** If not, provide details about how often the problem happens and under which conditions it normally happens.

Include details about your configuration and environment:

### Suggesting Enhancements

This section guides you through submitting an enhancement suggestion for Atom, including completely new features and minor improvements to existing functionality. Following these guidelines helps maintainers and the community understand your suggestion and find related suggestions.

#### Before Submitting An Enhancement Suggestion

* **Check the STAR manual and Release Notes** — you might discover that the enhancement is already available. Most importantly, check if you're using the latest version of STAR.

* **Perform a cursory search** to see if the enhancement has already been suggested. If it has, add a comment to the existing issue instead of opening a new one.

#### How Do I Submit A (Good) Enhancement Suggestion?

Feature requests and enhancement suggestions are tracked as [GitHub issues](https://guides.github.com/features/issues/) on https://github.com/alexdobin/STAR/issues.

* **Use a clear and descriptive title** for the issue to identify the suggestion.

* **Provide a step-by-step description of the suggested enhancement** in as many details as possible.

* **Provide specific examples to demonstrate the steps**. Include copy/pasteable snippets which you use in those examples, as [Markdown code blocks](https://help.github.com/articles/markdown-basics/#multiple-lines).

* **Describe the current behavior** and **explain which behavior you expected to see instead** and why.

* **Explain why this enhancement would be useful** to many STAR users.

* **List some other tools where this enhancement exists.**

### Pull Requests

Please read the guides on creating good pull requests (PR) and follow these guidelines:

* **Use a clear and descriptive title** for the pull request.

* **State the purpose of the PR**: is it a bug-fix, new feature implementation, documentation improvement, or cosmetic change? Why is it important?

* **Explain the expected changes in STAR behavior**. Make sure that the default STAR behavior does not change.

* **Provide detailed code documentation and commit messages**.

Adopted from https://github.com/atom/atom/blob/master/CONTRIBUTING.md

STAR

Spliced Transcripts Alignment to a Reference

© Alexander Dobin, 2009-2015

MIT License

STAR is a free open source software distributed under GPLv3

Copyright (c) 2019 Alexander Dobin

This program is free software: you can redistribute it and/or modify

it under the terms of the GNU General Public License as published by

the Free Software Foundation, either version 3 of the License, or

(at your option) any later version.

Permission is hereby granted, free of charge, to any person obtaining a copy

of this software and associated documentation files (the "Software"), to deal

in the Software without restriction, including without limitation the rights

to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

copies of the Software, and to permit persons to whom the Software is

furnished to do so, subject to the following conditions:

This program is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

GNU General Public License for more details.

The above copyright notice and this permission notice shall be included in all

copies or substantial portions of the Software.

For details, see <http://www.gnu.org/licenses/>.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE

AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,

OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE

SOFTWARE.

```bash

# Get latest STAR source from releases

wget https://github.com/alexdobin/STAR/archive/2.7.1a.tar.gz

tar -xzf 2.7.1a.tar.gz

cd STAR-2.7.1a

wget https://github.com/alexdobin/STAR/archive/2.7.2b.tar.gz

tar -xzf 2.7.2b.tar.gz

cd STAR-2.7.2b

# Alternatively, get STAR source using git

git clone https://github.com/alexdobin/STAR.git