Developer

This part of the Wiki provides instructions to get set up for contributing to breseq development and a roadmap for ongoing coding projects.

Developer Information

• Developer Quickstart
• Developer Installation
• Code of Conduct
• List of Proposed Coding Projects
• Coding Style Guide

In-Progress Coding Projects

• Add Interactivity to HTML output [Core:HTML/Javascript/C++]
• Parallelize breseq execution [Core:C++]
• Predict copy number variation [Test:R→Core:C++]
• Detect discontinuity (soft-clipping) evidence [Core:C++]

Available Coding Projects

• Compare across samples to improve predictions of low-frequency variants [Test:Python/R→Core:C++]
• Update/improve Circos visualization [Extension:Python/Javascript]
• Treatment similarity/specificity statistics [Extension:Python/R]
• Summarize data quality/coverage across many runs [Extension:Python/R]
• Phylogenetic tree generation [Extension:R]
• Predict structural variation from mate-pair mapping [Test:Python→Core:C++]