CLAUDE

CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Repository overview

This is the GitHub wiki source for breseq, a bacterial genome resequencing/mutation-calling tool. It is cloned from breseq.wiki.git and renders at github.com/barricklab/breseq/wiki. There is no source code, build system, or test suite here — only Markdown pages and an images/ folder of screenshots/diagrams. Editing is just changing Markdown/images and committing/pushing; there is no build or CI step.

Structure & conventions

• Every .md file at the repo root becomes a wiki page named after its filename (dashes render as spaces in the page title).
• Home.md is the wiki landing page; _Sidebar.md renders as the persistent nav sidebar on every page. Keep both in sync when pages are added, removed, or renamed. Note: their link sets are already slightly inconsistent with each other — treat that as a known pre-existing gap, not something to silently "fix" as a side effect of unrelated edits.
• Internal links use GitHub wiki syntax:
  • [[Page Name]] when the link text should equal the page title.
  • [Custom Text](Page-Name) when the display text differs from the page's URL slug.
  • Preserve this convention rather than switching to relative .md-style links.
• images/ holds all screenshots/diagrams referenced by pages (mostly PNG, plus a couple PDF/DOCX). Reference existing images rather than duplicating them.

Page groups

• Installation/Quickstart: Installation.md, Test-Drive.md
• Usage reference: Usage-breseq.md, Usage-gdtools.md
• File formats: GenomeDiff-File-Format.md, Reference-Sequence-File-Formats.md
• Conceptual docs: Methods.md, Output.md, FAQ.md, Bibliography.md
• Tutorials: Tutorial-*.md, including a Tutorial-Curation-* sub-series
• Developer docs: Developer.md, Developer-Quickstart.md, Developer-Installation.md, Coding-Style-Guide.md, Code-of-Conduct.md — these describe contributing to the breseq source repo (a separate C++/R codebase from this wiki), including its C++11-only/no-Boost policy and Google style guide conventions.