Skip to content

CLAUDE.md

Latest commit

 

History

History
74 lines (52 loc) · 2.37 KB

CLAUDE.md

File metadata and controls

74 lines (52 loc) · 2.37 KB

CLAUDE.md

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

Package Overview

valr is an R package for genome interval arithmetic, providing BEDtools-like functionality natively in R with full dplyr/tidyverse integration.

Build and Test Commands

# Run tests
devtools::test()

# Run a single test file
devtools::test(filter = "intersect")

# Full R CMD check
devtools::check()

# Generate documentation after modifying roxygen comments
devtools::document()

# Install dev dependencies
devtools::install_dev_deps()

Architecture

Core Data Structures

  • Interval dataframe (ivl_df): tibble with required columns chrom, start, end
  • Genome dataframe (genome_df): tibble with required columns chrom, size

Code Organization

  • R/ - R functions (~34 files)
    • bed_*.r - Main interval operations (intersect, merge, closest, etc.)
    • read_*.r - File I/O (BED, VCF, genome files)
    • tbls.r - Data validation (check_interval, check_genome)
    • utils.r - Helpers including valr_example() for example data
  • src/ - C++ implementations via Rcpp (~14 .cpp files)
    • Performance-critical operations use IntervalTree data structure
    • Headers in inst/include/
  • tests/testthat/ - Test suite (~33 test files)
    • Uses testthat edition 3 with parallel execution
    • Visual regression tests via vdiffr

C++ Integration

The package uses Rcpp with an IntervalTree library for efficient interval lookups. Key headers in inst/include/:

  • IntervalTree.h - Core interval tree implementation
  • grouped_dataframe.h - Handles grouped operations
  • DataFrameBuilder.h - Efficient dataframe construction

Code Style

  • Follow tidyverse style guide (https://style.tidyverse.org)
  • Use styler::style_pkg() but don't restyle unrelated code
  • Documentation uses roxygen2 with Markdown syntax
  • Code formatter: air (configured in air.toml for tribble formatting)

Key Conventions

  • Use .data[["column"]] syntax for column references in NSE operations
  • Use all_of() for column selection in dplyr verbs
  • Output columns from operations use . prefix (e.g., .overlap, .dist)
  • All bed_* functions support grouped dataframes via dplyr::group_by()

Contributing

  • Add tests for new functionality
  • Update NEWS.md for user-facing changes
  • Run devtools::check() before submitting PRs