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echofinemap 1.0.0

New features

  • FINEMAP: Added early runnability check via FINEMAP_check_runnable() — validates the binary can execute before preparing data, with platform-specific error messages for Apple Silicon dylib issues.
  • FINEMAP: Added automatic x86_64 dynamic library setup on Apple Silicon via FINEMAP_setup_dylibs(). Builds/downloads x86_64 libzstd, libomp, and gcc runtime libraries, then rewrites binary paths with install_name_tool.
  • FINEMAP: System PATH detection — checks for conda-installed FINEMAP before downloading from GitHub releases.
  • PAINTOR: Wired functional annotation pipeline end-to-end. PAINTOR_prepare_annotations() is a pure-R reimplementation of the original Python 2.7 AnnotateLocus.py, converting BED files to binary annotation matrices and passing annotation names to the PAINTOR executable.
  • PAINTOR: New annot_paintor parameter for downloading the comprehensive PAINTOR functional annotation library (~7GB, 10,000+ annotations) from BOX. Annotations are cached locally after first download.
  • PAINTOR: New PAINTOR_fetch_annotations() and PAINTOR_list_annotations() functions for managing the annotation library.
  • POLYFUN: Fixed parametric mode filename pattern — parametric output has no chromosome in the filename, so the import now matches correctly.

Bug fixes

  • FINEMAP: Fixed sparse matrix (dsCMatrix) handling in FINEMAP_construct_data() by converting to dense matrix before fwrite().
  • POLYFUN: Fixed silent error swallowing in POLYFUN_import_priors() — replaced try({}) with proper exit code checking and output file verification.
  • POLYFUN: Fixed requireNamespace("Ckmeans.1d.dp") to properly error with an informative message instead of silently continuing.
  • POLYFUN: Fixed POLYFUN_install() blocking non-interactive sessions by gating readline() behind interactive() check.
  • POLYFUN: Removed hardcoded path override in POLYFUN_compute_priors() that was overwriting the properly resolved polyfun path.
  • PAINTOR: Removed setup_gcc(version="clang") call from PAINTOR_install() that required sudo for symlink creation.
  • setup_gcc(): Rewritten for Apple Silicon support — checks both /opt/homebrew (ARM) and /usr/local (Intel) Homebrew paths, handles multiple gcc installation formats.
  • Tests: Split monolithic test-multifinemap.R into focused subtests (BST1, LRRK2 with network skip, POLYFUN_SUSIE with dependency checks).
  • Tests: Added proper skip guards for FINEMAP, PAINTOR, and POLYFUN tests with direct function checks instead of tryCatch wrappers.
  • Local R CMD check fixes and compatibility updates.

echofinemap 0.99.7

Bug fixes

  • Local R CMD check fixes and compatibility updates.

echofinemap 0.99.6

New features

  • Standardize rworkflows.yml with canonical template: enable Docker on ghcr.io, set write-all permissions, use GITHUB_TOKEN, add devel branch trigger.

echofinemap 0.99.5

New features

  • Implement rworkflows

echofinemap 0.99.4

New features

  • Pass more arg down to method-level via finemap_args.
  • Add check_args function to handle finemap_args.
  • Offload piggyback functions to echodata (echodata::get_data)
  • SUSIE:
    • Condense manual_var_y and var_name into one arg: var_y
    • Replace dataset_type with more appropriate case_control arg.
  • Fully documented all functions.
  • Remove POLYFUN_plot (redundant code with echoplot)
  • POLYFUN_: fixed or deleted functions
    • POLYFUN_munge_summ_stats
    • POLYFUN_compute_priors

Bug fixes

  • Make Rfast an Import to avoid downstream issues with echolocatoR.
  • Fix GHA: @master --> @v2
  • Remove unnecessary deps:
    • ggplot2
  • Adjust .Rbuildignore to not cause issues with large inst/tools subfolder.
  • require_cols:
    • Now takes the more accurate case_control arg instead of dataaset_type.

echofinemap 0.99.3

New features

  • COJO:
    • Now working with echoverse.
    • Added 3 COJO modes to list of finemapping methods: run_stepwise,run_conditional,run_joint
    • Automated installation of GCTA.
    • Added unit tests.
  • PAINTOR:
    • Now working with echoverse.
    • Generalized to any data input type (GWAS/QTL/TWAS) to avoid hard-coded args.
    • Streamlined functions and reduced clutter.
    • Automated installation of PAINTOR.
    • Can now handle multi-trait and multi-ancestry fine-mapping.
    • Added unit tests.
  • multifinemap:
    • Automatically checks finemap_methods
    • Passes seed all the way to finemapping functions.
    • Expanded finemapping methods.
  • check_required_cols: Add coloring via cli.
  • required_cols: Add URLS to GitHub repos and citations.
  • Added functions for checking each fine-mapping CLI method's version:
    • <method>_check_version
    • Changed POLYFUN_find_polyfun_folder --> POLYFUN_find_folder for consistency.

Bug fixes

  • FINEMAP: Figured out solution to get FINEMAP v1.4 working on Mac. Instructions in messages now updated.
  • create_method_path: Use basename(LD_reference) for file naming.
  • Require "MAF" columns for coloc, as it now seems to be required by the error message when it's missing: dataset : please give MAF if using p values

echofinemap 0.99.2

New features

  • Updated GHA.
  • POLYFUN:
    • Can now use FINEMAP or SUSIE as a method.
    • Change column "POLYFUN_h2" --> "POLYFUN.h2" to make consistent with other cols.
    • Automatically installs itself from the GitHub submodule.
    • POLYFUN_help now exported.
  • Use Rfast to speed up SUSIE.
  • remove_na_rows: Remove rows with NAs in tool-specific essential cols.
  • Update FINEMAP to v1.4.1.
  • Make separate columns for FINEMAP results:
    • PP: Conditional PP (from .cred file(s))
    • PP_snp: Marginal PP (from .snp file)
    • PP_config: Configuration PP (from .config file)
    • k: Optimized number of causal SNPs (<= n_causal).
  • Got FINEMAP to use priors via data.k file.

Bug fixes

  • Switch SUSIE method from susie_suff_stat to susie_rss for parameter consistency.
  • Fix ABF.
    • Use mean proportion_cases
  • Test FINEMAP v1.4 and v1.3.1 on Linux.
  • Actually pass force_new_finemap all the way down.
  • Dynamically infer "data.cred*" file name.
  • Fill NAs in FINEMAP CS/PP.
  • SUSIE:
    • susieR v0.11 contained serious bugs that caused susie_rss to fail. This was fixed in v0.12 (which is now a version requirement for echofinemap). See here for details: stephenslab/susieR#167

echofinemap 0.99.1

New features

  • Updated conda env to echoR_mini.
  • Add prior_k as argument to FINEMAP.
  • Add message about gcc8 to FINEMAP v1.4 error.

Bug fixes

  • Minor fixes to POLYFUN method checks.

echofinemap 0.99.0

  • Added a NEWS.md file to track changes to the package.