Changelog • echofinemap

echofinemap 1.0.0

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.

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.

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

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

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.

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.

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

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.

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: https://github.com/stephenslab/susieR/issues/167