Changelog

All notable changes to IDEAL-GENOM will be documented in this file.

Version 1.1.0 (Current)

Released: January 2026

New Features:

• Modules for visualization of GWAS results

  • Manhattan plot

  • Miami plot

  • QQ plot

  • LD heatmap

  • Trumpet plot

  • Effect size comparison plot (beta-beta plot)

• Module to fetch example datasets for testing and tutorials

Improvements:

• Example notebooks for visualization modules

Version 1.0.0

Released: January 2026

Major Changes:

• Complete redesign of configuration system from JSON to YAML

• Unified pipeline framework with step-based execution

• New command-line interface with subcommands (run, validate, template)

• Package renamed from ideal-genom-qc to ideal-genom

New Features:

• GWAS Pipeline: Complete GWAS workflow with GLM and GLMM support

• VCF Processing: Post-imputation VCF processing and PLINK conversion

• Population Analysis: Enhanced population structure tools (PCA, UMAP, t-SNE, Fst)

• Pipeline Executor: Automated pipeline execution with dependency management

• Configuration Validation: Built-in YAML configuration validation

• Variable Substitution: Support for dynamic variable references in configurations

Improvements:

• Enhanced error handling and logging

• Improved memory management for large datasets

• Parallel processing support across all modules

• Better documentation with comprehensive examples

• Rich reporting and visualization capabilities

• Docker support with pre-configured environment

API Changes:

• YAML configuration replaces JSON configuration files

• New Python API with consistent class interfaces

• Module reorganization: ideal_genom.qc, ideal_genom.gwas, ideal_genom.post_imputation

• Simplified class initialization patterns

Bug Fixes:

• Fixed kinship calculation memory issues

• Improved VCF parsing for large files

• Corrected reference genome download paths

• Fixed PCA projection edge cases

Dependencies:

• Python 3.11+ required (up from 3.8+)

• PLINK 2.0 now required alongside PLINK 1.9

• GCTA 1.95.0 or higher

• BCFtools 1.10+ for VCF processing

Version 0.1.0

Released: 2024

Initial Release:

• Basic QC pipeline (Sample QC, Ancestry QC, Variant QC)

• JSON-based configuration

• Command-line interface for basic operations

• Integration with PLINK 1.9

• 1000 Genomes reference panel support

• Basic UMAP visualization

Migration Guide (0.1.0 → 0.2.0)

Configuration Files:

Old (JSON):

{
    "sample_qc": {
        "mind": 0.1,
        "maf": 0.01
    }
}

New (YAML):

pipeline:
  steps:
    - name: "sample_qc"
      module: "ideal_genom.qc.sample_qc"
      class: "SampleQC"
      execute_params:
        mind: 0.1
        maf: 0.01

Command-Line Interface:

Old:

python -m ideal_genom_qc \
    --path_params parameters.json \
    --file_folders paths.json \
    --steps steps.json

New:

ideal-genom run --config pipeline.yaml

Python API:

Old:

from ideal_genom_qc import SampleQC

qc = SampleQC(...)
qc.run(...)

New:

from ideal_genom.qc.sample_qc import SampleQC

qc = SampleQC(...)
qc.execute_sample_qc_pipeline(...)

For detailed migration instructions, see the Getting Started guide.

Contributing

We welcome contributions! Please see Contributing Guide for guidelines.

For bug reports and feature requests, please use our GitHub Issues.