Changes in version 1.2 (Sep 2019)
====================================
	- "parameters" section in the configuration file was changed to "input_parameters"
	- Configuration file sections are checked for consistency
	- Output file names are changed from SNPs to vars. This is because they might contain INDELs too.
	- Merging of data sets are done with data.table method instead of merge() function.
	- Vignette is updated.
	- Added compatibility for older versions of R.

Changes in version 1.3 (Nov 2019)
====================================
	- S4 object system is used for defining classes and main functions. Package is now much more disciplined compared to the previous version which was in S3.
	- Printing of all log messages to the terminal can now be disabled by using suppressMessages() function.
	- Minor improvement in code.

Changes in version 1.4 (Jan 2020)
====================================
	- Allele matching for Insertion/Deletion multi-allelic variants were improved.
	- Report files were edited.
	- Minor bug fixes.
	- sample.inspector function is renamed to demo.inspector.

Changes in version 1.4.7 (Apr 2020)
====================================
	- data.table package (1.12.8) is now capable of directly writing gz files. This will be used for saving output zipped files.
	- R.utils package is now added to dependecy list. This will be used to read gz files with data.table::fread() function.

Changes in version 1.4.7.1 (May 2020)
====================================
	- Summary statistics are generated seprately for HQ variants.

Changes in version 1.4.8 (Jul 2020)
====================================
	- Messages to the terminal can be supressed using `verbose` parameter.
	- New columns can be added to the output files indicating multi-allelic or HQ variants.
	- Allele-frequency and RSID from the reference file can be added to the result files.

Changes in version 1.4.8.3 (Dec 2020)
====================================
	- A new column containing CHR:POS:EFF_ALL_OTHER_ALL can be added to the output files.

Changes in version 1.4.8.4 (Jan 2021)
====================================
	- File order can be set with a string parameter.
	- Allele frequency scatter plot is replaced with Smooth Scatter.
	- Search of variants in the reference dataset is improved.

Changes in version 1.5.7 (Jan 2022)
====================================
	- Some minor debugging was done.

Changes in version 1.6.0 (Nov 2022)
====================================
	- Due to problems with Java and rJava, XLSX package was replaced by OPENXLSX.

Changes in version 1.6.4 (May 2023)
====================================
	- Minor changes for compatibility with R v4.3.
	- Main function names were renamed by replacing dot with underline.

Changes in version 1.7.2 (Mar 2025)
====================================
	- Minor changes for compatibility with R v4.4.
	- LOG10P will be converted to PVALUE, if not in the input file.

Changes in version 1.7.4 (Dec 2025)
====================================
	- futile.logger package was replaced with logger

