Changes in version 1.2 (Sep 2019)
====================================
	- ".QC$parameters" is renamed to ".QC$input_parameters"
	- checkConfigFileSections() function was added to checkConfigFile.R
	- Below variables are changed:
		* study$SNPs_invalid.path
		* study$SNPs_removed.path
		* study$SNPs_improbable_values.path
		* study$SNPs_duplicates.path
		* study$SNPs_mismatches.path
		* study$SNPs_monomorphic.path
		* study$SNPs_multi_allelic.path
		* study$SNPs_ambiguous.path
		* study$SNPs_significant.path
	- Add compatibility for older versions of R
		* save.alternate.reference() ==> saveRDS(... , version = '2')
		* save.rds.file() ==> saveRDS(... , version = '2')

Changes in version 1.3 (Nov 2019)
====================================
	- New classes are defined using the S4 object system in R:
		* Inspector
		* Study
		* StudyList
	- New functions are developed for creating and running the algorithm:
		* setup.inspector()
		* run.inspector()
		* result.inspector()
		* sample.inspector()

Changes in version 1.4 (Jan 2020)
====================================
	- Allele matching was improved for Insertion/Deletion multi-allelic variants.
	- Manhattan plot function was made dependent from the rest of the package.
	- Report files were synchronized.
	- Minor bugs were fixed.
	- sample.inspector() is renamed to demo.inspector().

Changes in version 1.4.7 (Apr 2020)
====================================
	- R.utils package is imported for reading gz files.
	- 'cmd' parameter is no more used in data.table::fread().
	- data.table V1.12.8 is required for directly writing gz files.

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)
====================================
	- New parameter added to run.inspectior() function. The `verbose` parameter can be used to suppress messages in the terminal.
	- New parameters aded to [output_parameters] section in the configuration file for saving additional columns in the result files:
		* add_column_multiallelic
		* add_column_AFmismatch
		* add_column_HQ
		* add_column_rsid
	- New parameter added to [output_parameters] section in the configuration file for ordering the variants in the result files based on CHR:POS values.
		* ordered

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 (add_column_hid).

Changes in version 1.4.8.4 (Jan 2021)
====================================
	- file_order_string added to configuration file.
	- smoothScatter() function used for AF correlation scatterplot.

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

Changes in version 1.6.0 (Nov 2022)
====================================
	- XLSX package was replaced by OPENXLSX.

Changes in version 1.6.4 (May 2023)
====================================
	- Minor changes for compatibility with R v4.3.
	- setup.inspector() is renamed to setup_inspector()
	- run.inspector() is renamed to run_inspector()
	- result.inspector() is renamed to result_inspector()
	- demo.inspector() is renamed to demo_inspector()
	- compare.GWASs() is renamed to compare_GWASs()
	- system.check() is renamed to system_check()
	- get.config() is renamed to get_config()
	- get.headerTranslation() is renamed to get_headerTranslation()
	- manhattan.plot() is renamed to manhattan_plot()