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.