Updated the documentation for v1.1.2

CHANGELOG.md

@@ -2,6 +2,13 @@
 
 All notable changes to this project will be documented in this file.
 
+## [1.1.2] - 2024-04-03
+
+### Added
+- Added a new boolean input variable "match_by_pos_only" to allow matching variants based on position only.
+- Added conditional execution of commands in the loop based on the "match_by_pos_only" flag. If "match_by_pos_only" is true, a tab-delimited file is created with the chromosome, position, reference allele, and alternate allele from the subset VCF file. The exact chromosome, position, reference allele, and alternate allele from the newly created file are then matched with the subset variants list, and a final VCF file with the matched alleles is created.
+- Updated the "VCF_FILES" variable to include the correct file name based on the "match_by_pos_only" condition.
+
 ## [1.1.1] - 2024-04-02
 
 ### Added

README.md

@@ -34,6 +34,7 @@ The output is a set of files containing the extracted information.
 - `prefix`: Prefix for the output files. (required)
 - `extract_item`: A string specifying the information to extract from the FORMAT field of the VCF file. The available choices are GT, DS, and GP. Please provide as a comma-separated string. Example: `GT,DS` (required)
 - `use_GT_from_PED`: A boolean flag indicating whether to source the genotype encoding from a PED file generated by Plink2 software. If set to true, the genotype encoding will be sourced from the PED file. If not specified or set to false, the genotype encoding will be extracted from the VCF file. (optional)
+- `match_pos_only`: A boolean flag indicating whether to match the variants based on position only. If set to true, the variants will be matched based on chromosome and position only. If not specified or set to false, the variants will be matched based on chromosome, position, reference allele, and alternate allele from the `query_variants` file. (optional)
 
 ## Workflow Outputs