Version 3.30

Update Latex code to use raw strings when printing
Force use of vcflib=1.0.12 building conda package

Version 3.29

Locale settings forced to decimal
Zero coverage chrom split to right most dash
Use explicit options over reference types

Version 3.28

Fixed bug in vsnp3_remove_from_analysis.py
Updated PDF header location to yaml file in dependencies directory

Version 3.27

• Compatible with Python >=3.8,<=3.12
• Compatible with Pandas >=1.3,<=2.2
• Updated PDF Sourmash reporting to correct column
• Record system environment used
• Improved version program usage capture
• Removed Singularity bcftools option
• Replaced vcflib and vcftools with Python implementations
• Added --show_groups step 2 option to display groups in SNP tables
• Added --html_tree step 2 option to output interactive HTML tree
• Added --dp step 2 option to show sample average depth of coverage in SNP tables
• Updated Excel merge functionality in organize_directories.sh
• Updated README

Version 3.26

Changed step 2 default, with no option, to not provide a "groupings" column in the SNP table. The "--show_groups" flag must be provided to show the groups assigned for each sample in the SNP tables.

Version 3.25

Groups shown in SNP tables
Removed "X" from average depth Excel column for numerical sorting
When step 2 is run, VCF files are removed from the directory immediately after being put into memory
Utility script to select VCF files on multiple positions
"-hash" option to run groups specified with a "#" in defining the SNP Excel worksheet; otherwise, these groups are not run
Python 3.8 - 3.11 compatible

Version 3.24

Update reporting when multiple positions define a group.
Addition of writer.book.use_zip64() for writing out large Excel worksheets.
Update HTML reporting of samples that do not have a quality-defining SNP to place them into a group.
Spoligotype count cutoff changed from 5 to 3 when calling a spacer positive.

Version 3.23

vsnp3_fasta_to_fastq.py for converting FASTAs to fake paired FASTQs
Fix collecting Q20 and Q30 from seqkit
Fix amino acid residue calling
Function added to print defining SNPs

Version 3.21

• Option to provide full path to reference type.
• Ability to use two or more defining SNPs to designate a group.
• New output option to write output file to a specific directory.