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.