v0.8.4

Modifications in Input Pogenom pipeline: Two aligners can be used now, bowtie2 and BWA-MEM2.
bowtie2 can be used with --score-min function as in the paper, or using default parameters (both --local or --end-to-end) together with CoverM filter. BWA-MEM2 (performing only local alignments) should be used together with CoverM filter.

v0.8.3

• Change in Input_POGENOM pipeline: made subsampling to “min_coverage” optional by new parameter “subsample”

v0.8.2

• Now removes loci lacking variants after splitting haplotypes
• Option to split fasta headers at space characters and only use part before first space
• Added documentation on how output parameters are calculated

v0.8.1

• Improved Input_POGENOM pipeline
• Fixed small bug related to single-sample VCFs

v0.8.0

• Calculates per codon and sample amino acid frequencies.
• Calculates normalized genome-wide pi based on estimated coverage breadth.
• Option to calculate permuted gene-wise FST (new argument --fst_perm).
• Option to restrict analysis to samples specified in file (new argument --sample_file).
• Option to only calculate genome-wide pi (new argument ---pi-only).
• Input_POGENOM pipeline for automatic VCF file generation.

v0.6.0

• Allows GATK format of VCF file (new argument -–vcf_format).
• Disabled old argument -–vcf_version. Now automatically finds out which fields to use irrespective of version.
• Takes a genome fasta file as optional input (new argument -–fasta_file).
• Calculates total coverage at position by summing allele counts rather than using the DP parameter.
• Fixed FST calculation when inter-pi = 0.
• Fixed bug in calc_per_gene_aminoacid_fst.

v0.5.0

updated readme