0.2.3

• correct typo errors, add parameters in xml wrapper
• correct '%' in vvv2_display.py help
• update Galaxy xml wrapper to get 2 additional arguments: linear scale for cov_depth and max variant threshold (%age)
• bug correction: 1 added to all covdepth at all positions to avoid log(0)=-inf
• updated yaml (conda recipe) and xml (galaxy wrapper)
• now ordinate scale use threshold provided as argument, not hardcoded (it was already the case for treshold line)
• bug correction: handle vardict LSEQ=ACC_NR:ddd-ddd instead of nucleotides and RSEQ=SNV
• set as default log10 display for covdepth graph, add -y option to set this scale linear
• add option -w to define the percentage threshold to consider significant a variant
• bug correction: handle now stem loop occuring when gene is expected in tab file for conversion to json file

0.2.2

• better distinguish gene and CDS
• compatibility with python 3.12 (regexp strings prefixed by r)
• handle various annotation contexts not taken into account until now
• handle two following gene without annotation in between.
• shorten protein names for graphics in R script

0.2.1

• update version 0.2.0 -> 0.2.1
• update img of README example
• correct bug when user does not provide cov_depth_corr_f file. Attribute some modifications to 0.2.1 instead of 0.2.0 because some were not taken into account in the 0.2.0 package (even if made in main, seems not to be possible to make several time package labelled with the same version)
• add contig names on figure
• correct error deactivating covdepth display when not needed in visualize_snp_v4.R
• correct setup.py for dependencies and one script path
• update dependencies versions

0.2.0

• correct bug in PYTHON_SCRIPTS/convert_vcffile_to_readablefile2.py that missed some variants in text summary file
• add boxes for genes under graph (to fit traditional display of viral genomes)
• add [optional] coverage depth display in final png (if no cov depth provided, part disabled) aligned of variant graph
  for positions

0.1.10

• Deals with more vadr model annotations
• Use colors for proteins, symbols for genes for each variant
• Add GPL3.0 headers
• Add contig limits in png (vertical dotted lines)
• Correct range of characters in protein names (add '[' and ']')

0.1.9-beta

• Correct contig name parsing to allow recognition of GenBank accession numbers too (more generic parsing of vadr annotation).
• Update Galaxy wrapper vvv2_display version used to 0.1.9-beta.

0.1.8-beta

Add parameters for all output files (even tmp files of subscripts) to improve Galaxy compatibility. Correct checking of max number of args. Add missing 'import re' in py script. Add device="png" in R ggsave call to allow Galaxy compatibility. Correct shebang of one py script.

0.1.7-beta

Correct output naming to ensure it fits the name given by user. Correct output file naming for one subscript, correct titles and pos in R display. Change str replacement for file extensions so as to be compatible with galaxy file naming. Version number update.

0.1.6-beta

correct call to python subscript, version update in setup

0.1.5-beta

change version of setup.py