CHANGELOG

0.2.3.5:
  - bug correction: in convert_tbl2json.py, modif to take into account of vadr flu annotation (sig_peptide, note just after gene, etc)
  - change version 0.2.3.4 -> 0.2.3.5
0.2.3.4:
  - bug correction: in convert_tbl2json.py, handle case of ncRNA when gene is expected (for dengue example)
  - correct a bug when gene displayed between product and protein_id
  - mask warnings and decrease default verbosity in convert_tbl2json.py (to avoid error status in Galaxy)
  - add na.rm=TRUE in gom_text geom_point of visualize_snp_v4.R to avoid warnings, and Galaxy error status
  - change version 0.2.3.3 -> 0.2.3.4
0.2.3.3:
  - in convert_tbl2json.py, now when no gene found in bed, deduce them from CDS and name them gene_1 .. gene_N (not ORFN 
    because some prot are named ORF2 prot in PCV2, for an ORF that is not the second one!). It avoids to get a bug
    for PCV2 viruses for instance
  - in convert_vcffile_to_readablefile2.py, NOW handle genes in reverse orientation (did not display genes/prot labels previously)
  - change version 0.2.3.2 -> 0.2.3.3
0.2.3.2:
  - correct max number of args from 25 to 30 for vvv2_display.py
  - change version 0.2.3.1 -> 0.2.3.2
  - remove '' surrounding last argument of Galaxy xml wrapper
0.2.3.1:
  - same, only to make release archives updated (not the case when deleting and creating again with the same tags)
0.2.3:
  - correct typo errors, add parameters in xml wrapper
  - remove '\%' 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 <int> 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 netween.
  - shorten protein names for graphics in R script
0.2.1:
  - correct bug when user does not provide cov_depth_corr_f file
  - update dependencies versions
  - correct bug in PYTHON_SCRIPTS/convert_vcffile_to_readablefile2.py that missed some variants in text summary file
0.2.0:
  - 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
0.1.11:
  - display prot instead of genes and genes instead of prot
  - add num in front of genes to ensure to keep apparition order
  - replace fstrings in vvv2_display.py to allow better compatibility
  - add src/correct_covdepth_f.py script to convert cov depth files of samtools depth so as to have cumulative positions for display
  - prepare vvv2_display to coverage depth addition in input
  - add new script to setup.py file and change version to 0.1.11
0.1.10:
  - now horizontal line colors are for proteins, dot shape is for genes. Added vertical dotted lines to show contig limits
  - correction in vadr parsing using different virus models
  - tested on calicivirus, dengue, flavivirus, coronavirus, sarscov2, hcv, norovirus
  - better parse stemp_loops
  - now write all contig limits to avoid empty file (those are not compatible with Galaxy)
0.1.9-beta:
  - working for 2 viruses
0.1.2-alpha:
  - sources set in _src_ directory. vvv2_display.py modified to better fit python package requirements
        - add CHANGELOG
0.1.1-alpha:
  - pyvcf replaced by pysam to improve compatibility / long term maintening
  - consequence: PYTHON_SCRIPTS/convert_vcffile_to_readablefile.py replaced by PYTHON_SCRIPTS/convert_vcffile_to_readablefile2.py
  - vvv2.py renamed vvv2_display.py (because this program replace only the visualization part of vvv)
0.1.0-alpha: first version