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 geom_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
• change version 0.2.3.1 -> 0.2.3.2
• remove '' surrounding last argument of Galaxy xml wrapper

0.2.3.1

• 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 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.