orange v1.10

• Classify each driver gene as wild-type in case:
  1. Purple fit is reliable
  2. No reportable events have been found in the gene.
• Various additions and improvements to selection of potentially interesting events:
  • Unreported variants with canonical synonymous impact but reportable worst impact are added as potentially interesting variants.
  • Unreported variants in splice regions of genes for which we report splice variants are added as potentially interesting variants.
  • Unreported variants near hotspots are added as potentially interesting.
  • Unreported fusions of all oncogenes are added as potentially interesting fusions.
  • Driver genes that are nearly amplified (2.5 < minRelCN < 3) are added as potentially interesting gains.
  • Non-driver amplifications and losses are preferentially selected for being suspicious in case they have associated evidence.
  • Non-driver losses that have associated evidence but also a reported loss in the same band are retained as suspicious loss.
  • Breakends that are disruptive inside a pathogenic exon range of a promiscuous fusion gene but did not lead to fusions are added as potentially interesting disruptions.
• Various new annotations of existing tables:
  • Gene disruptions are annotated by their cluster ID to be able to determine whether multiple events happened in same event.
    • New input: linx_structural_variant_tsv
  • Expression entries in the RNA chapter are annotated with their tumor CN
• Clinical evidence is now grouped by event rather than treatment.
• Various minor and technical improvements:
  • Add optional parameter experiment_date which, when provided in YYMMDD format, sets the experiment date. If param is not provided, the current date is used (as before).
  • Variants with identical phased inframe canonical effect are dedup'ed prior to reporting.
  • Treatment counts on the front page are retrieved from general evidence only and no longer include trials.
  • Average chromosome arm copy numbers are calculated and stored in ORANGE JSON:
    • New input: purple_somatic_copy_number_tsv
  • All potentially interesting sections are now also written to the JSON output.
  • The structural variant driver table has been removed as all interesting events where duplicated with events in other sections
  • Add optional parameter limit_json_output, which if set limits the size of the JSON output to facilitate manual inspection of JSON datamodel.