linx v1.14

Functional:

• reportable added as first factor in fusion prioritisation
• IG fusions:
  • require IG downstream gene to face towards coding region if post-coding or downstream
  • IG known pairs using longer 100K upstream limit for 3' transcript
  • SVs IG region are considered outside of chain context as well as in their chain
• process AMP and DEL drivers regardless of gene category (ie TSG or ONCO)

Technical:

• write single-sample double minute file if annotations on ('-annotations DM')
• support wildcards for purple and sample data dir usage
• writes driver catalog with 'linx' prefix
• optional config sample_data_dir instead of VCF file, purple data dir and output dir
• only upload alt-mapping SGL breakand data to database if in a fusion
• fixed database loading for breakends and fusions