linx v1.15

Functional:

• link SGL with mapping to INF and process as a synthetic SV in Linx, suppress SGL and INF from svAnnotations
• process AMP and DEL drivers regardless of gene category
• require IG downstream gene to face towards coding region if post-coding or downstream

Technical:

• deletion drivers crash - protect against missing genes
• write empty driver catalog file if sample has no passing SVs
• write single-sample ecDNA file if annotations on (config: -annotations DM)
• only upload alt-mapping SGL breakand data if in a fusion
• writes driver catalog with 'linx' prefix, Cuppa loads this instead purple if exists
• optionally config sample_data_dir instead of VCF file, purple data dir and output dir