linx 1.13

Functional:

• write fusion neo-epitope data - use config option write_neo_epitopes
• ignore fusions with non-disruptive upstream chains
• Ensembl data cache: include same gene's transcript when determining first pre-transcript splice acceptor position
• write calculated JCN rather than SV JCN to breakend file
• separate routine for germline processing - with config -germline

Technical:

• accept 37 or HG37 for ref genome version
• added amplicon-architect comparison routine
• run multiple samples from file using wildcard '*' ror sampleId in VCF and purple directory
• visualiser circos: favour fusion over driver transcripts for
• optionally restrict genes to those specified in gene_id_file
• remove max sample config
• lower case for breakeand and fusion file headers
• de-merging simple groups was making redundant clusters

Bugs:

• Ensembl data cache: ignore first exon in first pre-transcript splice acceptor position
• optionally write cohort files for single sample - config -write_cohort