linx-v1.8

Functional:

• Visualiser - when specifying a gene to display, this can now be referenced in the Ensembl data cache rather than the more limited internal gene panel by providing a path to the data cache with config: 'gene_transcripts_dir'
• cluster 3 or more overlapping DELs and DUPs with matching copy number and forming potential links
• added INDEL annotation for shattering analysis with config: 'indel_annotation' and 'indel_input_file'
• chain consistency now checks for valid centromere traversal
• re-search for chained foldbacks once chaining is complete
• germline SVs disruption logic added
• Double Minutes:
  • criteria to identify possible BFB ploidy, pairs of SGL breakends
  • allow closed DM loops to amplify centromere
  • check all arms in cluster for telo/centro CN vs DM ploidy or require 50x sample ploidy

Technical

• fail if fusion reference files aren't found, DEV-1121