sv-linx v1.5

Functional changes:

• Fusion likelihood calcs - implemented gene-pairs, skip non-coding same-gene fusions
• known fusions don't require upstream transcript to be disruptive but will still fail on chain termination
• TIs limited by min of achor distances now less sum of breakend homologies
• BFB_AMP does not require max ploidy x8
• dominant foldback must exceed ploidy 4
• DMs can have a single SV and need to be 5x sample ploidy or 2.3x telomere/centromere
• dissolve simple groups unless all SVs in LOH or all assembled
• set intronic transcripts from LINE clusters to be non-disruptive

Bugs:

• only reconfigure chains for RECIP_INV_DUPs if can form positive TI
• determination of unique non-reported fusions was skipping first element