ISOFOX: integrate tars support (AUS-418)

[shiv-hartwig]

Functional:

• only works with Tars and Redux, not STAR BAMs
• removed all enriched gene logic, and enriched gene perc from statistics file
• alt-sj check splice junctions vs known to ensure novel is selected where multiple exist in a read
• fusion soft-clips reads no longer have a max bases of 10
• fusion supporting fragments include junction and discordant, not realigned
• fusion reads are more permissive keeping trans-exon refs related to an exon
• fusion hard filter if no supplementary has map qual >= 10 (not applied to known pairs and promiscous genes)
• fusion check for position adjustment from junction base overlap between primary and supplementary from BWA

Bugs:

• alt-SJs skip homology shift only if both ends of splice junction match the same transcript's exon boundaries
• trim adapter sequences prior to testing exon boundaries
• trim adapters based on matched alignment positions, not read ends (to handle inconsistent split reads in fragment)
• fusion fragments from primary and supp ensure the same pairing is used

Technical:

• no slice of duplicates, instead extract duplicate count from consensus read attribute

Config:

• removed RNA excluded regions config, now handled by Tars and Redux