redux v2.0

Functional:

• support for SBX and Ultima
• jitter UMI duplicate collapsing allows no edit distance
• write msi model prediction file if configured
• support MSK UMIs (variable length)

Bugs:

• fix failing to plot BQR due to BQR file columns renamed from lowerCamelCase to UpperCamelCase

Technical:

• runs BQR instead of Sage
• removed use of jitter read cache
• refactored jitter duplicate and poly-G UMI collapsing
• optimised read cache for intense regions (> 100K reads per 400 bases)
• add R dependencies for BQR plot to Dockerfile

Config:

• sequencing_type
  -msi_model_error_rates - per cohort
  -msi_model_coefficients - uses HMF WGS cohort
• support umi_type MSK
• support umi_type KAPA