redux v1.1

Changes from MarkDups:

Functional

• write MSI jitter files for Sage
• unmap secondaries and drop from BAM
• drop supplementaries with alignment score < 30 (BWA default)

Technical:

• optimised UMI collapsing, MSI jitter analysis and BAM writing
• significantly lower memory usage
• handle hard-clipped reads
• use 'redux' in TSV output files

Bugs:

• fixes a couple of minor & rare issues which could result in either dropped or duplicate reads
  -unmap read in unmap region if map becomes unmapped and vice versa

Config:

• requires samtools instead of sambamba for final BAM concatenation