redux v1.0-rc.1

Functional

• write MSI jitter files for Sage
• unmap secondaries and drop from BAM
• use median base qual from selected consensus base
• no dual fragment marking if not duplex UMIs
• drop supplementaries with alignment score < 30 (BWA default)

Technical

• handle hard-clipped reads
• minor memory and performance optimisations

Bugs
-unmap read in unmap region if map becomes unmapped and vice versa

• rare repeated writing of supplementaries