Merge branch 'feature-gears' into 'develop'

Refactoring of gears

@wyleung @h.mei 

Resolves #219, #165 and #232

Features to be added:

* [x] Kraken-report to JSON -> for html Sunflare plot display
* [x] R2, distinguish Single End or Paired End, this is used in Kraken for pairing and possible downstream alignments
* [x] Kraken-json to summary-json
* ~~[ ] Add bedtools genomecoverage (or similar tool to determine horizontal coverage and output bedgraph/wiggle)~~
* [x] Support for RNA aligners aligned bams, these may contain multiple alignments for 1 sequence. SamToFastq is not handling this.
* [x] Add report (sunflare plot)
* [x] Add tests

See merge request !241