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
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala 0 → 100644
public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/report/ext/js/gears.js 0 → 100644