Reduction of Promoter Annotation Size

[jleechung]

• Remove reducedExonRanges slot and integrate data into promoterCoordinates slot
  • Update calculateJunctionReadCounts function to use promoterCoordinates instead of exonRanges
• Remove code in annotation-data-helper.R used to calculate metadata that is not used in creating reduced promoter annotation object
• Replace promoterAnnotationData.gencode.v19.rda with promoterAnnotation.gencode.v19.rda (compressed)
  • Update R version 3.5.0 for serialized objects in DESCRIPTION
• Minor Fixes
  • Shift genome check for BAM file to proActiv wrapper
  • Add dplyr imports to annotation-data-helper.R functions
  • Remove deprecated link to preparePromoterIdMapping and update to preparePromoterAnnotation (estimate-promoter-activity.R)