bioRxiv v2

• set --max-intronlength-ends to 500kb, this is due to cases
  where GMAP soft-clips the terminal exon(s) if they are over
  10kb (default value)
• set chimeric alignment option to match min clip length
• consider partial novel junctions when checking for presence of
  novel intron (may also be novel exon). This may occur in cases
  of overlapping exons that can obscure novel exons.