Output flags

• Basic output flags
  • --statistics
  • --statistics-at-every-step
  • --create-simple-gtf
  • --create-gff3
• Fasta required output flags
  • --get-fasta-with-introns
  • --get-fasta-without-introns
  • --get-protein-fasta
  • --create-gtf
• Distributions flags
  • --distributions [option] [option] …
  • exon_lengths
  • intron_lengths
  • CDS_lengths
  • gene_lengths
  • exon_position
  • exon_position_data
  • intron_position
  • intron_position_data
• Compatibility flags
  • --compatibility [option] [option] etc…
  • SnpEff
  • EVM_1.1.1_gene_prediction
  • EVM_1.1.1_alignment