Options for clc_extract_consensus

Usage information:
  -a / --cas                   Specify the input cas file (required).
  -o / --output                Specify fasta file to output consensus sequence into (required).
  -r / --conflictresolution    Set the consensus sequence base conflict resolution. Must be either
				vote: select A, C, G or T by vote (default),
				ambiguity: use ambiguity nucleotides (R, Y, etc.), ort
				unknown: use unknown nucleotide (N).
  -c / --coverage              Specify minimum coverage to apply difference (default 2).
  -z / --zerocoverage          Set how regions with zero coverage is written in the consensus sequences. Must be either
				reference: use reference nucleotide (default)
				unknown: use unknown nucleotide (N), or
				none: remove zero coverage regions in consensus sequences.
  -i / --ignoreindels          Ignore indels completely in the analysis.
  -w / --outputzerocoverage    Output regions where coverage is zero to stdout.