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.