usage: fc_consensus.py [-h] [--n_core N_CORE] [--min_cov MIN_COV]
                       [--min_cov_aln MIN_COV_ALN] [--max_cov_aln MAX_COV_ALN]
                       [--min_len_aln MIN_LEN_ALN] [--min_n_read MIN_N_READ]
                       [--max_n_read MAX_N_READ] [--trim] [--output_full]
                       [--output_multi] [--min_idt MIN_IDT]
                       [--edge_tolerance EDGE_TOLERANCE]
                       [--trim_size TRIM_SIZE]

a simple multi-processor consensus sequence generator

optional arguments:
  -h, --help            show this help message and exit
  --n_core N_CORE       number of processes used for generating consensus; 0
                        for main process only (default: 24)
  --min_cov MIN_COV     minimum coverage to break the consensus (default: 6)
  --min_cov_aln MIN_COV_ALN
                        minimum coverage of alignment data; a seed read with
                        less than MIN_COV_ALN average depth of coverage will
                        be completely ignored (default: 10)
  --max_cov_aln MAX_COV_ALN
                        maximum coverage of alignment data; a seed read with
                        more than MAX_COV_ALN average depth of coverage of the
                        longest alignments will be capped, excess shorter
                        alignments will be ignored (default: 0)
  --min_len_aln MIN_LEN_ALN
                        minimum length of a sequence in an alignment to be
                        used in consensus; any shorter sequence will be
                        completely ignored (default: 0)
  --min_n_read MIN_N_READ
                        1 + minimum number of reads used in generating the
                        consensus; a seed read with fewer alignments will be
                        completely ignored (default: 10)
  --max_n_read MAX_N_READ
                        1 + maximum number of reads used in generating the
                        consensus (default: 500)
  --trim                trim the input sequence with k-mer spare dynamic
                        programming to find the mapped range (default: False)
  --output_full         output uncorrected regions too (default: False)
  --output_multi        output multi correct regions (default: False)
  --min_idt MIN_IDT     minimum identity of the alignments used for correction
                        (default: 0.7)
  --edge_tolerance EDGE_TOLERANCE
                        for trimming, the there is unaligned edge leng >
                        edge_tolerance, ignore the read (default: 1000)
  --trim_size TRIM_SIZE
                        the size for triming both ends from initial sparse
                        aligned region (default: 50)