Usage: cnD [OPTION] [FILE]
Parse FILE and call copy number variants. 
FILE is the output from "samtools pileup -c BAM | pileup2win.pl" see the README

    --prefix=STR         Use STR has the prefix for the output files
    --window=NUM         The window size of the input file (default: 1000)
    --learn=NUM          Perform Viterbi learning for NUM steps (default: 4)
    --repeat-cutoff=NUM  Flag all windows with a uniqueness score less than NUM as repeats
    --nohet              Do not use heterozygous SNP information
    --strict-OOR         Flag windows with out-of-range values as being repetitive instead of clamping the values
    --help               Print this message and exit
    --verbose            Print status and model parameters during processing