Program: cnvhmm (copy number analysis using hidden markov algorithm)
Version: 1.0.1
Author: Ken Chen & Xiaoqi Shi

Usage:   cnvhmm <command> [options]

Key commands:
        cnsdepth        create depth file
        hmm             run HMM analysis
       
===========================================================================
Usage:   cnvhmm cnsdepth [options] cnsfile outputfile

Optional Arguments:
 -y  STRING      assign marker file[defaul=NULL]
 -q  INT         map quality cutoff[defaul=40]
 -w  INT         window size[defaul=1000]
 -b  INT         mininum position[defaul=1]
 -e  DOUBLE      maximus position[defaul=1000000000000]
 -m  INT         GC window size[defaul=1000]
 -c  FLOAT       GC cutoff[defaul=0.5]

===========================================================================
Usage:   cnvhmm hmm [options]  [cnsfile] [infile]

Optional Arguments:
 -i                 if present program will use file created from cnsdepth as input[infile], otherwise take marker[markerfile] and cns[cnsfile] file as inputs

parameters for depth&GC data preparation:
 -y  STRING          assign marker file[defaul=NULL]
 -d  STRING          create and write out depth file from marker and cns file
 -o  STRING          results file(states and region information)
 -q  INT             map quality cutoff[defaul=40]
 -w  INT             window size[defaul=1000]
 -b  INT             mininum position[defaul=1]
 -e  DOUBLE          maximus position[defaul=999999999]
 -m  INT             GC window size[defaul=1000]
 -c  FLOAT           GC cutoff[defaul=0.5]

parameters for HMM process:
 -a  STRING          HMM algorithm [defaul='viterbi']
 -n  INT             max copy number[defaul=3]
 -f  INT             median filter size[defaul=3]
 -g  INT             GC correction 1:apply 0:not apply[defaul=1]
 -t  INT             transition probability 1:update 0:not update[defaul=0]
 -r  DOUBLE          cnv rate[defaul=0.001]
 -s  DOUBLE          nv size[defaul=0.1]
 -k  INT             minimum number of markers[defaul=5]
 -x  INT             The maximum # of bases a cnv can extend without evidence[defaul=450000]
 -l  DOUBLE          Log Likelihood Ratio Cut off[defaul=10]