VcfGenomeStat

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Purpose

vcfGenomeStat - print flanking sequences and how often they appear for input vcf file.

Usage

   ../bin/vcfGenomeStat  [-L <integer>] [-w <integer>] [-l <string>] -o
                         <string> -i <string> -r <string> [-v] [--]
                         [--version] [-h]


Where: 

   -L <integer>,  --max-line-length <integer>
     Maximun Line Length of the VCF file (default:1048576)

   -w <integer>,  --win <integer>
     Window size for HomPolymerRun (default:10)

   -l <string>,  --log <string>
     Log file - [out].log is default

   -o <string>,  --out <string>
     (required)  Output file

   -i <string>,  --in <string>
     (required)  Input VCF file

   -r <string>,  --reference <string>
     (required)  Karma's reference sequence

   -v,  --verbose
     Turn on verbose mode

   --,  --ignore_rest
     Ignores the rest of the labeled arguments following this flag.

   --version
     Displays version information and exits.

   -h,  --help
     Displays usage information and exits.