MANUAL: apt-chp-to-txt (apt-1.12.0)

apt-chp-to-txt writes expression and genotyping CHP files in tab-delimited text format.

This tool converts text/binary CHP files to tab-delimited text output. One output file is generated per CHP file, with the same base name and the extension .txt, and any previously-generated file of the same name is silently overwritten.

Quick Start

To convert text/binary CHP files to tab-delimited text output, use:

apt-chp-to-txt [options] file1.chp ... fileN.chp

Options:

apt-chp_to_txt - Writes copynumber CHP files in tab-delimited text format.

usage:
	apt-chp_to_txt  \
       --o results --chp-files chpfiles.txt

options:
   -h, --help                    This message. [default 'false'] 
     --version Display version information. [default 'false'] 
   -v, --verbose How verbose to be with status messages 0 = quiet, 
                   1 - usual messages, 2 - more messages. [default
                   '1'] 
   -o, --out-dir Directory to write result files into. [default 
                   '.'] 
     --cdf-file CDF file to pull probe set names from. [default 
                   ''] 
     --no-header If set to true, then the file header will not be
                   output. [default 'false'] 
     --no-body If set to true, then the file body will not be
                   output. [default 'false'] 
     --chp-files Text file specifying chp files to process, one per
                   line with the first line being 'chp_files'.
                   [default ''] 
     --log-file The name of the log file. Generally defaults to 
                   the program name in the out-dir folder. [default
                   '']