Class CheckPedigree

java.lang.Object
  CheckPedigree

public class CheckPedigree
extends java.lang.Object

This program reads in LINKAGE a pedigree file, and checks that the pedigree information is correctly formatted and self consistent. The checked file is then output. Error and warning messages are printed to the screen.

Note that only the pedigree information is checked for correct formatting. To check that the phenotype and genotype information is correctly formatted it's necessary to know the contents of the appropriate LINKAGE parameter file. So use CheckFormat for this.

See my LINKAGE format page for information about the way this suite of programs uses this format, including the difference between "pre-makeped" and standard "post-makeped" formats.

Usage : java CheckFormat < input.ped > output.ped [-pre]

where

• input.ped is the input LINKAGE pedigree file.
• output.ped is the checked output LINKAGE pedigree file.
• -pre If this option is specified the data is assumed to be in so called "pre-makeped" format and interpreted appropritately. The output will be in regular format not "pre-makeped" format.

Constructor Summary

CheckPedigree()

Method Summary

static void

main(java.lang.String[] args)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CheckPedigree

public CheckPedigree()

Method Detail

main

public static void main(java.lang.String[] args)