IBS clustering constraint: population concordance test (--ppc, --ppc-gap)

[davidonlaptop]

Description

This feature adds the --ppc and --ppc-gap constraint(s) on the --cluster option described in issue #7. For more info, check: http://pngu.mgh.harvard.edu/~purcell/plink/strat.shtml#options

The input file is the model created in #3.

Analysis

Add a comment to this issue with:

• plink version used as reference (1.07 or 1.90 beta 3)
• relevant C++ function name(s) and the file name(s) where they appear
• Document the structure of the hh file generated by plink (not always present).
• Document the algorithm and/or mathematical formula to compute:
  • --ppc option
  • --ppc-gap option

Design

Add a comment to this issue describing how this will be implemented in Spark, and how it differs from plink.

Implementation

The implementation should use:

• Scala
• Spark RDD
• Spark MLlib / GraphX (if appropriate)