IBS clustering constraint: maximum cluster size (--mc, --mcc)

[davidonlaptop]

Description

Similar to plink --cluster with --mc or --mcc options. See the wiki on IBS-MDS Process and the diagram for the Genome file.

More information can be found on the --cluster and --genome-full options in the section on Pairwise IBD estimation of plink manual.

The input file is the model created in #3.

This feature adds a constraint on the --cluster option described in issue #7.

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:
  • --mc option
  • --mcc 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)