Core Classes and Functions

There are three main classes in Diem. Namely,

• DiemType which is the main data structure that holes the core functions for polarizing the data

• Contig class which simply holds the sequence of intervals that form a contig

• Intervals a class which describes a single interval, i.e. a contiguous region of a single state in a given individual

DiemType → Contig → Interval: DiemType contains the diem-formatted data as well as a matrix of Contigs (one per individual per chromosome), each Contig contains a list of Intervals representing contiguous ancestry tracts.

DiemType Class

The central data structure that holds:

• DMBC: Diem Matrix By Chromosome (state matrices)

• Genomic positions and chromosome information

• Individual metadata including ploidy and exclusions

• Polarization results including polarity, diagnostic indices, and support values

• Contigs which are per-chromosome per-interval lists of tracts

Key methods:

• polarize(): Run polarization analysis

• apply_threshold(): Filter markers by diagnostic index

• smooth(): Apply kernel smoothing

• sort(): Sort individuals by hybrid index

• ‘create_contig_matrix(): builds the contigs from the processed data

Contig Class

The Contig class represents a collection of genomic intervals for a specific individual and chromosome, essentially describing the complete ancestry structure along that chromosome.

Key attributes:

• chrName: Chromosome name

• indName: Individual name

• intervals: List of Interval objects making up the contig

• num_intervals: Number of intervals in the contig

Key methods:

• printIntervals(): Display interval information in a readable format

• get_my_intervals_of_state(): Filter intervals by ancestry state

Interval Class

The Interval class represents a contiguous genomic region with consistent ancestry state for a specific individual and chromosome.

Key attributes:

• chrName: Chromosome name

• indName: Individual name

• idxl, idxr: Left and right indices (inclusive) in the state matrix

• l, r: Left and right physical positions

• state: Ancestry state of the interval (0=uncalled, 1-3=called states)

Key methods:

• span(): Calculate and return the physical span of the interval

• mapSpan(chrLength): Calculate the relative span as fraction of chromosome length. chrLength must be provided