recombination Class Reference

Provides utilities for handling recombination rates and genetic maps. More...

#include <recombination.hpp>

Classes
struct	map_file_line
	Representation of a single line from a genetic map file. More...

Static Public Member Functions
static bool	parse_map_file (const std::string &map_file_path, std::vector< target_variant > &sites, float recom_min)
	Parse and align a genetic recombination map file to a set of target variants.
static double	haldane (double cm)
	Haldane’s mapping function.
static double	cm_to_switch_prob (double cm)
	Convert genetic distance to switch probability (default decay rate).
static double	cm_to_switch_prob (double cm, double decay_rate)
	Convert genetic distance to switch probability with a custom decay rate.
static double	haldane_inverse (double recom_prob)
	Inverse Haldane’s mapping function.
static double	switch_prob_to_cm (double recom_prob)
	Convert switch probability to genetic distance.

Detailed Description

Provides utilities for handling recombination rates and genetic maps.

The recombination class is responsible for parsing genetic map files, interpolating recombination rates across target variant sites, and converting between genetic map units (centiMorgans) and switch probabilities used in haplotype inference.

Responsibilities

• Parse and align genetic map files to variant sites.
• Interpolate recombination map values for variants without direct entries.
• Convert between genetic distances (cM) and recombination/switch probabilities using models such as Haldane’s map function.

Key Components

• struct map_file_line: Represents a single line in the map file, including chromosome, base-pair position, and map value.
• parse_map_file(): Aligns recombination map data with target variants and computes switch probabilities.
• read_entry(): Reads a line from the map file (supports both old and new formats).
• Utility functions:
  • haldane() and haldane_inverse() for recombination ↔ cM conversions.
  • cm_to_switch_prob() and switch_prob_to_cm() for cM ↔ switch probability conversions.

Notes

• The last recombination probability in the sequence is always set to zero to ensure proper backward traversal during haplotype inference.
• Supports both the old PLINK-style map format and new three-column format.

Member Function Documentation

cm_to_switch_prob() [1/2]

static double recombination::cm_to_switch_prob ( double cm )

inlinestatic

Convert genetic distance to switch probability (default decay rate).

Parameters

cm	Genetic distance in centiMorgans.

Returns

Switch probability.

\[ p = 1 - e^{-d/100} \]

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cm_to_switch_prob() [2/2]

static double recombination::cm_to_switch_prob ( double cm, double decay_rate )

inlinestatic

Convert genetic distance to switch probability with a custom decay rate.

Parameters

cm	Genetic distance in centiMorgans.
decay_rate	Custom decay factor scaling the conversion.

Returns

Switch probability.

\[ p = 1 - e^{-\lambda d/100} \]

where \(\lambda\) is the decay rate.

haldane()

static double recombination::haldane ( double cm )

inlinestatic

Haldane’s mapping function.

Converts a genetic distance (in centiMorgans) into the probability of recombination between two loci.

Parameters

cm	Genetic distance in centiMorgans.

Returns

Recombination probability.

\[ r = \frac{1 - e^{-d/50}}{2} \]

where \(d\) is the distance in cM.

haldane_inverse()

static double recombination::haldane_inverse ( double recom_prob )

inlinestatic

Inverse Haldane’s mapping function.

Converts a recombination probability back into genetic distance (in cM).

Parameters

recom_prob

Recombination probability.

Returns

Genetic distance (cM).

\[ d = 50 \cdot \ln\left(\frac{1}{1 - 2r}\right) \]

where \(r\) is the recombination probability.

parse_map_file()

bool recombination::parse_map_file ( const std::string & map_file_path, std::vector< target_variant > & sites, float recom_min )

static

Parse and align a genetic recombination map file to a set of target variants.

This function reads a genetic map file and assigns recombination rates (in cM) to each target variant in the provided vector. It aligns the genetic map to the given chromosome, interpolates recombination values between map positions, and converts the aligned genetic map into switch probabilities for HMM traversal.

The recombination probability at each site is computed based on the genetic distance between consecutive variants and is adjusted to ensure non-negative values, respecting the provided minimum recombination threshold.

Parameters

map_file_path	Path to the genetic map file. Must contain either standard format or a header-prefixed "new" format (three tab-delimited columns).
sites	Vector of target variants (with chromosome, position, and recombination fields). The recombination field (recom) is updated in-place.
recom_min	Minimum recombination probability to enforce for each site.

Returns

true if parsing and recombination assignment succeeded, false if the map file was malformed, empty, or chromosome mismatch occurred.

Note

• Assumes sites is sorted by position and belongs to a single chromosome.
• Sites before the first map entry and after the last entry are extrapolated linearly.
• The last site’s recombination probability is always set to zero.
• Uses an exponential model for recombination probability conversion:

  \[ \text{recom} = \max\left(\frac{1 - e^{-\Delta / 50}}{2}, \text{recom_min}\right) \]

  where \(\Delta\) is the genetic distance between consecutive variants.

Warning

Assertions are used to check for invalid map entries (duplicate positions, overflow). These should be handled gracefully in production code.

switch_prob_to_cm()

static double recombination::switch_prob_to_cm ( double recom_prob )

inlinestatic

Convert switch probability to genetic distance.

Parameters

recom_prob

Switch probability.

Returns

Genetic distance (cM).

\[ d = 100 \cdot \ln\left(\frac{1}{1 - p}\right) \]

where \(p\) is the switch probability.

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The documentation for this class was generated from the following files:

• src/recombination.hpp
• src/recombination.cpp