A reader and interpolator for genetic map files. More...

#include <recombination.hpp>

Classes
struct	record
	A single line entry from the genetic map file. More...

Public Member Functions
	genetic_map_file (const std::string &map_file_path, const std::string &chrom)
	Constructs a genetic_map_file object for reading recombination map data.

bool	good () const
	Check whether the genetic map file was loaded successfully.

	operator bool () const
	Implicit conversion to bool for validity checking.

double	interpolate_centimorgan (std::size_t variant_pos)
	Interpolate the genetic map position (in centimorgans) for a variant.

Detailed Description

A reader and interpolator for genetic map files.

The genetic_map_file class provides an interface to read recombination rate data from a genetic map file and interpolate genetic distances (in centimorgans) for arbitrary variant positions.

The file may be in one of two formats:

New format: Three columns — chrom pos cM
Legacy format: Four columns — chrom <discard> cM pos

Only entries corresponding to the specified target chromosome are processed.

See also: record, read_record(), interpolate_centimorgan()

Constructor & Destructor Documentation

◆ genetic_map_file()

genetic_map_file::genetic_map_file	(	const std::string &	map_file_path,
		const std::string &	chrom )

Constructs a genetic_map_file object for reading recombination map data.

This constructor opens a genetic map file and prepares it for iterating over recombination map records associated with a specific chromosome.

The constructor:

Opens the map file stream.
Detects whether the file is in "new format" (three-column format with tab separators) or the older PLINK-style format.
Skips header lines (those beginning with #).
Searches for the first record matching the requested chromosome.
Reads and buffers the first two records (prev_rec_ and cur_rec_) for iteration.

Parameters

map_file_path	Path to the genetic map file.
chrom	Chromosome identifier to extract records for.

Note

If the file contains invalid header formatting, an error is printed and the object is marked invalid (good_ = false).
If no records for the target chromosome are found, or only a single record exists, the object is marked invalid.
The validity of the object should be checked with good() before use.

Example:

genetic_map_file gmap("genetic_map_chr1.txt", "1");
if (!gmap.good()) {
  throw std::runtime_error("Failed to load map file");
}

Member Function Documentation

◆ good()

bool genetic_map_file::good ( ) const

inline

Check whether the genetic map file was loaded successfully.

This function returns the internal state flag that indicates whether the constructor succeeded in opening and preparing the file.

Returns: true if the object is valid and ready for use, false otherwise.

◆ interpolate_centimorgan()

double genetic_map_file::interpolate_centimorgan ( std::size_t variant_pos )

Interpolate the genetic map position (in centimorgans) for a variant.

Given a genomic coordinate (basepair position), this method estimates the corresponding centimorgan (cM) value using linear interpolation between records in the genetic map file. The interpolation relies on two adjacent map records (prev_rec_ and cur_rec_).

If the position is before the first record, interpolation assumes a proportional relationship between basepairs and cM using the first record as reference.
If the position falls between two known records, interpolation is performed linearly between their map values.
If the position extends beyond the current block, additional records are read until the correct interval is found or until the chromosome ends.

Parameters

variant_pos The genomic coordinate (basepair position) of the variant.

Returns: The interpolated centimorgan (cM) value. If the object is invalid (good_ == false), returns NaN.

Note: Assertions ensure that consecutive map records have different positions. These cases should ideally be handled more gracefully.

Warning: Extrapolation beyond the last record assumes constant recombination rate (basepair_cm). Interpret with caution.

See also: good()

Here is the caller graph for this function:

◆ operator bool()

genetic_map_file::operator bool ( ) const

inline

Implicit conversion to bool for validity checking.

Provides a shorthand way to test whether the object is in a usable state. Equivalent to calling good().