genomicSimulationC 0.2.6
Data Fields
gsc_GenOptions Struct Reference

A type that contains choices of settings for gsc_SimData functions that create a new gsc_AlleleMatrix/generation. More...

#include <sim-operations.h>

+ Collaboration diagram for gsc_GenOptions:

Data Fields

_Bool will_name_offspring
 A boolean: whether generated offspring should be given names. More...
 
const char * offspring_name_prefix
 If will_name_offspring is true, generated offspring are named with the concatenation {offspring_name_prefix}{index}. More...
 
unsigned int family_size
 The number of offspring to produce from each cross. More...
 
_Bool will_track_pedigree
 A boolean: whether to track parentage of generated offspring. More...
 
_Bool will_allocate_ids
 A boolean: whether to allocate generated offspring session- unique IDs. More...
 
const char * filename_prefix
 A string used in save-as-you-go file names. More...
 
_Bool will_save_pedigree_to_file
 A boolean. More...
 
gsc_EffectID will_save_bvs_to_file
 If equal to NO_EFFECTSET, no bvs are calculated or saved. More...
 
_Bool will_save_alleles_to_file
 A boolean. More...
 
_Bool will_save_to_simdata
 A boolean. More...
 

Detailed Description

A type that contains choices of settings for gsc_SimData functions that create a new gsc_AlleleMatrix/generation.

The family_size parameter will affect how many offspring are produced.

The will_name_offspring, will_track_pedigree, and will_allocate_ids parameters affect how much extra detail about the offspring is generated/saved.

The will_save_to_simdata toggle allows you the option of generating offspring without saving them in memory. This may be useful in combination with save-as-you-go toggles will_save_pedigree_to_file, will_save_bvs_to_file, and will_save_alleles_to_file, to generate a larger number of offspring than will fit in memory.

Has short name: GenOptions

Definition at line 638 of file sim-operations.h.

Field Documentation

◆ family_size

unsigned int gsc_GenOptions::family_size

The number of offspring to produce from each cross.

Definition at line 643 of file sim-operations.h.

◆ filename_prefix

const char* gsc_GenOptions::filename_prefix

A string used in save-as-you-go file names.

Definition at line 651 of file sim-operations.h.

◆ offspring_name_prefix

const char* gsc_GenOptions::offspring_name_prefix

If will_name_offspring is true, generated offspring are named with the concatenation {offspring_name_prefix}{index}.

Definition at line 640 of file sim-operations.h.

◆ will_allocate_ids

_Bool gsc_GenOptions::will_allocate_ids

A boolean: whether to allocate generated offspring session- unique IDs.

IDs are used for pedigree tracking. The offspring of an anonymous individual (one without an ID) cannot identify that individual as their parent.

Definition at line 646 of file sim-operations.h.

◆ will_name_offspring

_Bool gsc_GenOptions::will_name_offspring

A boolean: whether generated offspring should be given names.

Definition at line 639 of file sim-operations.h.

◆ will_save_alleles_to_file

_Bool gsc_GenOptions::will_save_alleles_to_file

A boolean.

If true, the set of alleles of every offspring generated in the cross are saved to "{filename_prefix}-genotype.txt", even if will_save_to_simdata is false. Genotypes are saved in the format of gsc_save_allele_matrix()

Definition at line 664 of file sim-operations.h.

◆ will_save_bvs_to_file

gsc_EffectID gsc_GenOptions::will_save_bvs_to_file

If equal to NO_EFFECTSET, no bvs are calculated or saved.

Otherwise, for each offspring in the cross, the breeding values according to the marker effect set with this gsc_EffectID are saved to "{filename_prefix}-bv.txt", even if will_save_to_simdata is false. BVs are saved in the format of gsc_save_bvs()

Definition at line 657 of file sim-operations.h.

◆ will_save_pedigree_to_file

_Bool gsc_GenOptions::will_save_pedigree_to_file

A boolean.

If true, the full/recursive pedigrees of every offspring generated in the cross are saved to "{filename_prefix}-pedigree.txt", even if will_save_to_simdata is false. Pedigrees are saved in the format of gsc_save_full_pedigree()

Definition at line 652 of file sim-operations.h.

◆ will_save_to_simdata

_Bool gsc_GenOptions::will_save_to_simdata

A boolean.

If true, the generated offspring exist in the gsc_SimData struct after the function executes. If false, they are discarded after creation.

Definition at line 675 of file sim-operations.h.

◆ will_track_pedigree

_Bool gsc_GenOptions::will_track_pedigree

A boolean: whether to track parentage of generated offspring.

Definition at line 645 of file sim-operations.h.


The documentation for this struct was generated from the following file: