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Selective Sweep based on reading from a file with rudimentary ability to… #2410

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e5ce243
Selective Sweep based on reading from a file with rudimentary ability…
Aalhad-Bhatt Sep 3, 2025
8882f9b
Selective Sweep based on reading from a file with rudimentary ability…
Aalhad-Bhatt Sep 3, 2025
fbf9243
Forward notebook
Aalhad-Bhatt Sep 24, 2025
bf83a13
Forward sim notebook
Aalhad-Bhatt Sep 24, 2025
a945691
Well-mixed test cases
Aalhad-Bhatt Dec 3, 2025
690c7cb
Fixed test params
Aalhad-Bhatt Dec 3, 2025
d5957a7
Test cases for the well-mixed case. 1D test-cases soon to follow.
Aalhad-Bhatt Dec 3, 2025
b399c36
Merge branch 'main' into main
Aalhad-Bhatt Dec 4, 2025
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610 changes: 601 additions & 9 deletions lib/msprime.c
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27 changes: 23 additions & 4 deletions lib/msprime.h
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Original file line number Diff line number Diff line change
Expand Up @@ -43,8 +43,9 @@
#define MSP_MODEL_DIRAC 4
#define MSP_MODEL_DTWF 5
#define MSP_MODEL_SWEEP 6
#define MSP_MODEL_WF_PED 7
#define MSP_MODEL_SMC_K 8
#define MSP_MODEL_SWEEP_REVERSE 7
#define MSP_MODEL_WF_PED 8
#define MSP_MODEL_SMC_K 9

/* Exit codes from msp_run to distinguish different reasons for exiting
* before coalescence. */
Expand Down Expand Up @@ -231,13 +232,28 @@ typedef struct _sweep_t {
void (*print_state)(struct _sweep_t *self, FILE *out);
} sweep_t;

typedef struct _sweep_reverse_t {
double position;
size_t num_steps;
int num_demes;
int tot_pop;
double migration_rate;
tsk_id_t *mut_pop;
tsk_id_t *mut_pop_final;
double *t_of_forward_ev;
tsk_id_t *ev_type;
tsk_id_t *start_deme;
tsk_id_t *end_deme;
} sweep_reverse_t;

typedef struct _simulation_model_t {
int type;
union {
smc_k_coalescent_t smc_k_coalescent;
beta_coalescent_t beta_coalescent;
dirac_coalescent_t dirac_coalescent;
sweep_t sweep;
sweep_reverse_t sweep_reverse;
} params;
/* If the model allocates memory this function should be non-null. */
void (*free)(struct _simulation_model_t *model);
Expand Down Expand Up @@ -352,7 +368,7 @@ typedef struct {
/* Arbitrary limit, saves us having to put in complex malloc/free
* logic in the demographic_events. Can easily be changed if
* needs be. */
#define MSP_MAX_EVENT_POPULATIONS 100
#define MSP_MAX_EVENT_POPULATIONS 500000

typedef struct {
population_id_t derived[MSP_MAX_EVENT_POPULATIONS];
Expand Down Expand Up @@ -491,7 +507,10 @@ int msp_set_simulation_model_dirac(msp_t *self, double psi, double c);
int msp_set_simulation_model_beta(msp_t *self, double alpha, double truncation_point);
int msp_set_simulation_model_sweep_genic_selection(msp_t *self, double position,
double start_frequency, double end_frequency, double s, double dt);

int msp_set_simulation_model_sweep_genic_selection_reverse(msp_t *self, double position,
size_t num_steps, int num_demes, int tot_pop, double migration_rate,
tsk_id_t *mut_pop, tsk_id_t *mut_pop_final, double *t_of_forward_ev,
tsk_id_t *ev_type, tsk_id_t *start_deme, tsk_id_t *end_deme);
int msp_set_start_time(msp_t *self, double start_time);
int msp_set_store_migrations(msp_t *self, bool store_migrations);
int msp_set_store_full_arg(msp_t *self, bool store_full_arg);
Expand Down
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