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Factor out distributed SMC logic #2303

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Factor out distributed SMC logic #2303

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738c617
Python: Factor out distributed SMC logic
jeromekelleher Aug 2, 2024
28b1b0b
Partially working SMC-K in refactoring
jeromekelleher Aug 2, 2024
0b60d27
Fixup GC left event and tests
jeromekelleher Aug 5, 2024
4951c58
fix smck migration
jeromekelleher Aug 5, 2024
873149b
Thrashing about
jeromekelleher Aug 5, 2024
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Fixup GC left event and tests
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@jeromekelleher
jeromekelleher committed Aug 5, 2024
commit 0b60d27a8b76828bbc2fdba5ecee82b0965c4a42
13 changes: 0 additions & 13 deletions lib/msprime.c
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Original file line number Diff line number Diff line change
Expand Up @@ -5190,7 +5190,6 @@ msp_gene_conversion_left_event(msp_t *self, label_id_t label)
population_id_t population;
lineage_t *lineage, *new_lineage;
segment_t *y, *x, *alpha;
hull_t *rhs_hull;
hull_t *lhs_hull = NULL;

lhs_hull = NULL;
Expand Down Expand Up @@ -5306,18 +5305,6 @@ msp_gene_conversion_left_event(msp_t *self, label_id_t label)
self->sequence_length);
msp_reset_hull_right(
self, lhs_hull, lhs_old_right, lhs_new_right, y->lineage->population, label);

// rhs
tsk_bug_assert(alpha->left < lhs_old_right);
rhs_hull = msp_alloc_hull(self, alpha->left, lhs_old_right, alpha->lineage);
if (rhs_hull == NULL) {
ret = MSP_ERR_NO_MEMORY;
goto out;
}
ret = msp_insert_hull(self, rhs_hull);
if (ret != 0) {
goto out;
}
}

out:
Expand Down
10 changes: 5 additions & 5 deletions lib/tests/test_ancestry.c
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Original file line number Diff line number Diff line change
Expand Up @@ -4201,7 +4201,6 @@ test_fenwick_rebuild_smc_k(void)
tsk_table_collection_free(&tables);
}

#if 0
static void
run_smc_k_gc_simulation(
double gc_rate, double tract_length, bool discrete_genome, double offset)
Expand Down Expand Up @@ -4230,10 +4229,12 @@ run_smc_k_gc_simulation(
CU_ASSERT_EQUAL_FATAL(msp_set_recombination_rate(&msp, recombination_rate), 0);
CU_ASSERT_EQUAL_FATAL(msp_set_gene_conversion_rate(&msp, gc_rate), 0);
CU_ASSERT_EQUAL_FATAL(msp_set_gene_conversion_tract_length(&msp, tract_length), 0);
ret = msp_initialise(&msp);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = msp_set_simulation_model_smc_k(&msp, offset);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = msp_initialise(&msp);
CU_ASSERT_EQUAL_FATAL(ret, 0);

msp_verify(&msp, 0);

ret = msp_run(&msp, DBL_MAX, ULONG_MAX);
CU_ASSERT_EQUAL(ret, 0);
Expand Down Expand Up @@ -4266,7 +4267,6 @@ test_smc_k_gc(void)
run_smc_k_gc_simulation(1.0, tract_lengths[j], false, 3.1);
}
}
#endif

int
main(int argc, char **argv)
Expand Down Expand Up @@ -4367,7 +4367,7 @@ main(int argc, char **argv)
{ "test_mixed_model_smc_k", test_mixed_model_smc_k },
{ "test_mixed_model_smc_k_large", test_mixed_model_smc_k_large },
{ "test_fenwick_rebuild_smc_k", test_fenwick_rebuild_smc_k },
/* { "test_smc_k_gc", test_smc_k_gc }, */
{ "test_smc_k_gc", test_smc_k_gc },
CU_TEST_INFO_NULL,
};

Expand Down