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One-bit encoding for genotypes #809

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Merged
merged 1 commit into from
Apr 5, 2023
Merged

One-bit encoding for genotypes #809

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57 changes: 24 additions & 33 deletions _tsinfermodule.c
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Original file line number Diff line number Diff line change
Expand Up @@ -92,20 +92,21 @@ AncestorBuilder_init(AncestorBuilder *self, PyObject *args, PyObject *kwds)
{
int ret = -1;
int err;
static char *kwlist[] = {"num_samples", "max_sites", NULL};
int num_samples, max_sites;
static char *kwlist[] = {"num_samples", "max_sites", "genotype_encoding", NULL};
int num_samples, max_sites, genotype_encoding;
int flags = 0;

self->builder = NULL;
if (!PyArg_ParseTupleAndKeywords(args, kwds, "ii", kwlist,
&num_samples, &max_sites)) {
if (!PyArg_ParseTupleAndKeywords(args, kwds, "ii|i", kwlist,
&num_samples, &max_sites, &genotype_encoding)) {
goto out;
}
self->builder = PyMem_Malloc(sizeof(ancestor_builder_t));
if (self->builder == NULL) {
PyErr_NoMemory();
goto out;
}
flags = genotype_encoding;
Py_BEGIN_ALLOW_THREADS
err = ancestor_builder_alloc(self->builder, num_samples, max_sites, flags);
Py_END_ALLOW_THREADS
Expand Down Expand Up @@ -274,34 +275,6 @@ AncestorBuilder_ancestor_descriptors(AncestorBuilder *self)
}
PyTuple_SET_ITEM(descriptors, j, py_descriptor);
}
/* j = 0; */
/* /1* It's not great that we're breaking encapsulation here and looking */
/* * directly in to the builder's data structures. However, it's quite an */
/* * awkward set of data to communicate, so it seems OK. *1/ */
/* for (f = self->builder->num_samples; f > 0; f--) { */
/* for (a = self->builder->frequency_map[f].head; a != NULL; a = a->next) { */
/* map_elem = (pattern_map_t *) a->item; */
/* dims = map_elem->num_sites; */
/* site_array = (PyArrayObject *) PyArray_SimpleNew(1, &dims, NPY_INT32); */
/* if (site_array == NULL) { */
/* goto out; */
/* } */
/* site_array_data = (int32_t *) PyArray_DATA(site_array); */
/* /1* The elements are listed backwards, so reverse them *1/ */
/* k = map_elem->num_sites - 1; */
/* for (s = map_elem->sites; s != NULL; s = s->next) { */
/* site_array_data[k] = (int32_t) s->site; */
/* k--; */
/* } */
/* descriptor = Py_BuildValue("kO", (unsigned long) f, site_array); */
/* if (descriptor == NULL) { */
/* Py_DECREF(site_array); */
/* goto out; */
/* } */
/* PyTuple_SET_ITEM(descriptors, j, descriptor); */
/* j++; */
/* } */
/* } */
ret = descriptors;
descriptors = NULL;
out:
Expand Down Expand Up @@ -335,13 +308,31 @@ AncestorBuilder_get_num_ancestors(AncestorBuilder *self, void *closure)
return ret;
}

static PyObject *
AncestorBuilder_get_memsize(AncestorBuilder *self, void *closure)
{
PyObject *ret = NULL;

if (AncestorBuilder_check_state(self) != 0) {
goto out;
}
ret = Py_BuildValue("k", (unsigned long) ancestor_builder_get_memsize(
self->builder));
out:
return ret;
}


static PyMemberDef AncestorBuilder_members[] = {
{NULL} /* Sentinel */
};

static PyGetSetDef AncestorBuilder_getsetters[] = {
{"num_sites", (getter) AncestorBuilder_get_num_sites, NULL, "The number of sites."},
{"num_ancestors", (getter) AncestorBuilder_get_num_ancestors, NULL, "The number of ancestors."},
{"num_ancestors", (getter) AncestorBuilder_get_num_ancestors, NULL,
"The number of ancestors."},
{"mem_size", (getter) AncestorBuilder_get_memsize, NULL,
"The number of allocated bytes."},
{NULL} /* Sentinel */
};

Expand Down
3 changes: 3 additions & 0 deletions docs/api.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,9 @@ Running inference

.. autofunction:: tsinfer.generate_ancestors

.. autoclass:: tsinfer.GenotypeEncoding
:members:

.. autofunction:: tsinfer.match_ancestors

.. autofunction:: tsinfer.match_samples
Expand Down
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