/*
* new_graph
*
* @graph: an uninitialized graph.
* @edges: the edges to add, the first two elements refer to
* the "from" and "to" items of the first edge respectively.
* @n: the number of vertices.
* @directed: specifies whether the created graph is directed.
*/
int new_graph(graph_t *graph, vector_int *edges,int n, int directed)
{
assert(0 == (vector_int_size(edges) % 2));
assert(0 <= vector_int_min(edges));
int max = vector_int_max(edges);
n = (n > max) ? n : (max + 1);
new_graph_empty(graph, n, directed);
if (vector_int_size(edges) > 0)
graph_add_edges(graph, edges,0);
return 0;
}
int graph_randomized_graph(graph_t *graph, int vc, int ec, int directed)
{
new_graph_empty(graph, vc, directed);
vector_int edges;
vector_int_init(&edges, 2);
graph_neimode_t mode = (directed) ? GRAPH_OUT : GRAPH_ALL;
int v = 0, w = 0, i = 0;
while(i < ec) {
while (v == w || graph_edge_contains(graph, v, w, mode)) {
v = random() % vc;
w = random() % vc;
}
VECTOR(edges)[0] = v;
VECTOR(edges)[1] = w;
graph_add_edges(graph, &edges, 0);
i++;
}
vector_int_destroy(&edges);
return 0;
}
dstring_t *haplo_split(GapIO *io, snp_t *snp, int nsnps, int verbose,
double min_score, int two_pass, int fast_mode,
double c_offset, int max_sets) {
graph *g;
edge *e;
dstring_t *ds;
verbosity = verbose;
g = graph_from_snps(io, snp, nsnps, c_offset);
if (verbosity >= 3)
print_matrix(g);
graph_add_edges(g);
graph_calc_chimeric_scores(g);
graph_calc_link_scores(g, 1);
if (verbosity >= 3)
graph_print(g, 0);
if (verbosity)
puts("Merging graph nodes");
while ((e = best_edge(g)) && (e->linkage_score > min_score)) {
if (verbosity >= 1) {
putchar('.');
fflush(stdout);
}
merge_node(g, e);
graph_calc_link_scores(g, fast_mode ? 0 : 1);
if (verbosity >= 4) {
print_matrix(g);
graph_print(g, 1);
}
}
if (verbosity >= 1)
puts("");
/* graph_print(g, 1); */
if (two_pass) {
/* Add fake zero-score edges if we want just 2-haplotypes */
add_zero_edges(g);
graph_calc_link_scores(g, 1);
if (verbosity >= 4)
graph_print(g, 1);
puts("===pass 2===");
while ((e = best_edge(g)) && (e->linkage_score > min_score)) {
merge_node(g, e);
graph_calc_link_scores(g, fast_mode ? 0 : 1);
/* graph_print(g, 1); */
}
/* graph_print(g, 1); */
}
/* Force number of groups to be X? */
if (max_sets) {
int ngroups = count_groups(g);
add_zero_edges(g);
for (; ngroups > max_sets; ngroups--) {
e = best_edge(g);
if (!e) {
printf("Bailed out as no edge connecting groups\n");
break;
}
merge_node(g, e);
graph_calc_link_scores(g, fast_mode ? 0 : 1);
}
}
/* print_groups(g); */
ds = list_groups(g);
graph_destroy(g);
return ds;
}
