void test_revwalk_basic__sorting_modes(void)
{
git_oid id;
git_oid_fromstr(&id, commit_head);
cl_git_pass(test_walk(_walk, &id, GIT_SORT_TIME, commit_sorting_time, 1));
cl_git_pass(test_walk(_walk, &id, GIT_SORT_TOPOLOGICAL, commit_sorting_topo, 2));
cl_git_pass(test_walk(_walk, &id, GIT_SORT_TIME | GIT_SORT_REVERSE, commit_sorting_time_reverse, 1));
cl_git_pass(test_walk(_walk, &id, GIT_SORT_TOPOLOGICAL | GIT_SORT_REVERSE, commit_sorting_topo_reverse, 2));
}
int main(int argc, char *argv[])
{
ATerm aBottom;
ATermBBTree aTree;
ATinit(argc, argv, &aBottom);
ATbbtreeInit();
aTree = makeTree(dataValues);
/*ATftreeToDot(stdout, aTree);*/
test_walk(aTree, sortedDataValues);
return 0;
}
for (i = 0; i < results_count; ++i) if (memcmp(possible_results[i], result_array, result_bytes) == 0) return GIT_SUCCESS; return GIT_ERROR; } BEGIN_TEST(walk0, "do a simple walk on a repo with different sorting modes") git_oid id; git_repository *repo; git_revwalk *walk; must_pass(git_repository_open(&repo, REPOSITORY_FOLDER)); must_pass(git_revwalk_new(&walk, repo)); git_oid_mkstr(&id, commit_head); must_pass(test_walk(walk, &id, GIT_SORT_TIME, commit_sorting_time, 1)); must_pass(test_walk(walk, &id, GIT_SORT_TOPOLOGICAL, commit_sorting_topo, 2)); must_pass(test_walk(walk, &id, GIT_SORT_TIME | GIT_SORT_REVERSE, commit_sorting_time_reverse, 1)); must_pass(test_walk(walk, &id, GIT_SORT_TOPOLOGICAL | GIT_SORT_REVERSE, commit_sorting_topo_reverse, 2)); git_revwalk_free(walk); git_repository_free(repo); END_TEST BEGIN_SUITE(revwalk) ADD_TEST(walk0); END_SUITE
ATF_TC_BODY(walk_nsec3, tc) {
test_walk(tc);
}
ATF_TC_BODY(walk, tc) {
test_walk(tc);
}
static void test_repeat_loop()
{
TASSERT(sizeof(FollowPath) == 20);
// Construct 1 colour graph with kmer-size=11
dBGraph graph;
size_t kmer_size = 11, ncols = 1;
// Set up alignment correction params
CorrectAlnParam params = {.ctpcol = 0, .ctxcol = 0,
.ins_gap_min = 0, .ins_gap_max = 0,
.one_way_gap_traverse = true, .use_end_check = true,
.max_context = 10,
.gap_variance = 0.1, .gap_wiggle = 5};
// Sequence with repeat
char seq[] = "ATTTGGAACTCCGGA"
"GATAGGGCCAGT"
"GATAGGGCCAGT"
"GATAGGGCCAGT"
"GATAGGGCCAGT"
"GATAGGGCCAGT"
"GATAGGGCCAGT"
"GATAGGGCCAGT"
"GATAGGGCCAGT"
"GATAGGGCCAGT"
"GATAGGGCCAGT"
"GATAGGGCCAGT"
"CGTCAGGAGCTAACT";
char p0[] = "ATTTGGAACTCCGGA""GATAGGGCCAGT""GATAGGGCCAGT";
char p1[] = "GATAGGGCCAGT""GATAGGGCCAGT""CGTCAGGAGCTAACT";
// Allocate graph, but don't add any sequence
_construct_graph_with_paths(&graph, kmer_size, ncols, NULL, 0, params);
GenPathWorker *gen_path_wrkr = gen_paths_workers_alloc(1, &graph, NULL);
GraphWalker gwlk;
RepeatWalker rptwlk;
graph_walker_alloc(&gwlk);
rpt_walker_alloc(&rptwlk, graph.ht.capacity, 12);
dBNodeBuffer nbuf;
db_node_buf_alloc(&nbuf, 1024);
// Construct graph but no paths
build_graph_from_str_mt(&graph, 0, seq, strlen(seq));
TASSERT2(graph.ht.num_kmers == 15+12+15, "%zu", (size_t)graph.ht.num_kmers);
// Find first node in sequence
dBNode node0 = db_graph_find_str(&graph, seq);
TASSERT(node0.key != HASH_NOT_FOUND);
// 1) With no paths
char ans0[] = "ATTTGGAACTCCGGA""GATAGGGCCAGT";
test_walk(&gwlk, &rptwlk, node0, &nbuf, &graph, 15+2, ans0);
// 2) Add small paths - produces collapsed down seq with two copy repeat
gen_paths_from_str_mt(gen_path_wrkr, p0, params);
gen_paths_from_str_mt(gen_path_wrkr, p1, params);
char ans1[] = "ATTTGGAACTCCGGA""GATAGGGCCAGT""GATAGGGCCAGT""CGTCAGGAGCTAACT";
test_walk(&gwlk, &rptwlk, node0, &nbuf, &graph, 15+12+12+5, ans1);
// 3) Add long paths
gen_paths_from_str_mt(gen_path_wrkr, seq, params);
test_walk(&gwlk, &rptwlk, node0, &nbuf, &graph, strlen(seq)+1-kmer_size, seq);
graph_walker_dealloc(&gwlk);
rpt_walker_dealloc(&rptwlk);
db_node_buf_dealloc(&nbuf);
gen_paths_workers_dealloc(gen_path_wrkr, 1);
db_graph_dealloc(&graph);
}
void test_repeat_walker()
{
test_status("Testing repeat_walker.h");
test_repeat_loop();
}
