static void snp_annotator_stream_free(GtNodeStream *ns)
{
GtUword i;
GtSNPAnnotatorStream *sas;
if (!ns) return;
sas = gt_snp_annotator_stream_cast(ns);
gt_region_mapping_delete(sas->rmap);
while (gt_queue_size(sas->snps) > 0) {
gt_genome_node_delete((GtGenomeNode*) gt_queue_get(sas->snps));
}
while (gt_queue_size(sas->outqueue) > 0) {
gt_genome_node_delete((GtGenomeNode*) gt_queue_get(sas->outqueue));
}
for (i = 0; i < gt_array_size(sas->instreams); i++) {
gt_node_stream_delete(*(GtNodeStream**) gt_array_get(sas->instreams, i));
}
for (i = 0; i < gt_array_size(sas->cur_gene_set); i++) {
gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(sas->cur_gene_set, i));
}
gt_array_delete(sas->cur_gene_set);
gt_node_stream_delete(sas->merge_stream);
gt_array_delete(sas->instreams);
gt_queue_delete(sas->snps);
gt_queue_delete(sas->outqueue);
}
static void select_visitor_free(GtNodeVisitor *nv)
{
GtSelectVisitor *select_visitor = select_visitor_cast(nv);
gt_str_delete(select_visitor->source);
gt_str_delete(select_visitor->seqid);
gt_queue_delete(select_visitor->node_buffer);
}
static void add_ids_visitor_free(GtNodeVisitor *nv)
{
GtAddIDsVisitor *add_ids_visitor = add_ids_visitor_cast(nv);
gt_hashmap_delete(add_ids_visitor->undefined_sequence_regions);
gt_cstr_table_delete(add_ids_visitor->defined_seqids);
gt_queue_delete(add_ids_visitor->node_buffer);
}
static void filter_stream_free(GtNodeStream *ns)
{
AgnFilterStream *stream = filter_stream_cast(ns);
gt_node_stream_delete(stream->in_stream);
gt_queue_delete(stream->cache);
gt_hashmap_delete(stream->typestokeep);
}
static void buffer_stream_free(GtNodeStream *ns)
{
GtBufferStream *bs = buffer_stream_cast(ns);
while (gt_queue_size(bs->node_buffer))
gt_genome_node_delete(gt_queue_get(bs->node_buffer));
gt_queue_delete(bs->node_buffer);
gt_node_stream_delete(bs->in_stream);
}
static void gtf_in_stream_free(GtNodeStream *ns)
{
GtGTFInStream *gtf_in_stream = gtf_in_stream_cast(ns);
gt_free(gtf_in_stream->filename);
gt_type_checker_delete(gtf_in_stream->type_checker);
while (gt_queue_size(gtf_in_stream->genome_node_buffer))
gt_genome_node_delete(gt_queue_get(gtf_in_stream->genome_node_buffer));
gt_queue_delete(gtf_in_stream->genome_node_buffer);
}
static void gff3_numsorted_out_stream_free(GtNodeStream *ns)
{
GtGFF3NumsortedOutStream *gff3_out_stream =
gff3_numsorted_out_stream_cast(ns);
gt_node_stream_delete(gff3_out_stream->in_stream);
gt_node_visitor_delete(gff3_out_stream->gff3_visitor);
gt_array_delete(gff3_out_stream->buffer);
gt_queue_delete(gff3_out_stream->outqueue);
}
void gt_orphanage_delete(GtOrphanage *o)
{
if (!o) return;
gt_cstr_table_delete(o->orphan_ids);
gt_cstr_table_delete(o->missing_parents);
while (gt_queue_size(o->orphans))
gt_genome_node_delete(gt_queue_get(o->orphans));
gt_queue_delete(o->orphans);
gt_free(o);
}
void gt_desc_buffer_delete(GtDescBuffer *db)
{
if (!db) return;
if (db->reference_count) {
db->reference_count--;
return;
}
gt_free(db->buf);
gt_queue_delete(db->startqueue);
gt_free(db);
}
static void feature_in_stream_free(GtNodeStream *ns)
{
GtFeatureInStream *stream = feature_in_stream_cast(ns);
gt_str_array_delete(stream->seqids);
while (gt_queue_size(stream->regioncache) > 0)
{
GtGenomeNode *gn = gt_queue_get(stream->regioncache);
gt_genome_node_delete(gn);
}
gt_queue_delete(stream->regioncache);
}
static void gff3_in_stream_plain_free(GtNodeStream *ns)
{
GtGFF3InStreamPlain *gff3_in_stream_plain = gff3_in_stream_plain_cast(ns);
gt_str_array_delete(gff3_in_stream_plain->files);
gt_str_delete(gff3_in_stream_plain->stdinstr);
while (gt_queue_size(gff3_in_stream_plain->genome_node_buffer)) {
gt_genome_node_delete(gt_queue_get(gff3_in_stream_plain
->genome_node_buffer));
}
gt_queue_delete(gff3_in_stream_plain->genome_node_buffer);
gt_gff3_parser_delete(gff3_in_stream_plain->gff3_parser);
gt_cstr_table_delete(gff3_in_stream_plain->used_types);
gt_file_delete(gff3_in_stream_plain->fpin);
}
void gt_bed_parser_delete(GtBEDParser *bed_parser)
{
if (!bed_parser) return;
gt_free(bed_parser->block_type);
gt_free(bed_parser->thick_feature_type);
gt_free(bed_parser->feature_type);
gt_str_delete(bed_parser->another_word);
gt_str_delete(bed_parser->word);
gt_hashmap_delete(bed_parser->seqid_to_str_mapping);
while (gt_queue_size(bed_parser->feature_nodes))
gt_genome_node_delete(gt_queue_get(bed_parser->feature_nodes));
gt_queue_delete(bed_parser->feature_nodes);
gt_region_node_builder_delete(bed_parser->region_node_builder);
gt_free(bed_parser);
}
GtNodeVisitor*
agn_gaeval_visitor_new(GtNodeStream *astream, AgnGaevalParams gparams)
{
agn_assert(astream);
// Create the node visitor
GtNodeVisitor *nv = gt_node_visitor_create(gaeval_visitor_class());
AgnGaevalVisitor *v = gaeval_visitor_cast(nv);
v->alignments = gt_feature_index_memory_new();
v->tsvout = NULL;
v->params = gparams;
// Check that sum of weights is 1.0
double weights_total = gparams.alpha + gparams.beta +
gparams.gamma + gparams.epsilon;
if(fabs(weights_total - 1.0) > 0.0001)
{
fprintf(stderr, "[AgnGaevalVisitor::agn_gaeval_visitor_new] warning: "
"sum of weights is not 1.0 %.3lf; integrity calculations will be "
"incorrect\n", weights_total);
}
// Set up node stream to load alignment features into memory
GtQueue *streams = gt_queue_new();
GtNodeStream *stream, *last_stream;
GtHashmap *typestokeep = gt_hashmap_new(GT_HASH_STRING, NULL, NULL);
gt_hashmap_add(typestokeep, "cDNA_match", "cDNA_match");
gt_hashmap_add(typestokeep, "EST_match", "EST_match");
gt_hashmap_add(typestokeep, "nucleotide_match", "nucleotide_match");
stream = agn_filter_stream_new(astream, typestokeep);
gt_queue_add(streams, stream);
last_stream = stream;
stream = gt_feature_out_stream_new(last_stream, v->alignments);
gt_queue_add(streams, stream);
last_stream = stream;
stream = gt_inter_feature_stream_new(last_stream, "cDNA_match", "match_gap");
gt_queue_add(streams, stream);
last_stream = stream;
stream = gt_inter_feature_stream_new(last_stream, "EST_match", "match_gap");
gt_queue_add(streams, stream);
last_stream = stream;
stream = gt_inter_feature_stream_new(last_stream, "nucleotide_match",
"match_gap");
gt_queue_add(streams, stream);
last_stream = stream;
// Process the node stream
GtError *error = gt_error_new();
int result = gt_node_stream_pull(last_stream, error);
if(result == -1)
{
fprintf(stderr, "[AEGeAn::AgnGaevalStream] error parsing alignments: %s\n",
gt_error_get(error));
gt_node_visitor_delete(nv);
return NULL;
}
gt_error_delete(error);
gt_hashmap_delete(typestokeep);
while(gt_queue_size(streams) > 0)
{
stream = gt_queue_get(streams);
gt_node_stream_delete(stream);
}
gt_queue_delete(streams);
return nv;
}
bool agn_infer_cds_visitor_unit_test(AgnUnitTest *test)
{
GtQueue *queue = gt_queue_new();
infer_cds_visitor_test_data(queue);
agn_assert(gt_queue_size(queue) == 4);
GtFeatureNode *fn = gt_queue_get(queue);
GtArray *cds = agn_typecheck_select(fn, agn_typecheck_cds);
bool grape1 = (gt_array_size(cds) == 4);
if(grape1)
{
GtGenomeNode *cds2 = *(GtGenomeNode **)gt_array_get(cds, 1);
GtRange range = gt_genome_node_get_range(cds2);
grape1 = (range.start == 349 && range.end == 522);
}
agn_unit_test_result(test, "grape test sans UTRs", grape1);
gt_genome_node_delete((GtGenomeNode *)fn);
gt_array_delete(cds);
fn = gt_queue_get(queue);
cds = agn_typecheck_select(fn, agn_typecheck_cds);
bool grape2 = (gt_array_size(cds) == 1);
if(grape2)
{
GtGenomeNode *cds1 = *(GtGenomeNode **)gt_array_get(cds, 0);
GtRange range = gt_genome_node_get_range(cds1);
GtStrand strand = gt_feature_node_get_strand((GtFeatureNode *)cds1);
grape2 = (range.start == 10747 && range.end == 11577 &&
strand == GT_STRAND_REVERSE);
}
agn_unit_test_result(test, "grape test with UTRs, strand check", grape2);
gt_genome_node_delete((GtGenomeNode *)fn);
gt_array_delete(cds);
fn = gt_queue_get(queue);
cds = agn_typecheck_select(fn, agn_typecheck_cds);
bool grape3 = (gt_array_size(cds) == 2);
if(grape3)
{
GtGenomeNode *cds2 = *(GtGenomeNode **)gt_array_get(cds, 1);
GtRange range = gt_genome_node_get_range(cds2);
grape3 = (range.start == 22651 && range.end == 23022);
}
agn_unit_test_result(test, "grape test 3", grape3);
gt_genome_node_delete((GtGenomeNode *)fn);
gt_array_delete(cds);
fn = gt_queue_get(queue);
cds = agn_typecheck_select(fn, agn_typecheck_cds);
bool grape4 = (gt_array_size(cds) == 12);
if(grape4)
{
GtGenomeNode *cds7 = *(GtGenomeNode **)gt_array_get(cds, 6);
GtRange range = gt_genome_node_get_range(cds7);
grape4 = (range.start == 27956 && range.end == 27996);
}
agn_unit_test_result(test, "grape test 4", grape4);
gt_genome_node_delete((GtGenomeNode *)fn);
gt_array_delete(cds);
while(gt_queue_size(queue) > 0)
{
GtGenomeNode *cds_n = gt_queue_get(queue);
gt_genome_node_delete(cds_n);
}
gt_queue_delete(queue);
return agn_unit_test_success(test);
}
// Main method
int main(int argc, char * const *argv)
{
GtError *error;
GtLogger *logger;
GtQueue *streams;
GtNodeStream *stream, *last_stream;
CanonGFF3Options options = { NULL, NULL, false };
gt_lib_init();
error = gt_error_new();
canon_gff3_parse_options(argc, argv + 0, &options, error);
streams = gt_queue_new();
logger = gt_logger_new(true, "", stderr);
stream = gt_gff3_in_stream_new_unsorted(argc - optind, (const char **)
argv+optind);
gt_gff3_in_stream_check_id_attributes((GtGFF3InStream *)stream);
gt_gff3_in_stream_enable_tidy_mode((GtGFF3InStream *)stream);
gt_queue_add(streams, stream);
last_stream = stream;
if(options.infer)
{
GtHashmap *type_parents = gt_hashmap_new(GT_HASH_STRING, gt_free_func,
gt_free_func);
gt_hashmap_add(type_parents, gt_cstr_dup("mRNA"), gt_cstr_dup("gene"));
gt_hashmap_add(type_parents, gt_cstr_dup("tRNA"), gt_cstr_dup("gene"));
stream = agn_infer_parent_stream_new(last_stream,
type_parents);
gt_hashmap_delete(type_parents);
gt_queue_add(streams, stream);
last_stream = stream;
}
stream = agn_gene_stream_new(last_stream, logger);
gt_queue_add(streams, stream);
last_stream = stream;
if(options.source != NULL)
{
GtNodeVisitor *ssv = gt_set_source_visitor_new(options.source);
stream = gt_visitor_stream_new(last_stream, ssv);
gt_queue_add(streams, stream);
last_stream = stream;
}
stream = gt_gff3_out_stream_new(last_stream, options.outstream);
if(!options.infer)
gt_gff3_out_stream_retain_id_attributes((GtGFF3OutStream *)stream);
gt_queue_add(streams, stream);
last_stream = stream;
if(gt_node_stream_pull(last_stream, error) == -1)
{
fprintf(stderr, "[CanonGFF3] error processing node stream: %s",
gt_error_get(error));
}
while(gt_queue_size(streams) > 0)
{
stream = gt_queue_get(streams);
gt_node_stream_delete(stream);
}
gt_queue_delete(streams);
if(options.source != NULL)
gt_str_delete(options.source);
if(options.outstream != NULL)
gt_file_delete(options.outstream);
gt_error_delete(error);
gt_logger_delete(logger);
gt_lib_clean();
return 0;
}
int gt_queue_unit_test(GtError *err)
{
long check_counter = 0, check_counter_reverse = 1023;
unsigned long i;
int had_err = 0;
GtQueue *q;
gt_error_check(err);
/* without wraparound */
q = gt_queue_new();
gt_ensure(had_err, !gt_queue_size(q));
for (i = 0; !had_err && i < 1024; i++) {
gt_queue_add(q, (void*) i);
gt_ensure(had_err, gt_queue_size(q) == i + 1);
}
if (!had_err)
had_err = gt_queue_iterate(q, check_queue, &check_counter, err);
if (!had_err) {
had_err = gt_queue_iterate_reverse(q, check_queue_reverse,
&check_counter_reverse, err);
}
gt_ensure(had_err, gt_queue_iterate(q, fail_func, NULL, NULL));
gt_ensure(had_err, gt_queue_iterate_reverse(q, fail_func, NULL, NULL));
if (!had_err) {
gt_queue_remove(q, (void*) 0);
gt_ensure(had_err, gt_queue_size(q) == 1023);
}
for (i = 1; !had_err && i < 1024; i++) {
gt_ensure(had_err, gt_queue_head(q) == (void*) i);
gt_ensure(had_err, gt_queue_get(q) == (void*) i);
gt_ensure(had_err, gt_queue_size(q) == 1024 - i - 1);
}
gt_ensure(had_err, !gt_queue_size(q));
gt_queue_delete(q);
/* with wraparound (without full queue) */
if (!had_err) {
q = gt_queue_new();
gt_ensure(had_err, !gt_queue_size(q));
for (i = 0; !had_err && i < 1024; i++) {
gt_queue_add(q, (void*) i);
gt_ensure(had_err, gt_queue_size(q) == i + 1);
}
check_counter = 0;
check_counter_reverse = 1023;
if (!had_err)
had_err = gt_queue_iterate(q, check_queue, &check_counter, err);
gt_ensure(had_err, gt_queue_iterate(q, fail_func, NULL, NULL));
gt_ensure(had_err, gt_queue_iterate_reverse(q, fail_func, NULL, NULL));
if (!had_err) {
had_err = gt_queue_iterate_reverse(q, check_queue_reverse,
&check_counter_reverse, err);
}
for (i = 0; !had_err && i < 512; i++) {
gt_ensure(had_err, gt_queue_head(q) == (void*) i);
gt_ensure(had_err, gt_queue_get(q) == (void*) i);
gt_ensure(had_err, gt_queue_size(q) == 1024 - i - 1);
}
for (i = 0; !had_err && i < 512; i++) {
gt_queue_add(q, (void*) (i + 1024));
gt_ensure(had_err, gt_queue_size(q) == 512 + i + 1);
}
check_counter = 512;
check_counter_reverse = 1535;
if (!had_err)
had_err = gt_queue_iterate(q, check_queue, &check_counter, err);
if (!had_err) {
had_err = gt_queue_iterate_reverse(q, check_queue_reverse,
&check_counter_reverse, err);
}
gt_ensure(had_err, gt_queue_iterate(q, fail_func, NULL, NULL));
gt_ensure(had_err, gt_queue_iterate_reverse(q, fail_func, NULL, NULL));
if (!had_err) {
gt_queue_remove(q, (void*) 512);
gt_ensure(had_err, gt_queue_size(q) == 1023);
}
for (i = 1; !had_err && i < 1024; i++) {
gt_ensure(had_err, gt_queue_head(q) == (void*) (512 + i));
gt_ensure(had_err, gt_queue_get(q) == (void*) (512 + i));
gt_ensure(had_err, gt_queue_size(q) == 1024 - i - 1);
}
gt_ensure(had_err, !gt_queue_size(q));
gt_queue_delete(q);
}
/* with wraparound (with full queue) */
if (!had_err) {
q = gt_queue_new();
gt_ensure(had_err, !gt_queue_size(q));
for (i = 0; !had_err && i < 1024; i++) {
gt_queue_add(q, (void*) i);
gt_ensure(had_err, gt_queue_size(q) == i + 1);
}
check_counter = 0;
check_counter_reverse = 1023;
if (!had_err)
had_err = gt_queue_iterate(q, check_queue, &check_counter, err);
if (!had_err) {
had_err = gt_queue_iterate_reverse(q, check_queue_reverse,
&check_counter_reverse, err);
}
gt_ensure(had_err, gt_queue_iterate(q, fail_func, NULL, NULL));
gt_ensure(had_err, gt_queue_iterate_reverse(q, fail_func, NULL, NULL));
for (i = 0; !had_err && i < 512; i++) {
gt_ensure(had_err, gt_queue_head(q) == (void*) i);
gt_ensure(had_err, gt_queue_get(q) == (void*) i);
gt_ensure(had_err, gt_queue_size(q) == 1024 - i - 1);
}
for (i = 0; !had_err && i < 1024; i++) {
gt_queue_add(q, (void*) (i + 1024));
gt_ensure(had_err, gt_queue_size(q) == 512 + i + 1);
}
check_counter = 512;
check_counter_reverse = 2047;
if (!had_err)
had_err = gt_queue_iterate(q, check_queue, &check_counter, err);
if (!had_err) {
had_err = gt_queue_iterate_reverse(q, check_queue_reverse,
&check_counter_reverse, err);
}
gt_ensure(had_err, gt_queue_iterate(q, fail_func, NULL, NULL));
gt_ensure(had_err, gt_queue_iterate_reverse(q, fail_func, NULL, NULL));
if (!had_err) {
gt_queue_remove(q, (void*) 512);
gt_ensure(had_err, gt_queue_size(q) == 1535);
}
for (i = 1; !had_err && i < 1536; i++) {
gt_ensure(had_err, gt_queue_head(q) == (void*) (512 + i));
gt_ensure(had_err, gt_queue_get(q) == (void*) (512 + i));
gt_ensure(had_err, gt_queue_size(q) == 1536 - i - 1);
}
gt_ensure(had_err, !gt_queue_size(q));
gt_queue_delete(q);
}
/* test a corner case */
if (!had_err) {
q = gt_queue_new();
gt_queue_add(q, (void*) 1);
gt_ensure(had_err, gt_queue_size(q) == 1);
if (!had_err)
gt_queue_add(q, (void*) 1);
gt_ensure(had_err, gt_queue_size(q) == 2);
gt_ensure(had_err, gt_queue_get(q));
gt_ensure(had_err, gt_queue_size(q) == 1);
if (!had_err)
gt_queue_add(q, (void*) 1);
gt_ensure(had_err, gt_queue_size(q) == 2);
gt_ensure(had_err, gt_queue_get(q));
gt_ensure(had_err, gt_queue_size(q) == 1);
if (!had_err)
gt_queue_add(q, (void*) 1);
gt_ensure(had_err, gt_queue_size(q) == 2);
gt_ensure(had_err, gt_queue_get(q));
gt_ensure(had_err, gt_queue_size(q) == 1);
gt_ensure(had_err, gt_queue_get(q));
gt_ensure(had_err, gt_queue_size(q) == 0);
if (!had_err)
gt_queue_add(q, (void*) 1);
gt_ensure(had_err, gt_queue_size(q) == 1);
gt_ensure(had_err, gt_queue_get(q));
gt_ensure(had_err, gt_queue_size(q) == 0);
gt_queue_delete(q);
}
/* gt_queue_remove() corner case */
if (!had_err) {
q = gt_queue_new();
gt_queue_add(q, (void*) 1);
gt_ensure(had_err, gt_queue_size(q) == 1);
gt_queue_remove(q, (void*) 1);
gt_ensure(had_err, gt_queue_size(q) == 0);
gt_queue_delete(q);
}
/* gt_queue_remove() corner case */
if (!had_err) {
q = gt_queue_new();
gt_queue_add(q, (void*) 0);
gt_queue_add(q, (void*) 1);
gt_queue_add(q, (void*) 2);
gt_queue_add(q, (void*) 3);
gt_ensure(had_err, gt_queue_get(q) == (void*) 0);
gt_ensure(had_err, gt_queue_get(q) == (void*) 1);
gt_queue_add(q, (void*) 4);
gt_queue_add(q, (void*) 5);
gt_queue_remove(q, (void*) 4);
gt_queue_remove(q, (void*) 2);
gt_queue_remove(q, (void*) 5);
gt_queue_remove(q, (void*) 3);
gt_ensure(had_err, gt_queue_size(q) == 0);
gt_queue_delete(q);
}
/* delete with contents */
if (!had_err) {
q = gt_queue_new();
gt_ensure(had_err, !gt_queue_size(q));
if (!had_err)
gt_queue_add(q, gt_calloc(1, 16));
gt_ensure(had_err, gt_queue_size(q) == 1);
if (!had_err)
gt_queue_add(q, gt_calloc(1, 32));
gt_ensure(had_err, gt_queue_size(q) == 2);
gt_queue_delete_with_contents(q);
}
return had_err;
}