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 int filter_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
GtError *error)
{
AgnFilterStream *stream;
GtFeatureNode *fn;
int had_err;
gt_error_check(error);
stream = filter_stream_cast(ns);
if(gt_queue_size(stream->cache) > 0)
{
*gn = gt_queue_get(stream->cache);
return 0;
}
while(1)
{
had_err = gt_node_stream_next(stream->in_stream, gn, error);
if(had_err)
return had_err;
if(!*gn)
return 0;
fn = gt_feature_node_try_cast(*gn);
if(!fn)
return 0;
GtFeatureNode *current;
GtFeatureNodeIterator *iter = gt_feature_node_iterator_new(fn);
for(current = gt_feature_node_iterator_next(iter);
current != NULL;
current = gt_feature_node_iterator_next(iter))
{
const char *type = gt_feature_node_get_type(current);
bool keepfeature = false;
if(gt_hashmap_get(stream->typestokeep, type) != NULL)
keepfeature = true;
if(keepfeature)
{
gt_genome_node_ref((GtGenomeNode *)current);
gt_queue_add(stream->cache, current);
}
}
gt_feature_node_iterator_delete(iter);
gt_genome_node_delete((GtGenomeNode *)fn);
if(gt_queue_size(stream->cache) > 0)
{
*gn = gt_queue_get(stream->cache);
return 0;
}
}
return 0;
}
GtGenomeNode* gt_orphanage_get_orphan(GtOrphanage *o)
{
gt_assert(o);
if (gt_queue_size(o->orphans))
return gt_queue_get(o->orphans);
return NULL;
}
void gt_desc_buffer_reset(GtDescBuffer *db)
{
GtUword laststartpos;
gt_assert(db);
if (!db->dirty) return;
if (gt_queue_size(db->startqueue) == 0) {
db->length = 0;
db->dirty = false;
return;
}
laststartpos = (GtUword) gt_queue_head(db->startqueue);
if (laststartpos != 0) {
laststartpos = (GtUword) gt_queue_get(db->startqueue);
db->length = db->length - laststartpos;
if (db->length >= laststartpos) {
/* strings overlap */
memmove(db->buf, db->buf + laststartpos, db->length * sizeof (char));
} else {
/* no overlap */
memcpy(db->buf, db->buf + laststartpos, db->length * sizeof (char));
}
gt_queue_add(db->startqueue, (void*) 0);
}
db->dirty = false;
}
int gt_queue_iterate_reverse(GtQueue *q, GtQueueProcessor gt_queue_processor,
void *info, GtError *err)
{
long i;
int rval;
gt_error_check(err);
gt_assert(q && gt_queue_processor);
if (gt_queue_size(q)) {
if (q->front < q->back) { /* no wraparound */
for (i = q->back-1; i >= q->front; i--) {
if ((rval = gt_queue_processor(q->contents + i, info, err)))
return rval;
}
}
else { /* wraparound */
for (i = q->back-1; i >= 0; i--) {
if ((rval = gt_queue_processor(q->contents + i, info, err)))
return rval;
}
for (i = q->size-1; i >= q->front; i--) {
if ((rval = gt_queue_processor(q->contents +i, info, err))) return rval;
}
}
}
return 0;
}
static int snp_annotator_stream_process_current_gene(GtSNPAnnotatorStream *sas,
GtError *err)
{
int had_err = 0;
GtUword i;
GtUword nof_genes = gt_array_size(sas->cur_gene_set);
gt_error_check(err);
if (gt_queue_size(sas->snps) > 0) {
/* we need to process SNPs for a gene cluster*/
gt_assert(gt_queue_size(sas->outqueue) == 0);
for (i = 0; !had_err && i < nof_genes; i++) {
GtNodeVisitor *sav;
GtFeatureNode *gene;
gene = *(GtFeatureNode**) gt_array_get(sas->cur_gene_set, i);
sav = gt_snp_annotator_visitor_new(gene, sas->tt, sas->rmap, err);
if (!sav)
had_err = -1;
if (!had_err) {
if (i < nof_genes-1) {
had_err = gt_queue_iterate(sas->snps,
snp_annotator_stream_process_snp,
sav, err);
} else {
while (!had_err && gt_queue_size(sas->snps) > 0) {
GtFeatureNode *snp = (GtFeatureNode*) gt_queue_get(sas->snps);
had_err = gt_genome_node_accept((GtGenomeNode*) snp, sav, err);
gt_queue_add(sas->outqueue, snp);
gt_genome_node_delete((GtGenomeNode*) snp);
}
}
gt_node_visitor_delete(sav);
}
gt_genome_node_delete((GtGenomeNode*) gene);
}
} else {
/* no SNPs for this gene cluster, delete it */
for (i = 0; !had_err && i < nof_genes; i++) {
gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(sas->cur_gene_set,
i));
}
}
gt_assert(gt_queue_size(sas->snps) == 0);
gt_array_reset(sas->cur_gene_set);
return had_err;
}
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);
}
void gt_orphanage_reset(GtOrphanage *o)
{
gt_assert(o);
while (gt_queue_size(o->orphans))
gt_genome_node_delete(gt_queue_get(o->orphans));
gt_cstr_table_reset(o->missing_parents);
gt_cstr_table_reset(o->orphan_ids);
}
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 queue_wrap(GtQueue *q, bool free_contents)
{
gt_assert(q);
if (free_contents) {
while (gt_queue_size(q))
gt_free(gt_queue_get(q));
}
gt_free(q->contents);
gt_free(q);
}
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);
}
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);
}
void* gt_queue_get(GtQueue *q)
{
void *contents;
gt_assert(q && gt_queue_size(q));
/* get contents */
contents = q->contents[q->front++];
/* adjust indices */
if (q->front == q->back)
q->front = q->back = 0; /* reset */
else if (q->front == q->size)
q->front = 0; /* wraparound */
return contents;
}
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);
}
static int gtf_in_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
GT_UNUSED GtError *err)
{
GtGTFInStream *is;
int had_err = 0;
gt_error_check(err);
is = gtf_in_stream_cast(ns);
if (!is->file_processed) {
had_err = gtf_in_stream_process_file(is, err);
is->file_processed = true;
}
if (!had_err && gt_queue_size(is->genome_node_buffer)) {
/* we still have a node in the buffer -> serve it from there */
*gn = gt_queue_get(is->genome_node_buffer);
return 0;
}
if (!had_err) {
/* the buffer is empty */
gt_assert(!gt_queue_size(is->genome_node_buffer));
*gn = NULL;
}
return had_err;
}
void gt_queue_remove(GtQueue *q, void *elem)
{
long i, elemidx;
gt_assert(q && gt_queue_size(q));
if (q->front < q->back) { /* no wraparound */
for (i = q->back-1; i >= q->front; i--) {
if (q->contents[i] == elem)
break;
}
elemidx = i;
gt_assert(elemidx >= q->front); /* valid element found */
for (i = elemidx+1; i < q->back; i++)
q->contents[i-1] = q->contents[i];
q->contents[q->back-1] = NULL;
q->back--;
if (q->front == q->back)
q->front = q->back = 0; /* reset */
}
else { /* wraparound */
for (i = q->back-1; i >= 0; i--) {
if (q->contents[i] == elem)
break;
}
elemidx = i;
if (elemidx >= 0) { /* element found */
for (i = elemidx+1; i < q->back; i++)
q->contents[i-1] = q->contents[i];
q->contents[q->back-1] = NULL;
q->back--;
if (q->back == 0) q->back = q->size;
return;
}
for (i = q->size-1; i >= q->front; i--) {
if (q->contents[i] == elem)
break;
}
elemidx = i;
gt_assert(elemidx >= q->front); /* valid element found */
for (i = elemidx+1; i < q->size; i++)
q->contents[i-1] = q->contents[i];
q->contents[q->size-1] = q->contents[0];
for (i = 1; i < q->back; i++)
q->contents[i-1] = q->contents[i];
q->contents[q->back-1] = NULL;
q->back--;
if (q->back == 0)
q->back = q->size;
}
}
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);
}
static int buffer_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err)
{
GtBufferStream *bs;
gt_error_check(err);
bs = buffer_stream_cast(ns);
if (bs->buffering) {
int had_err = gt_node_stream_next(bs->in_stream, gn, err);
if (!had_err && *gn)
gt_queue_add(bs->node_buffer, gt_genome_node_ref(*gn));
return had_err;
}
else {
*gn = gt_queue_size(bs->node_buffer) ? gt_queue_get(bs->node_buffer) : NULL;
return 0;
}
}
static int feature_in_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
GtError *error)
{
GtFeatureInStream *stream = feature_in_stream_cast(ns);
gt_error_check(error);
if (!stream->init)
{
feature_in_stream_init(stream);
stream->init = true;
}
if (gt_queue_size(stream->regioncache) > 0)
{
GtGenomeNode *region = gt_queue_get(stream->regioncache);
*gn = region;
return 0;
}
if (stream->featurecache == NULL || gt_array_size(stream->featurecache) == 0)
{
if (stream->featurecache != NULL)
{
gt_array_delete(stream->featurecache);
stream->featurecache = NULL;
}
if (stream->seqindex == gt_str_array_size(stream->seqids))
{
*gn = NULL;
return 0;
}
const char *seqid = gt_str_array_get(stream->seqids, stream->seqindex++);
stream->featurecache = gt_feature_index_get_features_for_seqid(stream->fi,
seqid,
error);
gt_array_sort(stream->featurecache, (GtCompare)gt_genome_node_compare);
gt_array_reverse(stream->featurecache);
}
GtGenomeNode *feat = *(GtGenomeNode **)gt_array_pop(stream->featurecache);
*gn = gt_genome_node_ref(feat);
return 0;
}
int gt_bed_parser_parse(GtBEDParser *bed_parser, GtQueue *genome_nodes,
const char *filename, GtError *err)
{
GtIO *bed_file;
int had_err;
gt_error_check(err);
gt_assert(bed_parser && genome_nodes);
bed_file = gt_io_new(filename, "r");
/* parse BED file */
had_err = parse_bed_file(bed_parser, bed_file, err);
/* process created region and feature nodes */
gt_region_node_builder_build(bed_parser->region_node_builder, genome_nodes);
gt_region_node_builder_reset(bed_parser->region_node_builder);
while (gt_queue_size(bed_parser->feature_nodes))
gt_queue_add(genome_nodes, gt_queue_get(bed_parser->feature_nodes));
gt_io_delete(bed_file);
return had_err;
}
static int gff3_numsorted_out_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
GtError *err)
{
GtGFF3NumsortedOutStream *gff3_out_stream;
int had_err = 0;
GtUword i = 0;
gt_error_check(err);
gff3_out_stream = gff3_numsorted_out_stream_cast(ns);
if (!gff3_out_stream->outqueue) {
gff3_out_stream->outqueue = gt_queue_new();
while (!(had_err =
gt_node_stream_next(gff3_out_stream->in_stream, gn, err))) {
if (!*gn) break;
gt_array_add(gff3_out_stream->buffer, *gn);
}
if (!had_err) {
gt_genome_nodes_sort_stable_with_func(gff3_out_stream->buffer,
(GtCompare) gt_genome_node_compare_numeric_seqids);
for (i = 0; !had_err && i < gt_array_size(gff3_out_stream->buffer); i++) {
GtGenomeNode *mygn = *(GtGenomeNode**)
gt_array_get(gff3_out_stream->buffer, i);
gt_queue_add(gff3_out_stream->outqueue, mygn);
}
}
}
if (gff3_out_stream->outqueue && !had_err) {
if (gt_queue_size(gff3_out_stream->outqueue) > 0) {
GtGenomeNode *mygn = (GtGenomeNode*)
gt_queue_get(gff3_out_stream->outqueue);
gt_assert(mygn);
had_err = gt_genome_node_accept(mygn, gff3_out_stream->gff3_visitor, err);
if (!had_err)
*gn = mygn;
}
}
return had_err;
}
static int gff3_in_stream_plain_next(GtNodeStream *ns, GtGenomeNode **gn,
GtError *err)
{
GtGFF3InStreamPlain *is = gff3_in_stream_plain_cast(ns);
GtStr *filenamestr;
int had_err = 0, status_code;
gt_error_check(err);
if (gt_queue_size(is->genome_node_buffer) > 1) {
/* we still have at least two nodes in the buffer -> serve from there */
*gn = gt_queue_get(is->genome_node_buffer);
return 0;
}
/* the buffer is empty or has one element */
gt_assert(gt_queue_size(is->genome_node_buffer) <= 1);
for (;;) {
/* open file if necessary */
if (!is->file_is_open) {
if (gt_str_array_size(is->files) &&
is->next_file == gt_str_array_size(is->files)) {
break;
}
if (gt_str_array_size(is->files)) {
if (strcmp(gt_str_array_get(is->files, is->next_file), "-") == 0) {
if (is->stdin_argument) {
gt_error_set(err, "multiple specification of argument file \"-\"");
had_err = -1;
break;
}
is->fpin = gt_file_xopen(NULL, "r");
is->file_is_open = true;
is->stdin_argument = true;
}
else {
is->fpin = gt_file_xopen(gt_str_array_get(is->files,
is->next_file), "r");
is->file_is_open = true;
}
is->next_file++;
}
else {
if (is->stdin_processed)
break;
is->fpin = NULL;
is->file_is_open = true;
}
is->line_number = 0;
if (!had_err && is->progress_bar) {
printf("processing file \"%s\"\n", gt_str_array_size(is->files)
? gt_str_array_get(is->files, is->next_file-1) : "stdin");
}
if (!had_err && is->fpin && is->progress_bar) {
gt_progressbar_start(&is->line_number,
gt_file_number_of_lines(gt_str_array_get(is->files,
is->next_file-1)));
}
}
gt_assert(is->file_is_open);
filenamestr = gt_str_array_size(is->files)
? gt_str_array_get_str(is->files, is->next_file-1)
: is->stdinstr;
/* read two nodes */
had_err = gt_gff3_parser_parse_genome_nodes(is->gff3_parser, &status_code,
is->genome_node_buffer,
is->used_types, filenamestr,
&is->line_number, is->fpin,
err);
if (had_err)
break;
if (status_code != EOF) {
had_err = gt_gff3_parser_parse_genome_nodes(is->gff3_parser, &status_code,
is->genome_node_buffer,
is->used_types, filenamestr,
&is->line_number, is->fpin,
err);
if (had_err)
break;
}
if (status_code == EOF) {
/* end of current file */
if (is->progress_bar) gt_progressbar_stop();
gt_file_delete(is->fpin);
is->fpin = NULL;
is->file_is_open = false;
gt_gff3_parser_reset(is->gff3_parser);
if (!gt_str_array_size(is->files)) {
is->stdin_processed = true;
break;
}
continue;
}
gt_assert(gt_queue_size(is->genome_node_buffer));
/* make sure the parsed nodes are sorted */
if (is->ensure_sorting && gt_queue_size(is->genome_node_buffer) > 1) {
GtGenomeNode *last_node = NULL;
/* a sorted stream can have at most one input file */
gt_assert(gt_str_array_size(is->files) == 0 ||
gt_str_array_size(is->files) == 1);
had_err = gt_queue_iterate(is->genome_node_buffer, buffer_is_sorted,
&last_node, err);
}
if (!had_err) {
*gn = gt_queue_get(is->genome_node_buffer);
}
return had_err;
}
gt_assert(!gt_queue_size(is->genome_node_buffer));
*gn = NULL;
return had_err;
}
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);
}
void* gt_queue_head(GtQueue *q)
{
gt_assert(q && gt_queue_size(q));
return q->contents[q->front];
}
static int snp_annotator_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
GtError *err)
{
GtSNPAnnotatorStream *sas;
int had_err = 0;
bool complete_cluster = false;
GtGenomeNode *mygn = NULL;
GtFeatureNode *fn = NULL;
const char *snv_type = gt_symbol(gt_ft_SNV),
*snp_type = gt_symbol(gt_ft_SNP),
*gene_type = gt_symbol(gt_ft_gene);
gt_error_check(err);
sas = gt_snp_annotator_stream_cast(ns);
/* if there are still SNPs left in the buffer, output them */
if (gt_queue_size(sas->outqueue) > 0) {
*gn = (GtGenomeNode*) gt_queue_get(sas->outqueue);
return had_err;
} else complete_cluster = false;
while (!had_err && !complete_cluster) {
had_err = gt_node_stream_next(sas->merge_stream, &mygn, err);
/* stop if stream is at the end */
if (had_err || !mygn) break;
/* process all feature nodes */
if ((fn = gt_feature_node_try_cast(mygn))) {
GtGenomeNode *addgn;
const char *type = gt_feature_node_get_type(fn);
GtRange new_rng = gt_genome_node_get_range(mygn);
if (type == snv_type || type == snp_type) {
/* -----> this is a SNP <----- */
if (gt_range_overlap(&new_rng, &sas->cur_gene_range)) {
/* it falls into the currently observed range */
gt_queue_add(sas->snps, gt_genome_node_ref((GtGenomeNode*) fn));
} else {
/* SNP outside a gene, this cluster is done
add to out queue and start serving */
gt_assert(gt_queue_size(sas->outqueue) == 0);
had_err = snp_annotator_stream_process_current_gene(sas, err);
gt_queue_add(sas->outqueue, mygn);
if (gt_queue_size(sas->outqueue) > 0) {
*gn = (GtGenomeNode*) gt_queue_get(sas->outqueue);
complete_cluster = true;
}
}
} else if (type == gene_type) {
/* -----> this is a gene <----- */
if (gt_array_size(sas->cur_gene_set) == 0UL) {
/* new overlapping gene cluster */
addgn = gt_genome_node_ref(mygn);
gt_array_add(sas->cur_gene_set, addgn);
sas->cur_gene_range = gt_genome_node_get_range(mygn);
} else {
if (gt_range_overlap(&new_rng, &sas->cur_gene_range)) {
/* gene overlaps with current one, add to cluster */
addgn = gt_genome_node_ref(mygn);
gt_array_add(sas->cur_gene_set, addgn);
sas->cur_gene_range = gt_range_join(&sas->cur_gene_range, &new_rng);
} else {
/* finish current cluster and start a new one */
had_err = snp_annotator_stream_process_current_gene(sas, err);
if (!had_err) {
addgn = gt_genome_node_ref(mygn);
gt_array_add(sas->cur_gene_set, addgn);
sas->cur_gene_range = gt_genome_node_get_range(mygn);
}
if (gt_queue_size(sas->outqueue) > 0) {
*gn = (GtGenomeNode*) gt_queue_get(sas->outqueue);
complete_cluster = true;
}
}
}
/* from now on, genes are kept in gene cluster arrays only */
gt_genome_node_delete(mygn);
}
} else {
/* meta node */
had_err = snp_annotator_stream_process_current_gene(sas, err);
if (!had_err) {
gt_queue_add(sas->outqueue, mygn);
}
if (gt_queue_size(sas->outqueue) > 0) {
*gn = (GtGenomeNode*) gt_queue_get(sas->outqueue);
complete_cluster = true;
}
}
}
return had_err;
}
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;
}
// 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;
}
unsigned long gt_select_visitor_node_buffer_size(GtNodeVisitor *nv)
{
GtSelectVisitor *select_visitor = select_visitor_cast(nv);
return gt_queue_size(select_visitor->node_buffer);
}
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;
}
GtUword gt_add_ids_visitor_node_buffer_size(GtNodeVisitor *nv)
{
GtAddIDsVisitor *add_ids_visitor = add_ids_visitor_cast(nv);
return gt_queue_size(add_ids_visitor->node_buffer);
}
