void af_router_process(af_router * router, const double time) {
if (router->sinks_count == 0) {
fprintf(stderr, "There is no sinks!");
} else {
router->time = 0;
while (router->time < time) {
process_blocks(router->sinks, router->sinks_count);
reset_blocks(router->blocks, router->blocks_count);
router->time += router->step_size;
}
}
}
void process_blocks(af_block ** blocks, const size_t count) {
af_block *block;
size_t i = 0;
while (i < count) {
block = blocks[i];
if (af_block_is_clear(block)) {
process_blocks(block->input->sources, block->input->size);
af_block_process(block);
}
i++;
}
}
int main(int argc, char* argv[])
{
char mybuf[4096], *str;
while (fread(mybuf, sizeof(mybuf), 1, stdin) >= 0) {
str = strtok(mybuf, DELIM);
while (str) {
add_block(str);
str = strtok(NULL, DELIM);
}
if (feof(stdin))
break;
}
process_blocks();
return 0;
}
static int bed_rest(GtBEDParser *bed_parser, GtIO *bed_file, GtError *err)
{
GtUword block_count = 0;
GtGenomeNode *gn = NULL;
GtRange range;
GtStr *seqid;
int had_err;
gt_error_check(err);
/* column 1.: chrom */
seqid = get_seqid(bed_parser);
had_err = skip_blanks(bed_file, err);
/* column 2.: chromStart */
if (!had_err) {
word(bed_parser->word, bed_file);
had_err = skip_blanks(bed_file, err);
}
/* column 3.: chromEnd */
if (!had_err) {
word(bed_parser->another_word, bed_file);
had_err = parse_bed_range(&range, bed_parser->word,
bed_parser->another_word, bed_parser->offset,
bed_file, false, err);
}
if (!had_err) {
/* add region */
gt_region_node_builder_add_region(bed_parser->region_node_builder,
gt_str_get(seqid), range);
/* create feature */
gn = gt_feature_node_new(seqid,
bed_parser->feature_type
? bed_parser->feature_type
: BED_FEATURE_TYPE,
range.start, range.end, GT_STRAND_BOTH);
gt_queue_add(bed_parser->feature_nodes, gn);
if (bed_separator(bed_file))
had_err = skip_blanks(bed_file, err);
}
/* optional column 4.: name */
if (!had_err) {
word(bed_parser->word, bed_file);
if (gt_str_length(bed_parser->word)) {
gt_feature_node_add_attribute((GtFeatureNode*) gn, GT_GFF_NAME,
gt_str_get(bed_parser->word));
}
if (bed_separator(bed_file))
had_err = skip_blanks(bed_file, err);
}
/* optional column 5.: score */
if (!had_err) {
word(bed_parser->word, bed_file);
if (gt_str_length(bed_parser->word)) {
bool score_is_defined;
float score_value;
had_err = gt_parse_score(&score_is_defined, &score_value,
gt_str_get(bed_parser->word),
gt_io_get_line_number(bed_file),
gt_io_get_filename(bed_file), err);
if (!had_err && score_is_defined)
gt_feature_node_set_score((GtFeatureNode*) gn, score_value);
}
}
if (!had_err && bed_separator(bed_file))
had_err = skip_blanks(bed_file, err);
/* optional column 6.: strand */
if (!had_err) {
word(bed_parser->word, bed_file);
if (gt_str_length(bed_parser->word)) {
GtStrand strand;
had_err = gt_parse_strand(&strand, gt_str_get(bed_parser->word),
gt_io_get_line_number(bed_file),
gt_io_get_filename(bed_file), err);
if (!had_err)
gt_feature_node_set_strand((GtFeatureNode*) gn, strand);
}
}
if (!had_err && bed_separator(bed_file))
had_err = skip_blanks(bed_file, err);
/* optional column 7.: thickStart */
if (!had_err) {
word(bed_parser->word, bed_file);
if (bed_separator(bed_file))
had_err = skip_blanks(bed_file, err);
}
/* optional column 8.: thickEnd */
if (!had_err) {
word(bed_parser->another_word, bed_file);
if (gt_str_length(bed_parser->another_word)) {
gt_assert(gt_str_length(bed_parser->word));
/* got a thickStart and a thickEnd -> construct corresponding feature */
had_err = parse_bed_range(&range, bed_parser->word,
bed_parser->another_word, bed_parser->offset,
bed_file, true, err);
if (!had_err && range.start <= range.end)
construct_thick_feature(bed_parser, (GtFeatureNode*) gn, range);
}
}
if (!had_err && bed_separator(bed_file))
had_err = skip_blanks(bed_file, err);
/* optional column 9.: itemRgb */
if (!had_err) {
word(bed_parser->word, bed_file);
/* we do not use the RGB values */
if (bed_separator(bed_file))
had_err = skip_blanks(bed_file, err);
}
/* optional column 10.: blockCount */
if (!had_err) {
word(bed_parser->word, bed_file);
if (gt_str_length(bed_parser->word)) {
if (gt_parse_uword(&block_count, gt_str_get(bed_parser->word))) {
gt_error_set(err,
"file \"%s\": line "GT_WU": could not parse blockCount",
gt_io_get_filename(bed_file),
gt_io_get_line_number(bed_file));
had_err = -1;
}
else {
/* reset to parse/process blockSizes and blockStarts properly */
gt_str_reset(bed_parser->word);
gt_str_reset(bed_parser->another_word);
}
}
}
if (!had_err && bed_separator(bed_file))
had_err = skip_blanks(bed_file, err);
/* optional column 11.: blockSizes */
if (!had_err) {
word(bed_parser->word, bed_file);
if (bed_separator(bed_file))
had_err = skip_blanks(bed_file, err);
}
/* optional column 12.: blockStarts */
if (!had_err) {
word(bed_parser->another_word, bed_file);
if (bed_separator(bed_file))
had_err = skip_blanks(bed_file, err);
}
/* process blocks if necessary */
if (!had_err && block_count) {
had_err = process_blocks(bed_parser, (GtFeatureNode*) gn, block_count,
bed_parser->word, bed_parser->another_word,
bed_file, err);
}
/* the end of the line should now be reached */
if (!had_err)
had_err = gt_io_expect(bed_file, GT_END_OF_LINE, err);
return had_err;
}
