static int skip_blanks(GtIO *bed_file, GtError *err)
{
gt_error_check(err);
if (!bed_separator(bed_file)) {
gt_error_set(err, "file \"%s\": line %lu: expected blank or tabulator, got "
"'%c'", gt_io_get_filename(bed_file),
gt_io_get_line_number(bed_file), gt_io_peek(bed_file));
return -1;
}
while (bed_separator(bed_file))
gt_io_next(bed_file);
return 0;
}
static int track_rest(GtBEDParser *bed_parser, GtIO *bed_file, GtError *err)
{
char cc;
int had_err = 0;
gt_error_check(err);
bed_parser->offset = 0; /* reset offset for new track line */
if (bed_separator(bed_file)) /* skip to first attribute=value pair */
had_err = skip_blanks(bed_file, err);
while (!had_err &&
(cc = gt_io_peek(bed_file)) != GT_END_OF_LINE &&
cc != GT_CARRIAGE_RETURN) {
/* parse attribute */
word(bed_parser->word, bed_file);
had_err = gt_io_expect(bed_file, PAIR_SEPARATOR, err);
/* parse value */
if (!had_err) {
if (gt_io_peek(bed_file) == QUOTE_CHAR)
had_err = quoted_word(bed_parser->another_word, bed_file, err);
else
word(bed_parser->another_word, bed_file);
}
/* process offset if necessary */
if (!had_err && !strcmp(gt_str_get(bed_parser->word), OFFSET_KEYWORD)) {
if (gt_parse_word(&bed_parser->offset,
gt_str_get(bed_parser->another_word))) {
gt_error_set(err,
"file \"%s\": line "GT_WU": could not parse offset value "
"'%s'", gt_io_get_filename(bed_file),
gt_io_get_line_number(bed_file),
gt_str_get(bed_parser->another_word));
had_err = -1;
}
}
/* skip blanks up to next attribute or end-of-line */
if (!had_err && bed_separator(bed_file))
had_err = skip_blanks(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;
}
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;
}