/******************************************************************************
* Read from the current position in the file to the first format line
* containing a new sequence. Update the value of the current sequence.
*
* Returns TRUE if it was able to advance to the next sequence, FALSE if
* EOF reached before the next sequence was found. Dies if other errors
* encountered.
*****************************************************************************/
BOOLEAN_T go_to_next_sequence_in_wiggle(
WIGGLE_READER_T *reader
) {
char *line = NULL;
char *prev_chrom = NULL;
BOOLEAN_T result = FALSE;
while((result = read_wiggle_line(reader, &line)) == TRUE) {
if (is_format_line(line) == TRUE) {
// Parse format lines and move to next line
if (reader->chrom) {
prev_chrom = strdup(reader->chrom);
}
parse_wiggle_format_line(reader, line);
int chrom_match = 1;
if (prev_chrom) {
chrom_match = strcmp(prev_chrom, reader->chrom);
myfree(prev_chrom);
}
if (chrom_match != 0) {
// We've reached a new sequence
result = TRUE;
break;
}
}
myfree(line);
}
myfree(line);
return result;
}
/******************************************************************************
* Reads the next data block from the wiggle file
*
* Returns TRUE if it was able to read the block, FALSE if it reaches
* a new sequence sequence or EOF. Dies if other errors encountered.
*****************************************************************************/
BOOLEAN_T get_next_data_block_from_wiggle(
WIGGLE_READER_T *reader,
char **chrom,
size_t *start,
size_t *step,
size_t *span,
double *value
) {
char *line = NULL;
// Mark current position
long save_pos = ftell(reader->wiggle_file);
BOOLEAN_T result = read_wiggle_line(reader, &line);
if (result == TRUE) {
if (is_track_line(line) == TRUE) {
// Skip track lines
myfree(line);
result = FALSE;
}
else if (is_format_line(line) == TRUE) {
// We've reached a new sequence, back up one line
// FIXME CEG add error handling
fseek(reader->wiggle_file, save_pos, SEEK_SET);
myfree(line);
result = FALSE;
}
else {
parse_wiggle_value_line(reader, line, start, value);
*chrom = strdup(reader->chrom);
*step = reader->step;
*span = reader->span;
myfree(line);
result = TRUE;
}
}
return result;
}
/******************************************************************************
* Reads the next data line from the wiggle file
*
* Returns TRUE if it was able to read the line, FALSE if it reaches
* a new sequence sequence or EOF. Dies if other errors encountered.
*****************************************************************************/
BOOLEAN_T get_next_data_line_from_wiggle(
WIGGLE_READER_T *reader,
char **chrom,
size_t *start,
size_t *step,
size_t *span,
double *value
) {
char *line = NULL;
BOOLEAN_T done_looking = FALSE;
BOOLEAN_T found_data = FALSE;
// Save current reader state
INPUT_FMT_T prev_format = reader->format;
long prev_prev_line_position = reader->prev_line_position;
size_t prev_start = reader->start;
size_t prev_step = reader->step;
size_t prev_span = reader->span;
char *prev_chrom = NULL;
if (reader->chrom) {
prev_chrom = strdup(reader->chrom);
}
long save_pos = ftell(reader->wiggle_file);
// Keep trying until we've read a data line or reached a new sequence
while (done_looking == FALSE) {
BOOLEAN_T read_line = read_wiggle_line(reader, &line);
if (read_line != TRUE) {
// We've reached EOF
found_data = FALSE;
done_looking = TRUE;
break;
}
// A wiggle file line is either a track line,
// a format line, or a data line.
if (is_track_line(line) == TRUE) {
// Skip track lines
continue;
}
else if (is_format_line(line) == TRUE) {
// A format line may indicate a new sequence
// or simply be setting the start, span or step.
// If it's a new sequence we should just back up
// and return FALSE since no more data blocs are
// available for this sequence.
parse_wiggle_format_line(reader, line);
// Check to see if we've reached a new sequence
int chrom_match = -1;
if (prev_chrom) {
chrom_match = strcmp(prev_chrom, reader->chrom);
}
if (chrom_match != 0) {
// We've reached a new sequence. Back up one and return FALSE
errno = 0;
int e = fseek(reader->wiggle_file, save_pos, SEEK_SET);
if (e) {
die(
"Error when trying to get data line in wiggle file: %s.\nError message: %s.\n",
reader->filename,
strerror(errno)
);
}
// Restore reader values
reader->format = prev_format;
reader->prev_line_position = prev_prev_line_position;
reader->start = prev_start;
reader->step = prev_step;
reader->span = prev_span;
myfree(reader->chrom);
reader->chrom = strdup(prev_chrom);
found_data = FALSE;
done_looking = TRUE;
}
}
else {
// We've reached a data line
parse_wiggle_value_line(reader, line, start, value);
if (*chrom) {
myfree(*chrom);
}
*chrom = strdup(reader->chrom);
*step = reader->step;
*span = reader->span;
reader->prev_line_position = save_pos;
found_data = TRUE;
done_looking = TRUE;
}
myfree(line);
}
myfree(prev_chrom);
return found_data;
}