Exemple #1
0
/******************************************************************************
 * 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;
}
Exemple #2
0
/******************************************************************************
 * 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;
}
Exemple #3
0
/******************************************************************************
 * 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;
}