Ejemplo n.º 1
0
int gt_hcr_decoder_decode_range(GtHcrDecoder *hcr_dec, const char *name,
                                GtUword start, GtUword end,
                                GtTimer *timer, GtError *err)
{
    char qual[BUFSIZ] = {0},
                        seq[BUFSIZ] = {0};
    GtStr *desc = gt_str_new();
    int had_err = 0;
    GtUword cur_width,
            cur_read;
    size_t i;
    FILE *output;
    GT_UNUSED GtHcrSeqDecoder *seq_dec;

    gt_error_check(err);
    gt_assert(hcr_dec && name);
    seq_dec = hcr_dec->seq_dec;
    gt_assert(start <= end);
    gt_assert(start < seq_dec->num_of_reads && end < seq_dec->num_of_reads);
    if (timer != NULL)
        gt_timer_show_progress(timer, "decode hcr", stdout);
    output = gt_fa_fopen_with_suffix(name, HCRFILEDECODEDSUFFIX, "w", err);
    if (output == NULL)
        had_err = -1;

    for (cur_read = start; had_err == 0 && cur_read <= end; cur_read++) {
        if (gt_hcr_decoder_decode(hcr_dec, cur_read, seq, qual, desc, err) != 0)
            had_err = -1;
        else {
            gt_xfputc(HCR_DESCSEPSEQ, output);
            if (hcr_dec->encdesc != NULL)
                gt_xfputs(gt_str_get(desc), output);
            else
                fprintf(output, ""GT_WU"", cur_read);
            gt_xfputc('\n', output);
            for (i = 0, cur_width = 0; i < strlen(seq); i++, cur_width++) {
                if (cur_width == HCR_LINEWIDTH) {
                    cur_width = 0;
                    gt_xfputc('\n', output);
                }
                gt_xfputc(seq[i], output);
            }
            gt_xfputc('\n', output);
            gt_xfputc(HCR_DESCSEPQUAL, output);
            gt_xfputc('\n', output);
            for (i = 0, cur_width = 0; i < strlen(qual); i++, cur_width++) {
                if (cur_width == HCR_LINEWIDTH) {
                    cur_width = 0;
                    gt_xfputc('\n', output);
                }
                gt_xfputc(qual[i], output);
            }
            gt_xfputc('\n', output);
        }
    }
    gt_fa_xfclose(output);
    gt_str_delete(desc);
    return had_err;
}
static int gt_compreads_decompress_benchmark(GtHcrDecoder *hcrd,
                                             unsigned long amount,
                                             GtTimer *timer,
                                             GtError *err) {
  char qual[BUFSIZ] = {0},
       seq[BUFSIZ] = {0};
  int had_err = 0;
  unsigned long rand,
                max_rand = gt_hcr_decoder_num_of_reads(hcrd) - 1,
                count;

  GtStr *timer_comment = gt_str_new_cstr("extracting ");
  GtStr *desc = gt_str_new();

  gt_str_append_ulong(timer_comment, amount);
  gt_str_append_cstr(timer_comment, " reads of ");
  gt_str_append_ulong(timer_comment, max_rand + 1);
  gt_str_append_cstr(timer_comment, "!");

  if (timer == NULL) {
    timer = gt_timer_new_with_progress_description("extract random reads");
    gt_timer_start(timer);
  }
  else {
    gt_timer_show_progress(timer, "extract random reads", stdout);
  }

  gt_log_log("%s",gt_str_get(timer_comment));
  for (count = 0; count < amount; count++) {
    if (!had_err) {
      rand = gt_rand_max(max_rand);
      gt_log_log("get read: %lu", rand);
      had_err = gt_hcr_decoder_decode(hcrd, rand, seq, qual, desc, err);
      gt_log_log("%s",gt_str_get(desc));
      gt_log_log("%s",seq);
      gt_log_log("%s",qual);
    }
  }
  gt_str_delete(timer_comment);
  gt_str_delete(desc);
  if (!gt_showtime_enabled())
    gt_timer_delete(timer);
  return had_err;
}