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;
}