static int gt_compreads_compress_runner(GT_UNUSED int argc,
GT_UNUSED const char **argv,
GT_UNUSED int parsed_args,
void *tool_arguments, GtError *err)
{
GtCsrHcrEncodeArguments *arguments = tool_arguments;
int had_err = 0;
GtAlphabet *alpha = NULL;
GtHcrEncoder *hcre = NULL;
GtTimer *timer = NULL;
gt_error_check(err);
gt_assert(arguments);
if (gt_showtime_enabled()) {
timer = gt_timer_new_with_progress_description("start");
gt_timer_start(timer);
gt_assert(timer);
}
if (gt_str_length(arguments->smap) > 0) {
alpha = gt_alphabet_new_from_file_no_suffix(gt_str_get(arguments->smap),
err);
if (!alpha)
had_err = 1;
}
else {
alpha = gt_alphabet_new_dna();
if (!alpha)
had_err = 1;
}
if (!had_err) {
if (timer != NULL)
gt_timer_show_progress(timer, "encoding", stdout);
hcre = gt_hcr_encoder_new(arguments->files, alpha, arguments->descs,
arguments->qrng, timer, err);
if (!hcre)
had_err = 1;
else {
if (arguments->pagewise)
gt_hcr_encoder_set_sampling_page(hcre);
else if (arguments->regular)
gt_hcr_encoder_set_sampling_regular(hcre);
gt_hcr_encoder_set_sampling_rate(hcre, arguments->srate);
if (gt_hcr_encoder_encode(hcre, gt_str_get(arguments->name),
timer, err) != 0)
had_err = 1;
}
gt_hcr_encoder_delete(hcre);
}
gt_alphabet_delete(alpha);
if (timer != NULL) {
gt_timer_show_progress_final(timer, stdout);
gt_timer_delete(timer);
}
return had_err;
}
GtAlphabet *gt_alphabet_new_from_file(const char *filename,
GtError *err)
{
GtStr *tmpfilename;
GtAlphabet *a;
gt_assert(filename);
tmpfilename = gt_str_new_cstr(filename);
gt_str_append_cstr(tmpfilename, GT_ALPHABETFILESUFFIX);
a = gt_alphabet_new_from_file_no_suffix(gt_str_get(tmpfilename), err);
gt_str_delete(tmpfilename);
return a;
}
static int gt_compreads_decompress_runner(GT_UNUSED int argc,
GT_UNUSED const char **argv,
GT_UNUSED int parsed_args,
void *tool_arguments, GtError *err)
{
GtCsrHcrDecodeArguments *arguments = tool_arguments;
int had_err = 0;
GtAlphabet *alpha = NULL;
GtHcrDecoder *hcrd = NULL;
GtTimer *timer = NULL;
unsigned long start,
end;
gt_error_check(err);
gt_assert(arguments);
if (gt_showtime_enabled()) {
timer = gt_timer_new_with_progress_description("start");
gt_timer_start(timer);
gt_assert(timer);
}
if (gt_str_length(arguments->smap) > 0) {
alpha = gt_alphabet_new_from_file_no_suffix(gt_str_get(arguments->smap),
err);
if (!alpha)
had_err = -1;
}
else {
alpha = gt_alphabet_new_dna();
if (!alpha)
had_err = -1;
}
if (!had_err) {
if (timer != NULL)
gt_timer_show_progress(timer, "decoding", stdout);
if (gt_str_length(arguments->name) == 0) {
char *basenameptr;
basenameptr = gt_basename(gt_str_get(arguments->file));
gt_str_set(arguments->name, basenameptr);
gt_free(basenameptr);
}
hcrd = gt_hcr_decoder_new(gt_str_get(arguments->file), alpha,
arguments->descs, timer, err);
if (hcrd == NULL)
had_err = -1;
else {
if (arguments->bench != 0) {
had_err = gt_compreads_decompress_benchmark(hcrd,
arguments->bench,
timer, err);
}
else {
if (arguments->rng.start != GT_UNDEF_ULONG
&& arguments->rng.end != GT_UNDEF_ULONG) {
if (arguments->rng.start >= gt_hcr_decoder_num_of_reads(hcrd)
|| arguments->rng.end >= gt_hcr_decoder_num_of_reads(hcrd)) {
gt_error_set(err, "range %lu-%lu includes a read number exceeding "
"the total number of reads (%lu)",
arguments->rng.start,
arguments->rng.end,
gt_hcr_decoder_num_of_reads(hcrd));
had_err = -1;
}
start = arguments->rng.start;
end = arguments->rng.end;
}
else {
start = 0;
end = gt_hcr_decoder_num_of_reads(hcrd) - 1;
}
if (!had_err) {
gt_log_log("filebasename: %s", gt_str_get(arguments->name));
if (gt_hcr_decoder_decode_range(hcrd, gt_str_get(arguments->name),
start, end, timer, err)
!= 0)
had_err = -1;
}
}
}
gt_hcr_decoder_delete(hcrd);
}
gt_alphabet_delete(alpha);
if (timer != NULL) {
gt_timer_show_progress_final(timer, stdout);
gt_timer_delete(timer);
}
if (had_err)
gt_assert(gt_error_is_set(err));
return had_err;
}
