GtHcrDecoder *gt_hcr_decoder_new(const char *name, GtAlphabet *alpha, bool descs, GtTimer *timer, GtError *err) { GtHcrDecoder *hcr_dec; int had_err = 0; gt_error_check(err); if (timer != NULL) gt_timer_show_progress(timer, "initialize hcr decoder", stdout); hcr_dec = gt_malloc(sizeof (GtHcrDecoder)); if (descs) { hcr_dec->encdesc = gt_encdesc_load(name, err); if (gt_error_is_set(err)) { had_err = -1; } } else hcr_dec->encdesc = NULL; if (!had_err) { hcr_dec->seq_dec = hcr_seq_decoder_new(alpha, name, err); if (!gt_error_is_set(err)) return hcr_dec; } gt_hcr_decoder_delete(hcr_dec); return NULL; }
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; }