static int gt_splitfasta_runner(GT_UNUSED int argc, const char **argv,
int parsed_args, void *tool_arguments,
GtError *err)
{
SplitfastaArguments *arguments = tool_arguments;
unsigned int num_files;
int had_err;
off_t file_size;
const char* filename;
gt_error_check(err);
gt_assert(arguments);
num_files = arguments->num_files;
filename = argv[parsed_args];
if (gt_str_length(arguments->splitdesc)) {
had_err = split_description(filename, arguments->splitdesc,
arguments->width, arguments->force, err);
}
else {
unsigned long max_filesize;
if (num_files) {
/* set the maxfile size based on requested number of files */
file_size = gt_file_estimate_size(filename);
max_filesize= file_size / num_files ;
}
else
max_filesize= arguments->max_filesize_in_MB << 20;
had_err = split_fasta_file(filename, max_filesize, arguments->force, err);
}
return had_err;
}
off_t gt_files_estimate_total_size(const GtStrArray *filenames)
{
GtUword filenum;
off_t totalsize = 0;
for (filenum = 0; filenum < gt_str_array_size(filenames); filenum++)
totalsize += gt_file_estimate_size(gt_str_array_get(filenames, filenum));
return totalsize;
}
int gt_hcr_encoder_encode(GtHcrEncoder *hcr_enc, const char *name,
GtTimer *timer, GtError *err)
{
int had_err = 0;
GtStr *name1;
gt_error_check(err);
if (timer != NULL)
gt_timer_show_progress(timer, "write encoding", stdout);
if (hcr_enc->encdesc_encoder != NULL) {
GtCstrIterator *cstr_iterator = gt_fasta_header_iterator_new(hcr_enc->files,
err);
had_err = gt_encdesc_encoder_encode(hcr_enc->encdesc_encoder,
cstr_iterator, name, err);
gt_cstr_iterator_delete(cstr_iterator);
}
if (!had_err)
had_err = hcr_write_seq_qual_data(name, hcr_enc, timer, err);
if (!had_err && gt_log_enabled()) {
name1 = gt_str_new_cstr(name);
gt_str_append_cstr(name1, HCRFILESUFFIX);
gt_log_log("sequences with qualities encoding overview:");
gt_log_log("**>");
if (hcr_enc->page_sampling)
gt_log_log("applied sampling technique: sampling every " GT_WU
"th page",
hcr_enc->sampling_rate);
else if (hcr_enc->regular_sampling)
gt_log_log("applied sampling technique: sampling every " GT_WU
"th read",
hcr_enc->sampling_rate);
else
gt_log_log("applied sampling technique: none");
gt_log_log("total number of encoded nucleotide sequences with qualities: "
GT_WU, hcr_enc->num_of_reads);
gt_log_log("total number of encoded nucleotides: " GT_LLU,
hcr_enc->seq_encoder->total_num_of_symbols);
gt_log_log("bits per nucleotide encoding: %f",
(gt_file_estimate_size(gt_str_get(name1)) * 8.0) /
hcr_enc->seq_encoder->total_num_of_symbols);
gt_log_log("<**");
gt_str_delete(name1);
}
return had_err;
}
