static int encseq_encoder_lua_set_input_dna(lua_State *L)
{
GtEncseqEncoder **encoder;
encoder = check_encseq_encoder(L, 1);
gt_assert(*encoder);
gt_encseq_encoder_set_input_dna(*encoder);
return 0;
}
static int gt_genomediff_runner(int argc, const char **argv,
int parsed_args, void *tool_arguments,
GtError *err)
{
bool mirrored = false;
int had_err = 0,
i;
GtEncseq *encseq = NULL;
GtGenomediffArguments *arguments = tool_arguments;
GtLogger *logger;
GtShuUnitFileInfo *unit_info = NULL;
GtTimer *timer = NULL;
gt_error_check(err);
gt_assert(arguments);
logger = gt_logger_new(arguments->verbose,
GT_LOGGER_DEFLT_PREFIX,
stdout);
gt_assert(logger);
for (i = parsed_args; i < argc; i++) {
gt_str_array_add_cstr(arguments->filenames, argv[i]);
}
if (gt_showtime_enabled()) {
timer = gt_timer_new_with_progress_description("start");
gt_timer_start(timer);
gt_assert(timer);
}
if (arguments->with_units) {
gt_logger_log(logger, "unitfile option set, filename is %s\n",
gt_str_get(arguments->unitfile));
}
if (timer != NULL)
gt_timer_show_progress(timer, "start shu search", stdout);
if (gt_str_array_size(arguments->filenames) > 1UL) {
GtEncseqEncoder *ee = gt_encseq_encoder_new();
gt_encseq_encoder_set_timer(ee, timer);
gt_encseq_encoder_set_logger(ee, logger);
/* kr only makes sense for dna, so we can check this already with ee */
gt_encseq_encoder_set_input_dna(ee);
had_err = gt_encseq_encoder_encode(ee, arguments->filenames,
gt_str_get(arguments->indexname), err);
gt_encseq_encoder_delete(ee);
}
else {
gt_str_append_str(arguments->indexname,
gt_str_array_get_str(arguments->filenames, 0));
if (arguments->with_esa || arguments->with_pck) {
GtStr *current_line = gt_str_new();
FILE *prj_fp;
const char *buffer;
char **elements = NULL;
prj_fp = gt_fa_fopen_with_suffix(gt_str_get(arguments->indexname),
GT_PROJECTFILESUFFIX,"rb",err);
if (prj_fp == NULL)
had_err = -1;
while (!had_err && gt_str_read_next_line(current_line, prj_fp) != EOF) {
buffer = gt_str_get(current_line);
if (elements != NULL) {
gt_free(elements[0]);
gt_free(elements[1]);
}
gt_free(elements);
elements = gt_cstr_split(buffer, '=');
gt_log_log("%s", elements[0]);
if (strcmp("mirrored", elements[0]) == 0) {
gt_log_log("%s", elements[1]);
if (strcmp("1", elements[1]) == 0) {
mirrored = true;
gt_log_log("sequences are treated as mirrored");
}
}
gt_str_reset(current_line);
}
gt_str_delete(current_line);
if (elements != NULL) {
gt_free(elements[0]);
gt_free(elements[1]);
}
gt_free(elements);
gt_fa_xfclose(prj_fp);
}
}
if (!had_err) {
GtEncseqLoader *el = gt_encseq_loader_new_from_options(arguments->loadopts,
err);
if (mirrored)
gt_encseq_loader_mirror(el);
encseq =
gt_encseq_loader_load(el, gt_str_get(arguments->indexname), err);
gt_encseq_loader_delete(el);
}
if (encseq == NULL)
had_err = -1;
if (!had_err) {
unit_info = gt_shu_unit_info_new(encseq);
if (arguments->with_units)
had_err = gt_shu_unit_file_info_read(arguments->unitfile, unit_info,
logger, err);
}
if (!had_err) {
uint64_t **shusums = NULL;
if (arguments->with_esa || arguments->with_pck) {
shusums = gt_genomediff_shulen_sum(arguments, unit_info,
logger, timer, err);
if (shusums == NULL)
had_err = -1;
}
else {
const bool doesa = true;
GenomediffInfo gd_info;
Suffixeratoroptions sopts;
sopts.beverbose = arguments->verbose;
sopts.indexname = arguments->indexname;
sopts.db = NULL;
sopts.encopts = NULL;
sopts.genomediff = true;
sopts.inputindex = arguments->indexname;
sopts.loadopts = arguments->loadopts;
sopts.showprogress = false;
sopts.idxopts = arguments->idxopts;
gt_assert(unit_info != NULL);
gt_array2dim_calloc(shusums, unit_info->num_of_genomes,
unit_info->num_of_genomes);
gd_info.shulensums = shusums;
gd_info.unit_info = unit_info;
had_err = gt_runsuffixerator(doesa, &sopts, &gd_info, logger, err);
}
if (!had_err && shusums != NULL) {
had_err = gt_genomediff_kr_calc(shusums, arguments, unit_info,
arguments->with_pck, logger, timer, err);
gt_array2dim_delete(shusums);
}
}
if (timer != NULL) {
gt_timer_show_progress_final(timer, stdout);
gt_timer_delete(timer);
}
gt_logger_delete(logger);
gt_encseq_delete(encseq);
gt_shu_unit_info_delete(unit_info);
return had_err;
}
