static int gt_kmer_database_runner(GT_UNUSED int argc, const char **argv,
int parsed_args, void *tool_arguments,
GtError *err)
{
GtKmerDatabaseArguments *arguments = tool_arguments;
int had_err = 0;
GtEncseq *es;
GtUword es_length,
nu_kmer_codes = 0;
GtKmerDatabase *compare_db = NULL,
*db = NULL;
GtLogger *logger;
FILE *fp = NULL;
GtHashmap *kmer_hash = NULL;
GtTimer *timer = NULL;
gt_error_check(err);
gt_assert(arguments);
if (arguments->use_hash)
kmer_hash = gt_hashmap_new(GT_HASH_DIRECT, NULL,
(GtFree) gt_kmer_database_delete_hash_value);
if (arguments->bench)
timer = gt_timer_new_with_progress_description("loading encoded sequence");
logger = gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX, stderr);
if (arguments->verbose && gt_str_length(arguments->print_filename) > 0UL) {
fp = gt_fa_fopen(gt_str_get(arguments->print_filename), "w", err);
gt_logger_set_target(logger, fp);
}
if (!had_err) {
GtEncseqLoader *es_l;
if (arguments->bench)
gt_timer_start(timer);
es_l = gt_encseq_loader_new();
es = gt_encseq_loader_load(es_l, argv[parsed_args], err);
if (arguments->bench)
gt_timer_show_progress(timer, "saving kmers (+iterating over file)",
stdout);
if (es == NULL) {
had_err = -1;
}
gt_encseq_loader_delete(es_l);
}
if (!had_err) {
es_length = gt_encseq_total_length(es);
if (es_length < (GtUword) arguments->kmersize) {
gt_error_set(err, "Input is too short for used kmersize. File length: "
GT_WU " kmersize: %u", es_length, arguments->kmersize);
had_err = -1;
}
}
if (!had_err) {
GtAlphabet *alphabet;
alphabet = gt_encseq_alphabet(es);
if (arguments->bench)
nu_kmer_codes = gt_power_for_small_exponents(
gt_alphabet_num_of_chars(alphabet),
arguments->kmersize);
if (!arguments->merge_only && !arguments->use_hash && !arguments->bench) {
compare_db = gt_kmer_database_new(gt_alphabet_num_of_chars(alphabet),
arguments->kmersize, arguments->sb_size, es);
}
if (!arguments->use_hash) {
db = gt_kmer_database_new(gt_alphabet_num_of_chars(alphabet),
arguments->kmersize,
arguments->sb_size, es);
if (arguments->cutoff) {
if (arguments->mean_cutoff)
gt_kmer_database_use_mean_cutoff(db, (GtUword) 2,
arguments->cutoff_value);
else
gt_kmer_database_set_cutoff(db, arguments->cutoff_value);
if (!arguments->prune)
gt_kmer_database_set_prune(db);
}
}
}
if (!had_err) {
GtUword startpos = 0,
endpos;
GtKmercodeiterator *iter;
const GtKmercode *kmercode = NULL;
iter = gt_kmercodeiterator_encseq_new(es, GT_READMODE_FORWARD,
arguments->kmersize, 0);
while (!had_err && startpos < es_length - (arguments->kmersize - 1)) {
GtUword startpos_add_kmer = startpos;
if (arguments->merge_only) {
endpos = startpos + (arguments->kmersize - 1) +
(gt_rand_max((arguments->sb_size - 1) * 2));
if (endpos > es_length)
endpos = es_length;
}
else {
endpos = startpos + (arguments->kmersize - 1) +
(gt_rand_max(arguments->sb_size - 1));
}
gt_kmercodeiterator_reset(iter, GT_READMODE_FORWARD, startpos);
while ((kmercode = gt_kmercodeiterator_encseq_next(iter)) != NULL &&
startpos_add_kmer <= endpos - (arguments->kmersize - 1)) {
if (!arguments->merge_only && !arguments->use_hash &&
!kmercode->definedspecialposition && !arguments->bench) {
gt_kmer_database_add_kmer(compare_db, kmercode->code,
startpos_add_kmer);
}
if (arguments->use_hash && !kmercode->definedspecialposition) {
gt_kmer_database_add_to_hash(kmer_hash, kmercode->code,
startpos_add_kmer);
}
startpos_add_kmer++;
}
if (!arguments->use_hash) {
gt_kmer_database_add_interval(db, startpos, endpos);
gt_kmer_database_print_buffer(db, logger);
if (!arguments->bench)
had_err = gt_kmer_database_check_consistency(db, err);
}
startpos = endpos + 1;
}
if (!arguments->use_hash) {
gt_kmer_database_flush(db);
gt_kmer_database_print_buffer(db, logger);
if (!had_err && !arguments->bench)
had_err = gt_kmer_database_check_consistency(db, err);
if (!arguments->merge_only && !had_err && !arguments->bench)
had_err = gt_kmer_database_check_consistency(compare_db, err);
if (!arguments->merge_only && !arguments->bench)
gt_kmer_database_print(compare_db, logger, true);
if (!arguments->merge_only && !had_err && !arguments->bench)
had_err = gt_kmer_database_compare(compare_db, db, err);
gt_kmer_database_print(db, logger, true);
}
gt_kmercodeiterator_delete(iter);
}
if (arguments->bench) {
GtKmerStartpos pos;
GtArrayGtUword *pos_hash;
GtUword rand_access = (GtUword) 50000000,
rand_code,
i,
sum = 0;
gt_timer_show_progress(timer, "random access", stdout);
for (i = 0; i < rand_access; i++) {
rand_code = gt_rand_max(nu_kmer_codes - 1);
if (arguments->use_hash) {
pos_hash = gt_hashmap_get(kmer_hash, (const void *) rand_code);
if (pos_hash != NULL)
sum += pos_hash->spaceGtUword[pos_hash->nextfreeGtUword - 1];
}
else {
pos = gt_kmer_database_get_startpos(db, rand_code);
if (pos.no_positions > 0)
sum += pos.startpos[pos.no_positions - 1];
}
}
printf("sum: " GT_WU "\n", sum);
gt_timer_show_progress(timer, "", stdout);
gt_timer_stop(timer);
gt_timer_delete(timer);
}
if (arguments->use_hash)
gt_hashmap_delete(kmer_hash);
gt_encseq_delete(es);
if (!arguments->use_hash)
gt_kmer_database_delete(db);
if (!arguments->merge_only && !arguments->bench)
gt_kmer_database_delete(compare_db);
gt_logger_delete(logger);
gt_fa_fclose(fp);
return had_err;
}
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 = 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;
}
static int gt_gdiffcalc_runner(int argc, const char **argv, int parsed_args,
void *tool_arguments, GT_UNUSED GtError *err)
{
GtGenomediffArguments *arguments = tool_arguments;
int had_err = 0, i;
GtUword lcounter = 0, zcounter = 0;
double **shusums = NULL;
GtEncseq *encseq = NULL;
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("load encseq");
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 (!had_err) {
GtEncseqLoader *el = gt_encseq_loader_new_from_options(arguments->loadopts,
err);
encseq =
gt_encseq_loader_load(el, gt_str_get(arguments->indexname), err);
gt_encseq_loader_delete(el);
}
if (encseq == NULL)
had_err = -1;
if (timer != NULL)
gt_timer_show_progress(timer, "load units", stdout);
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 (timer != NULL)
gt_timer_show_progress(timer, "read table", stdout);
if (!had_err) {
GtIO *table_file = NULL;
GtTokenizer *tokenizer = NULL;
GtStr *line = NULL;
gt_assert(unit_info != NULL);
gt_array2dim_calloc(shusums, unit_info->num_of_genomes,
unit_info->num_of_genomes);
table_file = gt_io_new(gt_str_array_get(arguments->filenames, 0), "r");
tokenizer = gt_tokenizer_new(table_file);
line = gt_tokenizer_get_token(tokenizer);
while (line != NULL && !had_err) {
char *cline = gt_str_get(line);
char *elem = strtok(cline, ";");
zcounter = 0;
while (elem != NULL && !had_err) {
if (*elem != '#') {
if (1 != sscanf(elem, "%lf",
&shusums[lcounter][zcounter])) {
had_err = 1;
gt_error_set(err, "couldn't scan");
break;
}
gt_logger_log(logger,"wert: %lf", shusums[lcounter][zcounter]);
zcounter++;
}
else {
gt_logger_log(logger, "name: %s", elem++);
}
elem = strtok(NULL, ";");
}
gt_tokenizer_next_token(tokenizer);
gt_str_delete(line);
line = gt_tokenizer_get_token(tokenizer);
lcounter++;
gt_logger_log(logger, "line "GT_WD"", lcounter);
}
}
if (!had_err) {
GtUword num_of_seq, file_idx, seq_idx, startpos;
GT_UNUSED GtUword oldpos = 0;
gt_assert(unit_info != NULL);
gt_assert(lcounter == zcounter);
gt_assert(lcounter == unit_info->num_of_genomes);
num_of_seq = gt_encseq_num_of_sequences(unit_info->encseq);
for (seq_idx = 0; seq_idx < num_of_seq; seq_idx++) {
startpos = gt_encseq_seqstartpos(unit_info->encseq, seq_idx);
file_idx = gt_encseq_filenum(unit_info->encseq, startpos);
gt_log_log("seq: "GT_WU" starts at: "GT_WU"\n"
"belonges to file: "GT_WU" which is part of genome: %s",
seq_idx, startpos, file_idx,
gt_str_array_get(unit_info->genome_names,
unit_info->map_files[file_idx]));
gt_assert(oldpos <= startpos);
oldpos = startpos;
}
}
if (!had_err && shusums != NULL) {
had_err = gt_genomediff_calculate_div_from_avg(shusums, arguments,
unit_info,
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;
}
static int gt_condenser_search_runner(GT_UNUSED int argc,
GT_UNUSED const char **argv,
GT_UNUSED int parsed_args,
void *tool_arguments,
GtError *err)
{
GtCondenserSearchArguments *arguments = tool_arguments;
int i, had_err = 0;
char *querypath = gt_str_get(arguments->querypath);
GtStr* coarse_fname = gt_str_new_cstr("coarse_");
char *db_basename = NULL;
char *suffix_ptr = NULL;
GtTimer *timer = NULL;
GtLogger *logger = NULL;
gt_error_check(err);
gt_assert(arguments);
logger = gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX, stderr);
db_basename = gt_basename(gt_str_get(arguments->dbpath));
/* if first char is '.' this might be a hidden file */
if (strlen(db_basename) > (size_t) 1 &&
(suffix_ptr = strrchr(db_basename + 1, '.')) != NULL) {
/* remove suffix */
*suffix_ptr = '\0';
}
gt_str_append_cstr(coarse_fname, db_basename);
gt_str_append_cstr(coarse_fname, ".fas");
gt_free(db_basename);
db_basename = NULL;
suffix_ptr = NULL;
if (arguments->blastn || arguments->blastp) {
GtMatch *match;
GtMatchIterator *mp = NULL;
GtNREncseq *nrencseq = NULL;
GtStr *fastaname = gt_str_clone(arguments->dbpath);
HitPosition *hits;
double eval,
raw_eval = 0.0;
GtUword coarse_db_len = 0;
GtMatchIteratorStatus status;
int curr_hits = 0,
max_hits = 100;
hits = gt_malloc(sizeof (*hits) * (size_t) max_hits);
gt_str_append_cstr(fastaname, ".fas");
for (i=0; i < max_hits; i++) {
hits[i].range = gt_malloc(sizeof (*hits[i].range) * (size_t) 1);
}
if (gt_showtime_enabled()) {
timer = gt_timer_new_with_progress_description("initialization");
gt_timer_start(timer);
}
/*extract sequences from compressed database*/
if (!had_err) {
nrencseq = gt_n_r_encseq_new_from_file(gt_str_get(arguments->dbpath),
logger, err);
if (nrencseq == NULL)
had_err = -1;
}
if (!had_err) {
if (arguments->ceval == GT_UNDEF_DOUBLE ||
arguments->feval == GT_UNDEF_DOUBLE) {
/* from NCBI BLAST tutorial:
E = Kmne^{-lambdaS}
calculates E-value for score S with natural scale parameters K for
search space size and lambda for the scoring system
E = mn2^-S'
m being the subject (total) length, n the length of ONE query
calculates E-value for bit-score S'
*/
GtFastaReader *reader;
GtCondenserSearchAvg avg = {0,0};
reader = gt_fasta_reader_rec_new(arguments->querypath);
had_err = gt_fasta_reader_run(reader, NULL, NULL,
gt_condenser_search_cum_moving_avg,
&avg,
err);
if (!had_err) {
GtUword S = arguments->bitscore;
gt_log_log(GT_WU " queries, avg query size: " GT_WU,
avg.count, avg.avg);
raw_eval = 1/pow(2.0, (double) S) * avg.avg;
gt_logger_log(logger, "Raw E-value set to %.4e", raw_eval);
gt_assert(avg.avg != 0);
}
gt_fasta_reader_delete(reader);
}
}
/*create BLAST database from compressed database fasta file*/
if (!had_err) {
if (timer != NULL)
gt_timer_show_progress(timer, "create coarse BLAST db", stderr);
if (arguments->blastn)
had_err = gt_condenser_search_create_nucl_blastdb(gt_str_get(fastaname),
err);
else
had_err = gt_condenser_search_create_prot_blastdb(gt_str_get(fastaname),
err);
}
if (!had_err) {
GtBlastProcessCall *call;
if (timer != NULL)
gt_timer_show_progress(timer, "coarse BLAST run", stderr);
if (arguments->blastp)
call = gt_blast_process_call_new_prot();
else
call = gt_blast_process_call_new_nucl();
gt_blast_process_call_set_db(call, gt_str_get(fastaname));
gt_blast_process_call_set_query(call, querypath);
gt_blast_process_call_set_evalue(call, arguments->ceval);
gt_blast_process_call_set_num_threads(call, arguments->blthreads);
mp = gt_match_iterator_blast_process_new(call, err);
if (!mp)
had_err = -1;
gt_blast_process_call_delete(call);
while (!had_err &&
(status = gt_match_iterator_next(mp, &match, err)) !=
GT_MATCHER_STATUS_END)
{
if (status == GT_MATCHER_STATUS_OK) {
GtUword hit_seq_id;
char string[7];
const char *dbseqid = gt_match_get_seqid2(match);
if (sscanf(dbseqid,"%6s" GT_WU, string, &hit_seq_id) == 2) {
gt_match_get_range_seq2(match, hits[curr_hits].range);
hits[curr_hits].idx = hit_seq_id;
gt_match_delete(match);
curr_hits++;
if (curr_hits == max_hits) {
HitPosition *hit_extention;
max_hits += 100;
hits = gt_realloc(hits, sizeof (*hit_extention) * max_hits);
for (i=max_hits - 100; i < max_hits; i++) {
hits[i].range = gt_malloc(sizeof (*hits[i].range));
}
}
} else {
gt_error_set(err, "could not parse unique db header %s", dbseqid);
had_err = -1;
}
} else if (status == GT_MATCHER_STATUS_ERROR) {
had_err = -1;
}
}
gt_match_iterator_delete(mp);
}
/*extract sequences*/
if (!had_err) {
GtNREncseqDecompressor *decomp;
GtFile *coarse_hits;
if (timer != NULL)
gt_timer_show_progress(timer, "extract coarse search hits", stderr);
decomp = gt_n_r_encseq_decompressor_new(nrencseq);
coarse_hits = gt_file_new(gt_str_get(coarse_fname),"w", err);
/* TODO DW do NOT extract complete uniques! these could be complete
chromosomes!! just extract something around it? maybe +- max query
length*/
for (i = 0; i < curr_hits; i++) {
gt_n_r_encseq_decompressor_add_unique_idx_to_extract(decomp,
hits[i].idx);
}
had_err =
gt_n_r_encseq_decompressor_start_unique_extraction(coarse_hits,
decomp,
&coarse_db_len,
err);
gt_assert(coarse_db_len != 0);
gt_file_delete(coarse_hits);
gt_n_r_encseq_decompressor_delete(decomp);
}
gt_n_r_encseq_delete(nrencseq);
/* create BLAST database from decompressed database file */
if (!had_err) {
if (timer != NULL)
gt_timer_show_progress(timer, "create fine BLAST db", stderr);
if (arguments->blastn)
had_err =
gt_condenser_search_create_nucl_blastdb(gt_str_get(coarse_fname),
err);
else
had_err =
gt_condenser_search_create_prot_blastdb(gt_str_get(coarse_fname),
err);
}
/* perform fine BLAST search */
if (!had_err) {
GtBlastProcessCall *call;
if (timer != NULL)
gt_timer_show_progress(timer, "fine BLAST run", stderr);
if (arguments->feval == GT_UNDEF_DOUBLE) {
eval = raw_eval * coarse_db_len;
} else {
eval = arguments->feval;
}
if (arguments->blastp)
call = gt_blast_process_call_new_prot();
else
call = gt_blast_process_call_new_nucl();
gt_blast_process_call_set_db(call, gt_str_get(coarse_fname));
gt_blast_process_call_set_query(call, querypath);
gt_blast_process_call_set_evalue(call, eval);
gt_blast_process_call_set_num_threads(call, arguments->blthreads);
gt_logger_log(logger, "Fine E-value set to: %.4e (len)" GT_WU, eval,
coarse_db_len);
mp = gt_match_iterator_blast_process_new(call, err);
if (!mp)
had_err = -1;
gt_blast_process_call_delete(call);
if (!had_err) {
GtUword numofhits = 0;
while (!had_err &&
(status = gt_match_iterator_next(mp, &match, err)) !=
GT_MATCHER_STATUS_END) {
if (status == GT_MATCHER_STATUS_OK) {
GtMatchBlast *matchb = (GtMatchBlast*) match;
char *dbseqid = gt_malloc(sizeof (*dbseqid) * 50);
GtRange range_seq1;
GtRange range_seq2;
numofhits++;
gt_match_get_range_seq1(match, &range_seq1);
gt_match_get_range_seq2(match, &range_seq2);
gt_file_xprintf(
arguments->outfp,
"%s\t%s\t%.2f\t" GT_WU "\t" GT_WU "\t" GT_WU "\t" GT_WU "\t"
GT_WU "\t%g\t%.3f\n",
gt_match_get_seqid1(match),
gt_match_get_seqid2(match),
gt_match_blast_get_similarity(matchb),
gt_match_blast_get_align_length(matchb),
range_seq1.start,
range_seq1.end,
range_seq2.start,
range_seq2.end,
gt_match_blast_get_evalue(matchb),
(double) gt_match_blast_get_bitscore(matchb));
gt_match_delete(match);
gt_free(dbseqid);
} else if (status == GT_MATCHER_STATUS_ERROR) {
had_err = -1;
}
}
gt_log_log(GT_WU " hits found\n", numofhits);
}
gt_match_iterator_delete(mp);
}
if (!had_err)
if (timer != NULL)
gt_timer_show_progress_final(timer, stderr);
gt_timer_delete(timer);
/*cleanup*/
for (i=0; i < max_hits; i++) {
gt_free(hits[i].range);
}
gt_free(hits);
gt_str_delete(fastaname);
}
gt_str_delete(coarse_fname);
gt_logger_delete(logger);
return had_err;
}
