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;
}
int gt_codon_iterator_encseq_unit_test(GtError *err)
{
int had_err = 0,
i, j;
const char *testseq = "gctgatcgactgaacatagctagcacggccgcgcgatcgtacgatg",
*testseq_rc = "catcgtacgatcgcgcggccgtgctagctatgttcagtcgatcagc",
*testseq_rv = "gtagcatgctagcgcgccggcacgatcgatacaagtcagctagtcg",
*testseq_cm = "cgactagctgacttgtatcgatcgtgccggcgcgctagcatgctac";
GtEncseq *encseq;
GtEncseqBuilder *eb;
GtCodonIterator *ci;
GtAlphabet *alpha;
char n1, n2, n3;
unsigned int frame;
gt_error_check(err);
alpha = gt_alphabet_new_dna();
eb = gt_encseq_builder_new(alpha);
gt_encseq_builder_add_cstr(eb, testseq, strlen(testseq), "foo");
encseq = gt_encseq_builder_build(eb, NULL);
/* forward tests */
had_err = gt_codon_iterator_encseq_single_test(encseq, testseq, testseq,
GT_READMODE_FORWARD, err);
/* complement tests */
had_err = gt_codon_iterator_encseq_single_test(encseq, testseq, testseq_cm,
GT_READMODE_COMPL, err);
/* revcompl tests */
had_err = gt_codon_iterator_encseq_single_test(encseq, testseq, testseq_rc,
GT_READMODE_REVCOMPL, err);
/* reverse tests */
had_err = gt_codon_iterator_encseq_single_test(encseq, testseq, testseq_rv,
GT_READMODE_REVERSE, err);
/* lengths < 3 */
for (j = 0; !had_err && j < 3; j++) {
ci = gt_codon_iterator_encseq_new_with_readmode(encseq, 10, j,
GT_READMODE_REVCOMPL, NULL);
i = 10;
while (!(gt_codon_iterator_next(ci, &n1, &n2, &n3, &frame, NULL))) {
gt_ensure(had_err, false);
}
gt_ensure(had_err, i == 10);
gt_codon_iterator_delete(ci);
}
gt_encseq_delete(encseq);
gt_encseq_builder_delete(eb);
gt_alphabet_delete(alpha);
return had_err;
}
GtAlphabet* gt_alphabet_guess(const char *sequence, unsigned long seqlen)
{
unsigned long i;
gt_assert(sequence && seqlen);
for (i = 0;
i < seqlen && i < (unsigned long) ALPHABET_GUESS_MAX_LENGTH;
i++) {
if (strchr(ALPHABET_GUESS_PROTEIN_CHARS, sequence[i]) != NULL)
return gt_alphabet_new_protein();
}
return gt_alphabet_new_dna();
}
static int alphabet_lua_new_dna(lua_State *L)
{
GtAlphabet **alpha;
gt_assert(L);
alpha = lua_newuserdata(L, sizeof *alpha);
gt_assert(alpha);
*alpha = gt_alphabet_new_dna();
gt_assert(*alpha);
luaL_getmetatable(L, ALPHABET_METATABLE);
lua_setmetatable(L, -2);
return 1;
}
static void gt_tyrsearchinfo_init(Tyrsearchinfo *tyrsearchinfo,
const Tyrindex *tyrindex,
unsigned int showmode,
unsigned int searchstrand)
{
unsigned long merbytes;
merbytes = gt_tyrindex_merbytes(tyrindex);
tyrsearchinfo->mersize = gt_tyrindex_mersize(tyrindex);
tyrsearchinfo->mertable = gt_tyrindex_mertable(tyrindex);
tyrsearchinfo->lastmer = gt_tyrindex_lastmer(tyrindex);
tyrsearchinfo->showmode = showmode;
tyrsearchinfo->searchstrand = searchstrand;
tyrsearchinfo->dnaalpha = gt_alphabet_new_dna();
ALLOCASSIGNSPACE(tyrsearchinfo->bytecode,NULL,GtUchar,merbytes);
ALLOCASSIGNSPACE(tyrsearchinfo->rcbuf,NULL,GtUchar,tyrsearchinfo->mersize);
}
GtHpolProcessor *gt_hpol_processor_new(GtEncseq *encseq, unsigned long hmin)
{
GtHpolProcessor *hpp;
hpp = gt_malloc(sizeof (GtHpolProcessor));
gt_assert(encseq != NULL);
gt_assert(hmin > 0);
hpp->encseq = encseq;
hpp->hmin = hmin;
hpp->read_hmin = 0;
hpp->qmax = 0;
hpp->mapqmin = 0;
hpp->covmin = 0;
hpp->allow_partial = false;
hpp->allow_multiple = false;
hpp->hdist = gt_disc_distri_new();
hpp->nof_h = 0;
hpp->hdist_e = gt_disc_distri_new();
hpp->nof_h_e = 0;
hpp->hlen_max = 0;
hpp->cds_oracle = NULL;
hpp->asp = NULL;
hpp->nof_complete_edited = 0;
hpp->nof_complete_not_edited = 0;
hpp->nof_skipped = 0;
hpp->nof_unmapped = 0;
hpp->nof_multihits = 0;
hpp->nof_replaced = 0;
hpp->clenmax = GT_UNDEF_ULONG;
hpp->altmax = (double) 1.0;
hpp->refmin = (double) 0.0;
hpp->alpha = gt_alphabet_new_dna();
hpp->adjust_s_hlen = false;
hpp->output_segments = false;
hpp->outfp_segments = NULL;
hpp->output_stats = false;
hpp->output_multihit_stats = false;
hpp->outfp_stats = NULL;
hpp->processed_segments = NULL;
hpp->reads_iters = NULL;
hpp->outfiles = NULL;
hpp->nfiles = 0;
return hpp;
}
int gt_ltrdigest_arguments_check(GT_UNUSED int rest_argc, void *tool_arguments,
GtError* err)
{
GtLTRdigestOptions *arguments = tool_arguments;
int had_err = 0;
if (arguments->nthreads > 0) {
gt_warning("The '-threads' option is deprecated. Please use the '-j'"
"option of the 'gt' call instead, e.g.:\n"
" gt -j %lu ltrdigest ...", arguments->nthreads);
}
/* -trnas */
if (!had_err && arguments->trna_lib && gt_str_length(arguments->trna_lib) > 0)
{
if (!gt_file_exists(gt_str_get(arguments->trna_lib)))
{
gt_error_set(err, "File '%s' does not exist!",
gt_str_get(arguments->trna_lib));
had_err = -1;
}
}
if (!had_err)
{
GtHMM *hmm;
GtAlphabet *alpha;
alpha = gt_alphabet_new_dna();
hmm = gt_ppt_hmm_new(alpha, &arguments->ppt_opts);
if (!hmm)
{
gt_error_set(err, "PPT HMM parameters are not valid!");
had_err = -1;
}
else
gt_hmm_delete(hmm);
gt_alphabet_delete(alpha);
}
return had_err;
}
int gt_alphabet_unit_test(GtError *err)
{
int had_err = 0;
GtAlphabet *a, *b, *c;
gt_error_check(err);
a = gt_alphabet_new_dna();
b = gt_alphabet_new_protein();
c = gt_alphabet_clone(a);
gt_ensure(had_err, gt_alphabet_equals(a, a));
gt_ensure(had_err, gt_alphabet_equals(b, b));
gt_ensure(had_err, gt_alphabet_equals(c, c));
gt_ensure(had_err, !gt_alphabet_equals(a, b));
gt_ensure(had_err, gt_alphabet_equals(a, c));
gt_alphabet_delete(a);
gt_alphabet_delete(b);
gt_alphabet_delete(c);
return had_err;
}
static int readfirstvaluesfromfile(GtEncseqMetadata *emd,
const char *indexname, GtError *err)
{
FILE *fp;
bool had_err = false;
unsigned long cc, byteoffset = 0, alphatype;
char *alphadef;
gt_error_check(err);
fp = gt_fa_fopen_with_suffix(indexname, GT_ENCSEQFILESUFFIX, "rb", err);
if (fp == NULL)
{
had_err = true;
}
NEXTFREAD(emd->is64bit);
if (!had_err)
{
if ((int) emd->is64bit > 1)
{
gt_error_set(err, "illegal platform code %u in \"%s%s\"", emd->is64bit,
indexname, GT_ENCSEQFILESUFFIX);
had_err = true;
}
if (!had_err && ((emd->is64bit && sizeof (unsigned long) != (size_t) 8)
|| (!emd->is64bit && sizeof (unsigned long) == (size_t) 8)))
{
gt_error_set(err, "trying to load 64-bit index \"%s%s\" on a 32-bit "
"system or vice versa -- please use correct index "
"for this platform", indexname, GT_ENCSEQFILESUFFIX);
had_err = true;
}
}
NEXTFREAD(emd->version);
if (!had_err)
{
if (emd->version < GT_ENCSEQ_VERSION) {
gt_error_set(err, "index \"%s%s\" is format version %lu, current is "
"%lu -- please re-encode",
indexname, GT_ENCSEQFILESUFFIX,
emd->version, GT_ENCSEQ_VERSION);
had_err = true;
}
}
NEXTFREAD(cc);
if (!had_err)
{
if (cc >= (unsigned long) GT_ACCESS_TYPE_UNDEFINED)
{
gt_error_set(err, "illegal type %lu in \"%s%s\"", cc,
indexname, GT_ENCSEQFILESUFFIX);
had_err = true;
}
}
if (!had_err) {
emd->sat = (GtEncseqAccessType) cc;
NEXTFREAD(emd->totallength);
NEXTFREAD(emd->numofdbsequences);
NEXTFREAD(emd->numofdbfiles);
NEXTFREAD(emd->lengthofdbfilenames);
NEXTFREAD(emd->specialcharinfo);
NEXTFREAD(emd->minseqlen);
NEXTFREAD(emd->maxseqlen);
}
NEXTFREAD(alphatype);
if (!had_err) {
if (alphatype > 2UL) {
gt_error_set(err, "illegal alphabet type %lu in \"%s%s\"", alphatype,
indexname, GT_ENCSEQFILESUFFIX);
had_err = true;
}
}
if (!had_err) {
NEXTFREAD(emd->lengthofalphadef);
switch (alphatype) {
case 0:
emd->alpha = gt_alphabet_new_dna();
break;
case 1:
emd->alpha = gt_alphabet_new_protein();
break;
case 2:
gt_assert(emd->lengthofalphadef > 0);
emd->customalphabet = true;
alphadef = gt_malloc(sizeof (char) * emd->lengthofalphadef);
NEXTFREADWSIZE(*(alphadef), emd->lengthofalphadef);
emd->alpha = gt_alphabet_new_from_string(alphadef,
emd->lengthofalphadef,
err);
if (!emd->alpha) {
had_err = true;
}
gt_free(alphadef);
break;
}
gt_assert(emd->alpha != NULL);
}
gt_fa_xfclose(fp);
return had_err ? -1 : 0;
}
GtPBSResults* gt_pbs_find(const char *seq,
const char *rev_seq,
GtLTRElement *element,
GtPBSOptions *o,
GtError *err)
{
GtSeq *seq_forward, *seq_rev;
GtPBSResults *results;
unsigned long j;
GtAlignment *ali;
GtAlphabet *a = gt_alphabet_new_dna();
GtScoreFunction *sf = gt_dna_scorefunc_new(a,
o->ali_score_match,
o->ali_score_mismatch,
o->ali_score_insertion,
o->ali_score_deletion);
gt_assert(seq && rev_seq && sf && a && element);
results = gt_pbs_results_new(element, o);
seq_forward = gt_seq_new(seq + (gt_ltrelement_leftltrlen(element))
- (o->radius),
2*o->radius + 1,
a);
seq_rev = gt_seq_new(rev_seq + (gt_ltrelement_rightltrlen(element))
- (o->radius),
2*o->radius + 1,
a);
for (j=0;j<gt_bioseq_number_of_sequences(o->trna_lib);j++)
{
GtSeq *trna_seq, *trna_from3;
char *trna_from3_full;
unsigned long trna_seqlen;
trna_seq = gt_bioseq_get_seq(o->trna_lib, j);
trna_seqlen = gt_seq_length(trna_seq);
trna_from3_full = gt_calloc(trna_seqlen, sizeof (char));
memcpy(trna_from3_full, gt_seq_get_orig(trna_seq),
sizeof (char)*trna_seqlen);
(void) gt_reverse_complement(trna_from3_full, trna_seqlen, err);
trna_from3 = gt_seq_new_own(trna_from3_full, trna_seqlen, a);
ali = gt_swalign(seq_forward, trna_from3, sf);
gt_pbs_add_hit(results->hits, ali, o, trna_seqlen,
gt_seq_get_description(trna_seq), GT_STRAND_FORWARD,
results);
gt_alignment_delete(ali);
ali = gt_swalign(seq_rev, trna_from3, sf);
gt_pbs_add_hit(results->hits, ali, o, trna_seqlen,
gt_seq_get_description(trna_seq), GT_STRAND_REVERSE,
results);
gt_alignment_delete(ali);
gt_seq_delete(trna_from3);
}
gt_seq_delete(seq_forward);
gt_seq_delete(seq_rev);
gt_score_function_delete(sf);
gt_alphabet_delete(a);
gt_array_sort(results->hits, gt_pbs_hit_compare);
return results;
}
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;
}
static int gt_linspace_align_runner(GT_UNUSED int argc,
GT_UNUSED const char **argv,
GT_UNUSED int parsed_args,
void *tool_arguments,
GtError *err)
{
GtLinspaceArguments *arguments = tool_arguments;
int had_err = 0;
GtAlignment *align;
GtWord left_dist = 0, right_dist = 0;
GtSequenceTable *sequence_table1, *sequence_table2;
GtLinspaceManagement *spacemanager;
GtScoreHandler *scorehandler = NULL;
GtTimer *linspacetimer = NULL;
GtAlphabet *alphabet = NULL;
gt_error_check(err);
gt_assert(arguments);
sequence_table1 = gt_sequence_table_new();
sequence_table2 = gt_sequence_table_new();
align = gt_alignment_new();
spacemanager = gt_linspace_management_new();
gt_linspace_management_set_TSfactor(spacemanager,arguments->timesquarefactor);
/* get sequences */
if (gt_str_array_size(arguments->strings) > 0)
{
get_onesequence(sequence_table1, arguments->strings, 0);
sequence_table1->size++;
get_onesequence(sequence_table2, arguments->strings, 1);
sequence_table2->size++;
}
else if (gt_str_array_size(arguments->files) > 0)
{
had_err = get_fastasequences(sequence_table1,
gt_str_array_get_str(arguments->files,0),err);
if (!had_err)
{
had_err = get_fastasequences(sequence_table2,
gt_str_array_get_str(arguments->files,1),err);
}
}
if (arguments->dna)
{
alphabet = gt_alphabet_new_dna();
} else
{
gt_assert(arguments->protein);
alphabet = gt_alphabet_new_protein();
}
gt_encode_sequence_table(alphabet,sequence_table1);
gt_encode_sequence_table(alphabet,sequence_table2);
if (!had_err)
{
scorehandler = gt_arguments2scorehandler(arguments,err);
if (scorehandler == NULL)
{
had_err = -1;
} else
{
if (arguments->global && arguments->protein && !arguments->has_costmatrix)
{
GtScoreHandler *costhandler = gt_scorehandler2costhandler(scorehandler);
gt_scorehandler_delete(scorehandler);
scorehandler = costhandler;
}
}
}
/* get diagonal band */
if (!had_err && arguments->diagonal)
{
if (gt_str_array_size(arguments->diagonalbonds) > 0)
{
had_err = gt_parse_score_value(__LINE__,&left_dist,
gt_str_array_get(arguments->diagonalbonds,0),
false, err);
if (!had_err)
{
had_err = gt_parse_score_value(__LINE__,&right_dist,
gt_str_array_get(arguments->diagonalbonds,1),
false, err);
}
}
}
if (!had_err && arguments->spacetime)
{
linspacetimer = gt_timer_new();
}
/* alignment functions with linear gap costs */
if (!had_err)
{
bool affine;
if (gt_str_array_size(arguments->linearcosts) > 0)
{
affine = false;
} else
{
gt_assert(gt_str_array_size(arguments->affinecosts) > 0);
affine = true;
}
had_err = gt_all_against_all_alignment_check (
affine, align, arguments,
spacemanager,
scorehandler,
gt_alphabet_characters(alphabet),
gt_alphabet_wildcard_show(alphabet),
sequence_table1,
sequence_table2,
left_dist,
right_dist,
linspacetimer,err);
}
/*spacetime option*/
if (!had_err && arguments->spacetime)
{
printf("# combined space peak in kilobytes: %f\n",
GT_KILOBYTES(gt_linspace_management_get_spacepeak(spacemanager)));
gt_timer_show_formatted(linspacetimer,"# TIME overall " GT_WD ".%02ld\n",
stdout);
}
gt_timer_delete(linspacetimer);
gt_linspace_management_delete(spacemanager);
gt_sequence_table_delete(sequence_table1);
gt_sequence_table_delete(sequence_table2);
gt_alignment_delete(align);
gt_alphabet_delete(alphabet);
gt_scorehandler_delete(scorehandler);
return had_err;
}
int gt_encseq_gc_unit_test(GtError *err)
{
int had_err = 0;
double *results;
GtEncseqBuilder *eb;
GtEncseq *encseq;
const char testseq1[] = "aaaaaa",
testseq2[] = "cccccc",
testseq3[] = "acgtacgt",
testseq4[] = "acgtn";
/* testseq5[] = "xxxxn"; */
GtAlphabet *alpha;
/*GtError *tmp_err;*/
gt_error_check(err);
alpha = gt_alphabet_new_dna();
/* test a-seq */
eb = gt_encseq_builder_new(alpha);
gt_encseq_builder_create_ssp_tab(eb);
gt_encseq_builder_enable_description_support(eb);
gt_encseq_builder_add_cstr(eb, testseq1, 6UL, "only a");
encseq = gt_encseq_builder_build(eb, err);
if ((results = gt_encseq_get_gc(encseq,
false,
true,
err)) != NULL)
{
gt_ensure(had_err, gt_double_equals_double(results[0], 0.0));
}
else
{
had_err = -1;
}
gt_free(results);
gt_encseq_builder_delete(eb);
gt_encseq_delete(encseq);
if (!had_err)
{
/* test c-seq */
eb = gt_encseq_builder_new(alpha);
gt_encseq_builder_create_ssp_tab(eb);
gt_encseq_builder_enable_description_support(eb);
gt_encseq_builder_add_cstr(eb, testseq2, 6UL, "only c");
encseq = gt_encseq_builder_build(eb, err);
if ((results = gt_encseq_get_gc(encseq,
false,
true,
err)) != NULL)
{
gt_ensure(had_err, gt_double_equals_one(results[0]));
}
else
{
had_err = -1;
}
gt_free(results);
gt_encseq_builder_delete(eb);
gt_encseq_delete(encseq);
}
if (!had_err)
{
/* test dna-seq and dna+special-seq*/
eb = gt_encseq_builder_new(alpha);
gt_encseq_builder_create_ssp_tab(eb);
gt_encseq_builder_enable_description_support(eb);
gt_encseq_builder_add_cstr(eb, testseq3, 8UL, "0.5");
gt_encseq_builder_add_cstr(eb, testseq4, 5UL, "0.5+special");
encseq = gt_encseq_builder_build(eb, err);
if ((results = gt_encseq_get_gc(encseq,
false,
true,
err)) != NULL)
{
gt_ensure(had_err, gt_double_equals_double(results[0], 0.5));
gt_ensure(had_err, gt_double_equals_double(results[1], 0.5));
}
else
{
had_err = -1;
}
gt_free(results);
if (!had_err)
{
/* count special chars */
if ((results = gt_encseq_get_gc(encseq,
true,
true,
err)) != NULL)
{
gt_ensure(had_err, gt_double_equals_double(results[0], 0.5));
gt_ensure(had_err, gt_double_equals_double(results[1], (2.0/5.0)));
}
else
{
had_err = -1;
}
gt_free(results);
}
gt_encseq_builder_delete(eb);
gt_encseq_delete(encseq);
}
if (!had_err)
{
/* test dna-seq and dna+special-seq*/
eb = gt_encseq_builder_new(alpha);
gt_encseq_builder_create_ssp_tab(eb);
gt_encseq_builder_enable_description_support(eb);
gt_encseq_builder_add_cstr(eb, testseq3, 8UL, "0.5");
gt_encseq_builder_add_cstr(eb, testseq4, 5UL, "0.5+special");
encseq = gt_encseq_builder_build(eb, err);
/*add mirrored sequence*/
had_err = gt_encseq_mirror(encseq, err);
/* sequence wise */
if ((results = gt_encseq_get_gc(encseq,
false,
true,
err)) != NULL)
{
gt_ensure(had_err, gt_double_equals_double(results[0], 0.5));
gt_ensure(had_err, gt_double_equals_double(results[1], 0.5));
gt_ensure(had_err, gt_double_equals_double(results[2], 0.5));
gt_ensure(had_err, gt_double_equals_double(results[3], 0.5));
}
else
{
had_err = -1;
}
gt_free(results);
if (!had_err)
{
/* count special chars */
if ((results = gt_encseq_get_gc(encseq,
true,
true,
err)) != NULL)
{
gt_ensure(had_err, gt_double_equals_double(results[0], 0.5));
gt_ensure(had_err, gt_double_equals_double(results[1], (2.0/5.0)));
gt_ensure(had_err, gt_double_equals_double(results[2], (2.0/5.0)));
gt_ensure(had_err, gt_double_equals_double(results[3], 0.5));
}
else
{
had_err = -1;
}
gt_free(results);
}
gt_encseq_builder_delete(eb);
gt_encseq_delete(encseq);
}
gt_alphabet_delete(alpha);
return had_err;
}
