GtSeqCol* gt_bioseq_col_new(GtStrArray *sequence_files, GtError *err)
{
GtSeqCol *sc;
GtBioseqCol *bsc;
GtUword i;
int had_err = 0;
gt_error_check(err);
gt_assert(sequence_files);
gt_assert(gt_str_array_size(sequence_files));
sc = gt_seq_col_create(gt_bioseq_col_class());
bsc = gt_bioseq_col_cast(sc);
bsc->num_of_seqfiles = gt_str_array_size(sequence_files);
bsc->bioseqs = gt_calloc(bsc->num_of_seqfiles, sizeof (GtBioseq*));
for (i = 0; !had_err && i < bsc->num_of_seqfiles; i++) {
bsc->bioseqs[i] = gt_bioseq_new(gt_str_array_get(sequence_files, i), err);
if (!bsc->bioseqs[i])
had_err = -1;
}
if (had_err) {
gt_bioseq_col_delete(sc);
return NULL;
}
bsc->matchdescstart = false;
return sc;
}
static void construct_description(GtStr *description, const char *type,
GtUword counter, bool join,
bool translate, GtStr *seqid,
GtStrArray *target_ids)
{
gt_assert(!gt_str_length(description));
gt_str_append_cstr(description, type);
gt_str_append_char(description, '_');
gt_str_append_ulong(description, counter);
if (join)
gt_str_append_cstr(description, " (joined)");
if (translate)
gt_str_append_cstr(description, " (translated)");
if (seqid) {
gt_assert(gt_str_length(seqid));
gt_str_append_cstr(description, " [seqid ");
gt_str_append_str(description, seqid);
gt_str_append_char(description, ']');
}
if (target_ids && gt_str_array_size(target_ids)) {
GtUword i;
gt_str_append_cstr(description, " [target IDs ");
gt_str_append_cstr(description, gt_str_array_get(target_ids, 0));
for (i = 1; i < gt_str_array_size(target_ids); i++) {
gt_str_append_char(description, ',');
gt_str_append_cstr(description, gt_str_array_get(target_ids, i));
}
gt_str_append_char(description, ']');
}
}
static void showsimpleoptions(const Cmppairwiseopt *opt)
{
if (gt_str_array_size(opt->strings) > 0)
{
if (!opt->showedist)
printf("# two strings \"%s\" \"%s\"\n", gt_str_array_get(opt->strings,0),
gt_str_array_get(opt->strings,1UL));
return;
}
if (gt_str_array_size(opt->files) > 0)
{
printf("# two files \"%s\" \"%s\"\n", gt_str_array_get(opt->files,0),
gt_str_array_get(opt->files,1UL));
return;
}
if (opt->charlistlen != NULL)
{
printf("# alphalen \"%s\" " GT_WU "\n",
gt_str_get(opt->charlistlen->charlist),
opt->charlistlen->len);
return;
}
if (gt_str_length(opt->text) > 0)
{
printf("# text \"%s\"\n", gt_str_get(opt->text));
return;
}
}
static GtUword applycheckfunctiontosimpleoptions(
Checkcmppairfuntype checkfunction,
const Cmppairwiseopt *opt)
{
if (gt_str_array_size(opt->strings) > 0)
{
bool forward = true;
while (true)
{
checkfunction(forward,
(const GtUchar *) gt_str_array_get(opt->strings,0),
(GtUword) strlen(gt_str_array_get(opt->strings,0)),
(const GtUchar *) gt_str_array_get(opt->strings,1UL),
(GtUword) strlen(gt_str_array_get(opt->strings,1UL)));
if (!forward)
{
break;
}
forward = false;
}
return 2UL; /* number of testcases */
}
if (gt_str_array_size(opt->files) > 0)
{
if (opt->fasta)
{
GtUword i, j;
for (i = 0; i < gt_str_array_size(opt->fastasequences0); i++)
{
for (j = 0; j < gt_str_array_size(opt->fastasequences1); j++)
{
checkfunction(true,
(const GtUchar *) gt_str_array_get(opt->fastasequences0,i),
(GtUword) strlen(gt_str_array_get(opt->fastasequences0,i)),
(const GtUchar *) gt_str_array_get(opt->fastasequences1,j),
(GtUword) strlen(gt_str_array_get(opt->fastasequences1,j)));
}
}
}
else
{
gt_runcheckfunctionontwofiles(checkfunction,
gt_str_array_get(opt->files,0),
gt_str_array_get(opt->files,1UL));
}
return 2UL;
}
if (opt->charlistlen != NULL)
{
return gt_runcheckfunctiononalphalen(checkfunction,
gt_str_get(opt->charlistlen->charlist),
opt->charlistlen->len);
}
if (gt_str_length(opt->text) > 0)
{
return gt_runcheckfunctionontext(checkfunction, gt_str_get(opt->text));
}
gt_assert(false);
return 0;
}
GtFastaBuffer* gt_fastabuffer_new(const GtStrArray *filenametab,
const GtUchar *symbolmap,
bool plainformat,
Filelengthvalues **filelengthtab,
GtQueue *descptr,
unsigned long *characterdistribution)
{
GtFastaBuffer *fb;
fb = gt_calloc(1, sizeof (GtFastaBuffer));
fb->plainformat = plainformat;
fb->filenum = 0;
fb->firstoverallseq = true;
fb->firstseqinfile = true;
fb->nextfile = true;
fb->nextread = fb->nextfree = 0;
fb->filenametab = filenametab;
fb->symbolmap = symbolmap;
fb->complete = false;
fb->lastspeciallength = 0;
fb->descptr = descptr;
if (filelengthtab)
{
*filelengthtab = gt_calloc(gt_str_array_size(filenametab),
sizeof (Filelengthvalues));
fb->filelengthtab = *filelengthtab;
} else
{
fb->filelengthtab = NULL;
}
fb->characterdistribution = characterdistribution;
GT_INITARRAY(&fb->headerbuffer, char);
return fb;
}
int gt_parse_algbounds(Sfxstrategy *sfxstrategy,
const GtStrArray *algbounds,
GtError *err)
{
bool haserr = false;
const char *arg;
GtWord readint;
if (gt_str_array_size(algbounds) != 3UL)
{
gt_error_set(err,"option -algbds must have exactly 3 arguments");
haserr = true;
}
GT_IDXOPTS_READMAXBOUND(maxinsertionsort, 0);
GT_IDXOPTS_READMAXBOUND(maxbltriesort, 1UL);
if (sfxstrategy->maxinsertionsort > sfxstrategy->maxbltriesort)
{
gt_error_set(err,"first argument of option -algbds must not be larger "
"than second argument");
haserr = true;
}
GT_IDXOPTS_READMAXBOUND(maxcountingsort, 2UL);
if (sfxstrategy->maxbltriesort > sfxstrategy->maxcountingsort)
{
gt_error_set(err,"second argument of option -algbds must not be larger "
"than third argument");
haserr = true;
}
return haserr ? -1 : 0;
}
int gt_seqiterator_fastq_next(GtSeqIterator *seqit,
const GtUchar **sequence,
unsigned long *len,
char **desc,
GtError *err)
{
int errstatus = 0;
GtSeqIteratorFastQ *seqitf;
gt_assert(seqit);
seqitf = gt_seqiterator_fastq_cast((GtSeqIterator*) seqit);
gt_assert(seqit && len && desc);
seqitf = gt_seqiterator_fastq_cast(seqit);
gt_str_reset(seqitf->qualsbuffer);
gt_str_reset(seqitf->qdescbuffer);
gt_str_reset(seqitf->sequencebuffer);
gt_str_reset(seqitf->descbuffer);
/* parse file */
errstatus = parse_fastq_block(seqitf, err);
if (!errstatus) {
*sequence = (GtUchar*) gt_str_get(seqitf->sequencebuffer);
*len = gt_str_length(seqitf->sequencebuffer);
*desc = gt_str_get(seqitf->descbuffer);
if (seqitf->qualities)
*seqitf->qualities = (GtUchar*) gt_str_get(seqitf->qualsbuffer);
errstatus = 1;
} else {
if (errstatus == EOF) {
/* we could not get a next entry from this file */
/* can we open another? */
if (seqitf->filenum+1 < gt_str_array_size(seqitf->filenametab)) {
const char *filename;
filename = gt_str_array_get(seqitf->filenametab, ++seqitf->filenum);
gt_file_delete(seqitf->curfile);
seqitf->curfile = gt_file_xopen(filename, "r");
seqitf->curline = 1;
/* get first entry from next file*/
errstatus = parse_fastq_block(seqitf, err);
if (!errstatus) {
*sequence = (GtUchar*) gt_str_get(seqitf->sequencebuffer);
*len = gt_str_length(seqitf->sequencebuffer);
*desc = gt_str_get(seqitf->descbuffer);
if (seqitf->qualities)
*seqitf->qualities = (GtUchar*) gt_str_get(seqitf->qualsbuffer);
errstatus = 1;
} else {
errstatus = -1;
}
} else {
/* all entries read from all files */
errstatus = 0;
}
} else {
errstatus = -1;
}
}
return errstatus;
}
static int encode_sequence_files(GtStrArray *infiles, GtEncseqOptions *opts,
const char *indexname, bool verbose,
bool esq_no_header,
GtError *err)
{
GtEncseqEncoder *encseq_encoder;
GtLogger *logger;
int had_err = 0;
gt_error_check(err);
gt_assert(infiles && gt_str_array_size(infiles) > 0 && opts);
logger = gt_logger_new(verbose, "# ", stderr);
encseq_encoder = gt_encseq_encoder_new_from_options(opts, err);
if (!encseq_encoder)
had_err = -1;
if (!had_err) {
gt_encseq_encoder_set_logger(encseq_encoder, logger);
if (esq_no_header)
{
gt_encseq_encoder_disable_esq_header(encseq_encoder);
}
had_err = gt_encseq_encoder_encode(encseq_encoder, infiles, indexname, err);
}
gt_encseq_encoder_delete(encseq_encoder);
gt_logger_delete(logger);
return had_err;
}
static int gt_idxlocali_runner (GT_UNUSED int argc,
GT_UNUSED const char **argv,
GT_UNUSED int parsed_args,
void *tool_arguments,
GtError * err)
{
IdxlocaliOptions *arguments = tool_arguments;
bool haserr = false;
unsigned long idx;
gt_error_check (err);
gt_assert (arguments != NULL);
gt_assert (parsed_args == argc);
printf ("# indexname(%s)=%s\n", arguments->withesa ? "esa" : "pck",
gt_str_get (arguments->indexname));
for (idx = 0; idx < gt_str_array_size (arguments->queryfiles); idx++)
{
printf ("# queryfile=%s\n",gt_str_array_get (arguments->queryfiles, idx));
}
printf ("# threshold=%lu\n", arguments->threshold);
if (!haserr && runidxlocali (arguments, err) != 0)
{
haserr = true;
}
return haserr ? -1 : 0;
}
static int inputthesequences(unsigned int *numofchars,
unsigned long *nextpostable,
Suffixarray *suffixarraytable,
const GtStrArray *indexnametab,
unsigned int demand,
GtLogger *logger,
GtError *err)
{
unsigned long idx;
const char *indexname;
gt_error_check(err);
for (idx=0; idx<gt_str_array_size(indexnametab); idx++)
{
indexname = gt_str_array_get(indexnametab,idx);
if (streamsuffixarray(&suffixarraytable[idx],
demand,
indexname,
logger,
err) != 0)
{
return -1;
}
if (idx == 0)
{
*numofchars =
gt_alphabet_num_of_chars(
gt_encseq_alphabet(suffixarraytable[idx].encseq));
}
nextpostable[idx] = 0;
}
return 0;
}
static int gt_seqids_runner(GT_UNUSED int argc, const char **argv,
int parsed_args,
GT_UNUSED void *tool_arguments, GtError *err)
{
GtNodeStream *in_stream, *v_stream;
GtCstrTable *cst;
int had_err = 0;
gt_error_check(err);
cst = gt_cstr_table_new();
in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
argv + parsed_args);
v_stream = gt_visitor_stream_new(in_stream, gt_collect_ids_visitor_new(cst));
had_err = gt_node_stream_pull(v_stream, err);
if (!had_err) {
GtStrArray *seqids;
GtUword i;
seqids = gt_cstr_table_get_all(cst);
for (i = 0; i < gt_str_array_size(seqids); i++) {
printf("%s\n", gt_str_array_get(seqids, i));
}
gt_str_array_delete(seqids);
}
gt_node_stream_delete(v_stream);
gt_node_stream_delete(in_stream);
gt_cstr_table_delete(cst);
return had_err;
}
/* single sequences (-ss)*/
static void get_onesequence(const GtSequenceTable *sequence_table,
const GtStrArray *strings,
GtUword idx)
{
gt_assert(sequence_table != NULL && strings != NULL &&
idx < gt_str_array_size(strings));
sequence_table->seqarray[0] = gt_str_new_cstr(gt_str_array_get(strings,idx));
}
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;
}
static unsigned long applycheckfunctiontosimpleoptions(
Checkcmppairfuntype checkfunction,
const Cmppairwiseopt *opt)
{
if (gt_str_array_size(opt->strings) > 0)
{
bool forward = true;
while (true)
{
checkfunction(forward,
(const GtUchar *) gt_str_array_get(opt->strings,0),
(unsigned long) strlen(gt_str_array_get(opt->strings,0)),
(const GtUchar *) gt_str_array_get(opt->strings,1UL),
(unsigned long) strlen(gt_str_array_get(opt->strings,1UL)));
if (!forward)
{
break;
}
forward = false;
}
return 2UL; /* number of testcases */
}
if (gt_str_array_size(opt->files) > 0)
{
gt_runcheckfunctionontwofiles(checkfunction,
gt_str_array_get(opt->files,0),
gt_str_array_get(opt->files,1UL));
return 2UL;
}
if (opt->charlistlen != NULL)
{
return gt_runcheckfunctiononalphalen(checkfunction,
gt_str_get(opt->charlistlen->charlist),
opt->charlistlen->len);
}
if (gt_str_length(opt->text) > 0)
{
return gt_runcheckfunctionontext(checkfunction,gt_str_get(opt->text));
}
gt_assert(false);
return 0;
}
void gt_lua_push_strarray_as_table(lua_State *L, GtStrArray *sa)
{
unsigned long i;
gt_assert(L && sa);
lua_newtable(L);
for (i = 0; i < gt_str_array_size(sa); i++) {
lua_pushinteger(L, i+1); /* in Lua we index from 1 on */
lua_pushstring(L, gt_str_array_get(sa, i));
lua_rawset(L, -3);
}
}
static int gt_ltr_cluster_stream_next(GtNodeStream *ns,
GtGenomeNode **gn,
GtError *err)
{
GtLTRClusterStream *lcs;
GtGenomeNode *ref_gn;
int had_err = 0;
unsigned long i = 0;
gt_error_check(err);
lcs = gt_ltr_cluster_stream_cast(ns);
if (lcs->first_next) {
while (!(had_err = gt_node_stream_next(lcs->in_stream, gn, err)) && *gn) {
gt_assert(*gn && !had_err);
ref_gn = gt_genome_node_ref(*gn);
gt_array_add(lcs->nodes, ref_gn);
had_err = gt_genome_node_accept(*gn, (GtNodeVisitor*) lcs->lcv, err);
if (had_err) {
gt_genome_node_delete(*gn);
*gn = NULL;
break;
}
}
lcs->feat_to_encseq =
gt_ltr_cluster_prepare_seq_visitor_get_encseqs(lcs->lcv);
lcs->feat_to_encseq_keys =
gt_ltr_cluster_prepare_seq_visitor_get_features(lcs->lcv);
if (!had_err) {
for (i = 0; i < gt_str_array_size(lcs->feat_to_encseq_keys); i++) {
had_err = process_feature(lcs,
gt_str_array_get(lcs->feat_to_encseq_keys, i),
err);
if (had_err)
break;
}
}
if (!had_err) {
*gn = *(GtGenomeNode**) gt_array_get(lcs->nodes, lcs->next_index);
lcs->next_index++;
lcs->first_next = false;
return 0;
}
} else {
if (lcs->next_index >= gt_array_size(lcs->nodes))
*gn = NULL;
else {
*gn = *(GtGenomeNode**) gt_array_get(lcs->nodes, lcs->next_index);
lcs->next_index++;
}
return 0;
}
return had_err;
}
GtQuerysubstringmatchiterator *gt_querysubstringmatchiterator_new(
const GtEncseq *dbencseq,
GtUword totallength,
const ESASuffixptr *suftabpart,
GtReadmode db_readmode,
GtUword numberofsuffixes,
const GtStrArray *query_files,
const GtEncseq *query_encseq,
GtReadmode query_readmode,
unsigned int userdefinedleastlength,
GtError *err)
{
GtQuerysubstringmatchiterator *qsmi = gt_malloc(sizeof *qsmi);
qsmi->dbencseq = dbencseq;
qsmi->suftabpart = suftabpart;
qsmi->db_readmode = db_readmode;
qsmi->numberofsuffixes = numberofsuffixes;
qsmi->totallength = totallength;
qsmi->userdefinedleastlength = (GtUword) userdefinedleastlength;
qsmi->queryunitnum = 0;
qsmi->desc = NULL;
qsmi->query_for_seqit = NULL;
qsmi->query_seqlen = 0;
qsmi->queryrep.sequence = NULL;
qsmi->queryrep.encseq = query_encseq;
qsmi->queryrep.readmode = query_readmode;
qsmi->queryrep.startpos = 0;
qsmi->dbstart = 0;
qsmi->matchlength = 0;
qsmi->querysubstring.queryrep = &qsmi->queryrep;
qsmi->mmsi = gt_mmsearchiterator_new_empty();
qsmi->mmsi_defined = false;
if (query_files == NULL || gt_str_array_size(query_files) == 0)
{
gt_assert(query_encseq != NULL);
qsmi->seqit = NULL;
qsmi->query_encseq_numofsequences
= (uint64_t) gt_encseq_num_of_sequences(query_encseq);
} else
{
gt_assert(query_encseq == NULL);
qsmi->seqit = gt_seq_iterator_sequence_buffer_new(query_files, err);
if (qsmi->seqit == NULL)
{
gt_querysubstringmatchiterator_delete(qsmi);
return NULL;
}
gt_seq_iterator_set_symbolmap(qsmi->seqit,
gt_alphabet_symbolmap(gt_encseq_alphabet(dbencseq)));
}
return qsmi;
}
static int extracttarget_from_seqfiles(const char *target,
GtStrArray *seqfiles,
GtError *err)
{
GtStr *unescaped_target;
char *escaped_target;
GtSplitter *splitter;
unsigned long i;
int had_err = 0;
gt_error_check(err);
gt_assert(target && seqfiles);
splitter = gt_splitter_new();
unescaped_target = gt_str_new();
escaped_target = gt_cstr_dup(target);
gt_splitter_split(splitter, escaped_target, strlen(escaped_target), ',');
for (i = 0; !had_err && i < gt_splitter_size(splitter); i++) {
GtSplitter *blank_splitter;
char *token = gt_splitter_get_token(splitter, i);
blank_splitter = gt_splitter_new();
gt_splitter_split(blank_splitter, token, strlen(token), ' ');
had_err = gt_gff3_unescape(unescaped_target,
gt_splitter_get_token(blank_splitter, 0),
strlen(gt_splitter_get_token(blank_splitter, 0)),
err);
if (!had_err) {
unsigned long j;
for (j = 0; j < gt_str_array_size(seqfiles); j++) {
unsigned long k;
GtBioseq *bioseq;
if (!(bioseq = gt_bioseq_new(gt_str_array_get(seqfiles, j), err))) {
had_err = -1;
break;
}
for (k = 0; k < gt_bioseq_number_of_sequences(bioseq); k++) {
TargetInfo target_info;
const char *desc = gt_bioseq_get_description(bioseq, k);
target_info.bioseq = bioseq;
target_info.seqnum = k;
gt_string_matching_bmh(desc, strlen(desc),
gt_str_get(unescaped_target),
gt_str_length(unescaped_target), show_target,
&target_info);
}
gt_bioseq_delete(bioseq);
}
}
gt_splitter_delete(blank_splitter);
}
gt_free(escaped_target);
gt_str_delete(unescaped_target);
gt_splitter_delete(splitter);
return had_err;
}
int gth_process_intermediate_files(GthInput *input, GtStrArray *consensusfiles,
GthSAProcessFunc saprocessfunc, void *data,
GthShowVerbose showverbose, GtError *err)
{
GtUword i;
GtFile *fp, *genfile;
int had_err = 0;
gt_error_check(err);
/* process all files */
if (gt_str_array_size(consensusfiles)) {
for (i = 0; !had_err && i < gt_str_array_size(consensusfiles); i++) {
/* open file */
fp = gt_file_xopen(gt_str_array_get(consensusfiles, i), "r");
if (showverbose) {
show_parse_file_status(showverbose, i,
gt_str_array_size(consensusfiles),
gt_str_array_get(consensusfiles, i));
}
had_err = gt_parse_intermediate_output(input, saprocessfunc, data,
gt_str_array_get(consensusfiles, i),
fp, err);
/* close file */
gt_file_delete(fp);
}
}
else {
genfile = gt_file_new_from_fileptr(stdin);
had_err = gt_parse_intermediate_output(input, saprocessfunc, data, "stdin",
genfile, err);
gt_file_delete_without_handle(genfile);
}
return had_err;
}
void vcfoutput_write(VcfOutput *v, ResultSet *r) {
gt_assert(v);
gt_assert(r);
GtStr *temp = gt_str_new();
unsigned long i =0;
unsigned long vcf_size = 0;
vcf_size = gt_str_array_size(resultset_get_vcf_array(r));
for(i=0;i<gt_str_array_size(resultset_get_vcf_array(r));i++) {
gt_str_set(temp, gt_str_array_get(resultset_get_vcf_array(r),i));
if(i == vcf_size-1) {
gt_str_append_cstr(temp,";");
if(resultset_get_exon(r) != 0) {
gt_str_append_cstr(temp,"EX;");
}
if(resultset_get_frms(r) != 0) {
gt_str_append_cstr(temp,"NSF;");
}
if(resultset_get_miss(r) != 0) {
gt_str_append_cstr(temp,"NSM;");
}
if(resultset_get_nons(r) != 0) {
gt_str_append_cstr(temp,"NSN;");
}
if(resultset_get_threeprime(r) != 0) {
gt_str_append_cstr(temp,"ASS;");
}
if(resultset_get_fiveprime(r) != 0) {
gt_str_append_cstr(temp,"DSS;");
}
}
gt_str_append_cstr(temp,"\t");
gt_file_xwrite(v->file,gt_str_get(temp),gt_str_length(temp));
gt_str_reset(temp);
}
gt_str_delete(temp);
}
GtTranslatorStatus gt_translator_find_codon(GtTranslator *translator,
GtStrArray *codons,
GtUword *pos,
GtError *err)
{
char n1, n2, n3;
unsigned int frame;
GtUword i;
GtCodonIteratorStatus retval;
gt_assert(translator && codons && pos);
gt_error_check(err);
for (i = 0; i<gt_str_array_size(codons); i++) {
int len;
if ((len = (int) strlen(gt_str_array_get(codons, i))) != GT_CODON_LENGTH) {
gt_error_set(err, "invalid codon length for codon %s: %d",
gt_str_array_get(codons, i), len);
return GT_TRANSLATOR_ERROR;
}
}
while (!(retval =
gt_codon_iterator_next(translator->ci,
&n1, &n2, &n3, &frame, err))) {
for (i = 0; i<gt_str_array_size(codons); i++) {
const char *codon;
codon = gt_str_array_get(codons, i);
if (n1 == codon[0] && n2 == codon[1] && n3 == codon[2]) {
*pos = gt_codon_iterator_current_position(translator->ci)-1;
return GT_TRANSLATOR_OK;
}
}
}
if (retval == GT_CODON_ITERATOR_END)
return GT_TRANSLATOR_END;
else
return GT_TRANSLATOR_ERROR;
}
static int gt_tyr_search_arguments_check(int rest_argc,
void *tool_arguments,
GtError *err)
{
Optionargmodedesc showmodedesctable[] =
{
{"qseqnum","query sequence number",SHOWQSEQNUM},
{"qpos","query position",SHOWQPOS},
{"counts","number of occurrence counts",SHOWCOUNTS},
{"sequence","mer-sequence",SHOWSEQUENCE}
};
Optionargmodedesc stranddesctable[] =
{
{"f","forward strand",STRAND_FORWARD},
{"p","reverse strand",STRAND_REVERSE},
{"fp","forward and reverse strand",STRAND_FORWARD | STRAND_REVERSE}
};
unsigned long idx;
Tyr_search_options *arguments = tool_arguments;
if (rest_argc != 0)
{
gt_error_set(err,"superfluous arguments");
return -1;
}
for (idx=0; idx<gt_str_array_size(arguments->showmodespec); idx++)
{
if (optionargaddbitmask(showmodedesctable,
sizeof (showmodedesctable)/
sizeof (showmodedesctable[0]),
&arguments->showmode,
"-output",
gt_str_array_get(arguments->showmodespec,idx),
err) != 0)
{
return -1;
}
}
if (optionargaddbitmask(stranddesctable,
sizeof (stranddesctable)/
sizeof (stranddesctable[0]),
&arguments->strand,
"-output",
gt_str_get(arguments->strandspec),err) != 0)
{
return -1;
}
return 0;
}
static int encseq_lua_filenames(lua_State *L)
{
GtEncseq **encseq;
const GtStrArray *filenames;
GtUword i;
encseq = check_encseq(L, 1);
filenames = gt_encseq_filenames(*encseq);
lua_newtable(L);
for (i = 0; i < gt_str_array_size(filenames); i++) {
lua_pushinteger(L, i+1); /* in Lua we index from 1 on */
lua_pushstring(L, gt_str_array_get(filenames, i));
lua_rawset(L, -3);
}
return 1;
}
static int sequence_node_add_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
GtError *err)
{
GtSequenceNodeAddStream *s;
int had_err;
gt_error_check(err);
s = gt_sequence_node_add_stream_cast(ns);
/* stream nodes as long as we have some, record seen seqids */
if (!(had_err = gt_node_stream_next(s->in_stream, gn, err)) && *gn) {
had_err = gt_genome_node_accept(*gn, s->collect_vis, err);
}
/* if there are no more */
if (!had_err && !*gn) {
if (!s->seqids) {
s->seqids = gt_cstr_table_get_all(s->seqid_table);
}
gt_assert(s->seqids);
if (s->cur_seqid >= gt_str_array_size(s->seqids)) {
*gn = NULL;
return 0;
} else {
GtGenomeNode *new_sn;
GtUword len;
char *seq = NULL;
GtStr *seqid = gt_str_new(),
*seqstr = gt_str_new();
gt_str_append_cstr(seqid, gt_str_array_get(s->seqids, s->cur_seqid));
had_err = gt_region_mapping_get_sequence_length(s->rm, &len, seqid, err);
if (!had_err) {
had_err = gt_region_mapping_get_sequence(s->rm, &seq, seqid, 1, len,
err);
}
if (!had_err) {
gt_str_append_cstr_nt(seqstr, seq, len);
new_sn = gt_sequence_node_new(gt_str_get(seqid), seqstr);
*gn = new_sn;
}
s->cur_seqid++;
gt_free(seq);
gt_str_delete(seqid);
gt_str_delete(seqstr);
}
}
return had_err;
}
int gt_trans_table_unit_test(GtError *err)
{
int had_err = 0;
GtStrArray *schemes;
gt_error_check(err);
/* check retrieval of table descriptions */
schemes = gt_trans_table_get_scheme_descriptions();
gt_ensure(
gt_str_array_size(schemes) == (GtUword) GT_NUMOFTRANSSCHEMES);
/* check switching translation scheme */
/* test_errnum = gt_translator_set_translation_scheme(tr, 3, test_err);
gt_ensure(!test_errnum && !gt_error_is_set(test_err)); */
/* check switching to invalid translation scheme */
/* test_errnum = gt_translator_set_translation_scheme(tr, 7, test_err);
gt_ensure(test_errnum && gt_error_is_set(test_err)); */
/* switch back to default translation scheme */
/* gt_error_unset(test_err);
test_errnum = gt_translator_set_translation_scheme(tr, 1, test_err);
gt_ensure(!test_errnum && !gt_error_is_set(test_err)); */
/* check single codon translation */
/*
* char *bases = "AaCcGgTt";
* gt_error_unset(test_err);
for (i=0; i<8; i++) {
char c1 = bases[i];
for (j=0; j<8; j++) {
char c2 = bases[j];
for (k=0; k<8; k++) {
char c3 = bases[k], ret1, ret2;
test_errnum = gt_translator_codon2amino(tr, c1, c2, c3, &ret1,
test_err);
gt_ensure(!test_errnum && !gt_error_is_set(test_err));
ret2 = gt_transa(tr->scheme->aminos, true, c1, c2, c3, NULL,
test_err);
gt_ensure(ret1 == ret2);
}
}
} */
return had_err;
}
int gt_esa2shulengthqueryfiles(unsigned long *totalgmatchlength,
const Suffixarray *suffixarray,
const GtStrArray *queryfilenames,
GtError *err)
{
bool haserr = false;
GtSeqIterator *seqit;
const GtUchar *query;
unsigned long querylen;
char *desc = NULL;
int retval;
GtAlphabet *alphabet;
gt_error_check(err);
alphabet = gt_encseq_alphabet(suffixarray->encseq);
gt_assert(gt_str_array_size(queryfilenames) == 1UL);
seqit = gt_seq_iterator_sequence_buffer_new(queryfilenames, err);
if (!seqit)
{
haserr = true;
}
if (!haserr)
{
gt_seq_iterator_set_symbolmap(seqit, gt_alphabet_symbolmap(alphabet));
for (; /* Nothing */; )
{
retval = gt_seq_iterator_next(seqit,
&query,
&querylen,
&desc,
err);
if (retval < 0)
{
haserr = true;
break;
}
if (retval == 0)
{
break;
}
*totalgmatchlength += gt_esa2shulengthquery(suffixarray,query,querylen);
}
gt_seq_iterator_delete(seqit);
}
return haserr ? -1 : 0;
}
static int m2i_change_target_seqids(GtFeatureNode *fn, const char *target,
GtRegionMapping *region_mapping,
GtError *err)
{
GtStrArray *target_ids;
GtArray *target_ranges, *target_strands;
GtStr *desc, *new_seqid;
unsigned long i;
int had_err;
gt_error_check(err);
gt_assert(fn && target && region_mapping);
target_ids = gt_str_array_new();
target_ranges = gt_array_new(sizeof (GtRange));
target_strands = gt_array_new(sizeof (GtStrand));
desc = gt_str_new();
new_seqid = gt_str_new();
had_err = gt_gff3_parser_parse_all_target_attributes(target, false,
target_ids,
target_ranges,
target_strands, "", 0,
err);
for (i = 0; !had_err && i < gt_str_array_size(target_ids); i++) {
GtStr *seqid;
gt_str_reset(desc);
gt_str_reset(new_seqid);
seqid = gt_str_array_get_str(target_ids, i);
had_err = gt_region_mapping_get_description(region_mapping, desc, seqid,
err);
if (!had_err)
gt_regular_seqid_save(new_seqid, desc);
gt_str_array_set(target_ids, i, new_seqid);
}
if (!had_err) {
GtStr *new_target = gt_str_new();
gt_gff3_parser_build_target_str(new_target, target_ids, target_ranges,
target_strands);
gt_feature_node_set_attribute(fn, GT_GFF_TARGET, gt_str_get(new_target));
gt_str_delete(new_target);
}
gt_str_delete(new_seqid);
gt_str_delete(desc);
gt_array_delete(target_strands);
gt_array_delete(target_ranges);
gt_str_array_delete(target_ids);
return had_err;
}
static int gt_encseq_encode_runner(GT_UNUSED int argc, const char **argv,
int parsed_args, GT_UNUSED void *tool_arguments,
GtError *err)
{
int had_err = 0,
i;
GtEncseqEncodeArguments *arguments =
(GtEncseqEncodeArguments*) tool_arguments;
GtStrArray *infiles;
gt_error_check(err);
infiles = gt_str_array_new();
for (i = parsed_args; i < argc; i++) {
gt_str_array_add_cstr(infiles, argv[i]);
}
if (gt_str_length(arguments->indexname) == 0UL) {
if (gt_str_array_size(infiles) > 1UL) {
gt_error_set(err,"if more than one input file is given, then "
"option -indexname is mandatory");
had_err = -1;
} else {
char *basenameptr;
basenameptr = gt_basename(gt_str_array_get(infiles, 0UL));
gt_str_set(arguments->indexname, basenameptr);
gt_free(basenameptr);
}
}
if (!had_err) {
gt_assert(gt_str_length(arguments->indexname) > 0UL);
had_err = encode_sequence_files(infiles,
arguments->eopts,
gt_str_get(arguments->indexname),
arguments->verbose,
arguments->no_esq_header,
err);
}
if (!had_err && arguments->showstats)
show_encoded_statistics(infiles, gt_str_get(arguments->indexname));
gt_str_array_delete(infiles);
return had_err;
}
int gt_mergeesa(int argc, const char **argv, GtError *err)
{
GtStr *storeindex;
GtStrArray *indexnametab;
bool haserr = false;
int parsed_args;
gt_error_check(err);
storeindex = gt_str_new();
indexnametab = gt_str_array_new();
switch (parse_options(storeindex, indexnametab, &parsed_args, argc, argv,
err)) {
case GT_OPTION_PARSER_OK:
break;
case GT_OPTION_PARSER_ERROR:
haserr = true;
break;
case GT_OPTION_PARSER_REQUESTS_EXIT:
return 0;
}
if (!haserr)
{
GtUword i;
GtLogger *logger;
printf("# storeindex=%s\n",gt_str_get(storeindex));
for (i=0; i<gt_str_array_size(indexnametab); i++)
{
printf("# input=%s\n",gt_str_array_get(indexnametab,i));
}
logger = gt_logger_new(false, GT_LOGGER_DEFLT_PREFIX, stdout);
if (gt_performtheindexmerging(storeindex,
indexnametab,
logger,
err) != 0)
{
haserr = true;
}
gt_logger_delete(logger);
}
gt_str_delete(storeindex);
gt_str_array_delete(indexnametab);
return haserr ? -1 : 0;
}
static int feature_in_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
GtError *error)
{
GtFeatureInStream *stream = feature_in_stream_cast(ns);
gt_error_check(error);
if (!stream->init)
{
feature_in_stream_init(stream);
stream->init = true;
}
if (gt_queue_size(stream->regioncache) > 0)
{
GtGenomeNode *region = gt_queue_get(stream->regioncache);
*gn = region;
return 0;
}
if (stream->featurecache == NULL || gt_array_size(stream->featurecache) == 0)
{
if (stream->featurecache != NULL)
{
gt_array_delete(stream->featurecache);
stream->featurecache = NULL;
}
if (stream->seqindex == gt_str_array_size(stream->seqids))
{
*gn = NULL;
return 0;
}
const char *seqid = gt_str_array_get(stream->seqids, stream->seqindex++);
stream->featurecache = gt_feature_index_get_features_for_seqid(stream->fi,
seqid,
error);
gt_array_sort(stream->featurecache, (GtCompare)gt_genome_node_compare);
gt_array_reverse(stream->featurecache);
}
GtGenomeNode *feat = *(GtGenomeNode **)gt_array_pop(stream->featurecache);
*gn = gt_genome_node_ref(feat);
return 0;
}
