GtHcrDecoder *gt_hcr_decoder_new(const char *name, GtAlphabet *alpha,
bool descs, GtTimer *timer, GtError *err)
{
GtHcrDecoder *hcr_dec;
int had_err = 0;
gt_error_check(err);
if (timer != NULL)
gt_timer_show_progress(timer, "initialize hcr decoder", stdout);
hcr_dec = gt_malloc(sizeof (GtHcrDecoder));
if (descs) {
hcr_dec->encdesc = gt_encdesc_load(name, err);
if (gt_error_is_set(err)) {
had_err = -1;
}
}
else
hcr_dec->encdesc = NULL;
if (!had_err) {
hcr_dec->seq_dec = hcr_seq_decoder_new(alpha, name, err);
if (!gt_error_is_set(err))
return hcr_dec;
}
gt_hcr_decoder_delete(hcr_dec);
return NULL;
}
GtStrArray* agn_seq_union(GtFeatureIndex *refrfeats, GtFeatureIndex *predfeats,
AgnLogger *logger)
{
// Fetch seqids from reference and prediction annotations
GtError *e = gt_error_new();
GtStrArray *refrseqids = gt_feature_index_get_seqids(refrfeats, e);
if(gt_error_is_set(e))
{
agn_logger_log_error(logger, "error fetching seqids for reference: %s",
gt_error_get(e));
gt_error_unset(e);
}
GtStrArray *predseqids = gt_feature_index_get_seqids(predfeats, e);
if(gt_error_is_set(e))
{
agn_logger_log_error(logger, "error fetching seqids for prediction: %s",
gt_error_get(e));
gt_error_unset(e);
}
gt_error_delete(e);
if(agn_logger_has_error(logger))
{
gt_str_array_delete(refrseqids);
gt_str_array_delete(predseqids);
return NULL;
}
GtStrArray *seqids = agn_gt_str_array_union(refrseqids, predseqids);
gt_str_array_delete(refrseqids);
gt_str_array_delete(predseqids);
return seqids;
}
FMindex *gt_loadvoidBWTSeqForSA(const char *indexname,
bool withpckbt,
GtError *err)
{
BWTSeq *bwtseq = NULL;
bool haserr = false;
GtEncseqMetadata *emd;
GtAlphabet *alphabet;
emd = gt_encseq_metadata_new(indexname, err);
if (emd == NULL) {
gt_assert(gt_error_is_set(err));
haserr = true;
}
if (!haserr) {
alphabet = gt_encseq_metadata_alphabet(emd);
if (alphabet == NULL)
{
gt_assert(gt_error_is_set(err));
haserr = true;
}
}
if (!haserr)
{
bwtseq = gt_loadBWTSeqForSA(indexname,
BWT_ON_BLOCK_ENC,
BWTDEFOPT_MULTI_QUERY,
alphabet,
err);
if (bwtseq == NULL)
{
gt_assert(gt_error_is_set(err));
haserr = true;
}
}
if (!haserr)
{
if (withpckbt && gt_pckbuckettable_exists(indexname))
{
unsigned int numofchars = gt_alphabet_num_of_chars(alphabet);
bwtseq->pckbuckettable = gt_pckbuckettable_map(indexname,numofchars,err);
if (bwtseq->pckbuckettable == NULL)
{
gt_assert(gt_error_is_set(err));
haserr = true;
}
} else
{
bwtseq->pckbuckettable = NULL;
}
}
gt_encseq_metadata_delete(emd);
if (haserr && bwtseq != NULL)
{
gt_deletevoidBWTSeq((FMindex *) bwtseq);
bwtseq = NULL;
}
return haserr ? NULL : (FMindex *) bwtseq;
}
static GtHcrSeqDecoder *hcr_seq_decoder_new(GtAlphabet *alpha, const char *name,
GtError *err)
{
GtHcrSeqDecoder *seq_dec = gt_malloc(sizeof (GtHcrSeqDecoder));
GtBaseQualDistr *bqd = NULL;
GtWord end_enc_start_sampling = 0;
FILE *fp = NULL;
GT_UNUSED size_t read,
one = (size_t) 1;
seq_dec->alpha = alpha;
seq_dec->alphabet_size = gt_alphabet_size(alpha);
seq_dec->cur_read = 0;
seq_dec->data_iter = NULL;
seq_dec->file_info_rbt = NULL;
seq_dec->fileinfos = NULL;
seq_dec->filename = gt_str_new_cstr(name);
seq_dec->huff_dec = NULL;
seq_dec->huffman = NULL;
seq_dec->sampling = NULL;
seq_dec->symbols = NULL;
gt_str_append_cstr(seq_dec->filename, HCRFILESUFFIX);
fp = gt_fa_fopen_with_suffix(name, HCRFILESUFFIX, "rb", err);
if (gt_error_is_set(err)) {
hcr_seq_decoder_delete(seq_dec);
seq_dec = NULL;
}
else {
hcr_read_file_info(seq_dec, fp);
bqd = hcr_base_qual_distr_new_from_file(fp, seq_dec->alpha);
seq_dec->qual_offset = bqd->qual_offset;
read = gt_xfread_one(&end_enc_start_sampling, fp);
gt_assert(read == one);
seq_dec->start_of_encoding = decoder_calc_start_of_encoded_data(fp);
seq_decoder_init_huffman(seq_dec, end_enc_start_sampling, bqd, err);
if (gt_error_is_set(err)) {
hcr_seq_decoder_delete(seq_dec);
seq_dec = NULL;
}
}
if (seq_dec != NULL) {
gt_xfseek(fp, end_enc_start_sampling, SEEK_SET);
seq_dec->sampling = gt_sampling_read(fp);
seq_dec->file_info_rbt = seq_decoder_init_file_info(seq_dec->fileinfos,
seq_dec->num_of_files);
}
hcr_base_qual_distr_delete(bqd);
gt_fa_fclose(fp);
return seq_dec;
}
static int canvas_cairo_file_lua_new_generic(lua_State *L, GtGraphicsOutType t)
{
GtCanvas **canvas;
GtImageInfo **ii;
unsigned int width,
height;
GtError *err;
GtStyle *style;
width = luaL_checkint(L, 1);
height = luaL_checkint(L, 2);
/* create canvas */
style = gt_lua_get_style_from_registry(L);
canvas = lua_newuserdata(L, sizeof (GtCanvas*));
gt_assert(canvas);
/* if a imageinfo object is passed, it must be correct type */
if (lua_isnil(L, 3)) {
err = gt_error_new();
*canvas = gt_canvas_cairo_file_new(style, t, width, height, NULL, err);
} else {
ii = check_imageinfo(L, 3);
err = gt_error_new();
*canvas = gt_canvas_cairo_file_new(style, t, width, height, *ii, err);
}
if (gt_error_is_set(err))
return gt_lua_error(L, err);
gt_error_delete(err);
luaL_getmetatable(L, CANVAS_METATABLE);
lua_setmetatable(L, -2);
return 1;
}
GtIntset *gt_intset_io(GtIntset *intset, FILE *fp, GtError *err)
{
int had_err = 0;
GtUword type;
if (intset == NULL) {
had_err = gt_intset_read_type_rewind(fp, &type, err);
if (!had_err && gt_intset_8_file_is_type(type))
intset = gt_intset_8_io(intset, fp, err);
else {
if (!had_err && gt_intset_16_file_is_type(type))
intset = gt_intset_16_io(intset, fp, err);
else {
if (!had_err && gt_intset_32_file_is_type(type))
intset = gt_intset_32_io(intset, fp, err);
else {
if (!gt_error_is_set(err))
gt_error_set(err, "could not identify intset type from file");
}
}
}
}
else {
gt_assert(intset->c_class != NULL);
gt_assert(intset->c_class->io_func != NULL);
intset = intset->c_class->io_func(intset, fp, err);
}
return intset;
}
GtAlphabet* gt_alphabet_new_from_string(const char *alphadef, unsigned long len,
GtError *err)
{
unsigned long i, j;
GtStrArray *sa;
GtAlphabet *alpha;
gt_assert(alphadef && len > 0);
gt_error_check(err);
alpha = gt_alphabet_new_empty();
gt_assert(alphadef);
sa = gt_str_array_new();
j = 0;
for (i = 0; i < len; i++) {
if (alphadef[i] == '\n' || i == len - 1) {
gt_str_array_add_cstr_nt(sa, alphadef+j, i - j);
j = i+1;
}
}
if (read_symbolmap_from_lines(alpha, NULL, sa, err) != 0) {
gt_str_array_delete(sa);
gt_assert(gt_error_is_set(err));
return NULL;
}
gt_str_array_delete(sa);
return alpha;
}
int gt_lua_error(lua_State *L, GtError *err)
{
gt_assert(L && err);
gt_assert(gt_error_is_set(err));
luaL_where(L, 1);
lua_pushstring(L, gt_error_get(err));
gt_error_delete(err);
lua_concat(L, 2);
return lua_error(L);
}
GtEncseqMetadata* gt_encseq_metadata_new(const char *indexname, GtError *err)
{
int had_err = 0;
GtEncseqMetadata *encseq_metadata;
gt_assert(indexname);
encseq_metadata = gt_malloc(sizeof (GtEncseqMetadata));
encseq_metadata->alpha = NULL;
encseq_metadata->customalphabet = false;
had_err = readfirstvaluesfromfile(encseq_metadata, indexname, err);
if (had_err) {
gt_assert(gt_error_is_set(err));
gt_free(encseq_metadata);
encseq_metadata = NULL;
}
return encseq_metadata;
}
static int feature_index_lua_get_first_seqid(lua_State *L)
{
GtFeatureIndex **feature_index;
char *seqid;
GtError *err;
feature_index = check_feature_index(L, 1);
err = gt_error_new();
seqid = gt_feature_index_get_first_seqid(*feature_index, err);
if (gt_error_is_set(err))
return gt_lua_error(L, err);
gt_error_delete(err);
if (seqid) {
lua_pushstring(L, seqid);
gt_free(seqid);
} else
lua_pushnil(L);
return 1;
}
GtAlphabet* gt_alphabet_new_from_sequence(const GtStrArray *filenametab,
GtError *err)
{
GtAlphabet *alpha;
int had_err = 0;
gt_error_check(err);
alpha = gt_alphabet_new_empty();
if (assign_protein_or_dna_alphabet(alpha,filenametab,err) != 0) {
had_err = -1;
gt_assert(gt_error_is_set(err));
}
if (had_err)
{
gt_alphabet_delete(alpha);
return NULL;
}
return alpha;
}
int gt_tooldriver(int(*tool)(int argc, const char **argv, GtError*),
int argc, char *argv[])
{
GtError *err;
int had_err;
gt_allocators_init();
err = gt_error_new();
gt_error_set_progname(err, argv[0]);
had_err = tool(argc, (const char**) argv, err);
if (gt_error_is_set(err)) {
fprintf(stderr, "%s: error: %s\n", gt_error_get_progname(err),
gt_error_get(err));
gt_assert(had_err);
}
gt_error_delete(err);
if (gt_allocators_clean())
return 2; /* programmer error */
if (had_err)
return EXIT_FAILURE;
return EXIT_SUCCESS;
}
static int layout_lua_new(lua_State *L)
{
GtLayout **layout;
GtDiagram **diagram;
unsigned int width;
GtStyle *style;
GtError *err;
diagram = check_diagram(L, 1);
width = luaL_checkint(L, 2);
/* create layout */
style = gt_lua_get_style_from_registry(L);
layout = lua_newuserdata(L, sizeof (GtLayout*));
gt_assert(layout);
err = gt_error_new();
*layout = gt_layout_new(*diagram, width, style, err);
if (gt_error_is_set(err))
return gt_lua_error(L, err);
gt_error_delete(err);
luaL_getmetatable(L, LAYOUT_METATABLE);
lua_setmetatable(L, -2);
return 1;
}
int gt_toolobjdriver(GtToolConstructor tool_constructor, int argc, char *argv[])
{
GtTool *tool;
GtError *err;
int had_err;
gt_allocators_init();
err = gt_error_new();
gt_error_set_progname(err, argv[0]);
tool = tool_constructor();
had_err = gt_tool_run(tool, argc, (const char**) argv, err);
gt_tool_delete(tool);
if (gt_error_is_set(err)) {
fprintf(stderr, "%s: error: %s\n", gt_error_get_progname(err),
gt_error_get(err));
gt_assert(had_err);
}
gt_error_delete(err);
if (gt_allocators_clean())
return 2; /* programmer error */
if (had_err)
return EXIT_FAILURE;
return EXIT_SUCCESS;
}
int gt_hcr_decoder_decode(GtHcrDecoder *hcr_dec, GtUword readnum,
char *seq, char *qual, GtStr *desc, GtError *err)
{
GtUword nearestsample = 0,
reads_to_read = 0,
idx,
current_read = hcr_dec->seq_dec->cur_read ;
size_t startofnearestsample = 0;
GtSampling *sampling;
HcrHuffDataIterator *data_iter;
GtHuffmanDecoder *huff_dec;
gt_error_check(err);
gt_assert(hcr_dec);
gt_assert(readnum < hcr_dec->seq_dec->num_of_reads);
gt_assert(seq != NULL && qual != NULL);
if (current_read == readnum) {
if (hcr_next_seq_qual(hcr_dec->seq_dec, seq, qual, err) == -1) {
gt_assert(gt_error_is_set(err));
return -1;
}
}
else {
sampling = hcr_dec->seq_dec->sampling;
data_iter = hcr_dec->seq_dec->data_iter;
huff_dec = hcr_dec->seq_dec->huff_dec;
if (sampling != NULL) {
gt_sampling_get_page(sampling,
readnum,
&nearestsample,
&startofnearestsample);
/* nearestsample <= cur_read < readnum: current sample is the right one */
if (nearestsample <= current_read && current_read <= readnum)
reads_to_read = readnum - current_read;
else { /* reset decoder to new sample */
reset_data_iterator_to_pos(data_iter, startofnearestsample);
(void) gt_huffman_decoder_get_new_mem_chunk(huff_dec, err);
if (gt_error_is_set(err))
return -1;
reads_to_read = readnum - nearestsample;
hcr_dec->seq_dec->cur_read = nearestsample;
}
gt_log_log("reads to read: "GT_WU", nearest sample: "GT_WU"",
reads_to_read,nearestsample);
gt_log_log("start of nearest: "GT_WU"", (GtUword) startofnearestsample);
}
else {
if (current_read <= readnum)
reads_to_read = readnum - current_read;
else {
reset_data_iterator_to_start(data_iter);
(void) gt_huffman_decoder_get_new_mem_chunk(huff_dec, err);
if (gt_error_is_set(err))
return -1;
reads_to_read = readnum;
hcr_dec->seq_dec->cur_read = 0;
}
}
for (idx = 0; idx < reads_to_read; idx++) {
if (hcr_next_seq_qual(hcr_dec->seq_dec, seq,qual, err) == -1) {
gt_assert(gt_error_is_set(err));
return -1;
}
gt_log_log("seq:\n%s\nqual:\n%s", seq, qual);
}
if (hcr_next_seq_qual(hcr_dec->seq_dec, seq, qual, err) == -1) {
gt_assert(gt_error_is_set(err));
return -1;
}
}
if (hcr_dec->encdesc != NULL) {
if (gt_encdesc_decode(hcr_dec->encdesc, readnum, desc, err) == -1) {
gt_error_set(err, "cannot retrieve description with number "GT_WU"."
"(%d)", readnum, __LINE__);
return -1;
}
}
return 0;
}
static int gt_ltrdigest_runner(GT_UNUSED int argc, const char **argv,
int parsed_args, void *tool_arguments,
GtError *err)
{
GtLTRdigestOptions *arguments = tool_arguments;
GtNodeStream *gff3_in_stream = NULL,
*gff3_out_stream = NULL,
*ltrdigest_stream = NULL,
*tab_out_stream = NULL,
*last_stream = NULL;
int had_err = 0,
tests_to_run = 0,
arg = parsed_args;
const char *indexname = argv[arg+1];
GtLogger *logger = gt_logger_new(arguments->verbose,
GT_LOGGER_DEFLT_PREFIX, stdout);
GtEncseqLoader *el;
GtEncseq *encseq;
gt_error_check(err);
gt_assert(arguments);
/* Set sequence encoder options. Defaults are ok. */
el = gt_encseq_loader_new();
gt_encseq_loader_set_logger(el, logger);
/* Open sequence file */
encseq = gt_encseq_loader_load(el, indexname, err);
if (!encseq)
had_err = -1;
/* Always search for PPT. */
tests_to_run |= GT_LTRDIGEST_RUN_PPT;
/* Open tRNA library if given. */
if (!had_err && arguments->trna_lib
&& gt_str_length(arguments->trna_lib) > 0)
{
tests_to_run |= GT_LTRDIGEST_RUN_PBS;
arguments->pbs_opts.trna_lib = gt_bioseq_new(gt_str_get(arguments->trna_lib),
err);
if (gt_error_is_set(err))
had_err = -1;
}
#ifdef HAVE_HMMER
/* Open HMMER files if given. */
if (!had_err && gt_str_array_size(arguments->pdom_opts.hmm_files) > 0)
{
tests_to_run |= GT_LTRDIGEST_RUN_PDOM;
if (!strcmp(gt_str_get(arguments->cutoffs), "GA")) {
arguments->pdom_opts.cutoff = GT_PHMM_CUTOFF_GA;
} else if (!strcmp(gt_str_get(arguments->cutoffs), "TC")) {
arguments->pdom_opts.cutoff = GT_PHMM_CUTOFF_TC;
} else if (!strcmp(gt_str_get(arguments->cutoffs), "NONE")) {
arguments->pdom_opts.cutoff = GT_PHMM_CUTOFF_NONE;
} else {
gt_error_set(err, "invalid cutoff setting!");
had_err = -1;
}
}
#endif
if (!had_err)
{
/* set up stream flow
* ------------------*/
last_stream = gff3_in_stream = gt_gff3_in_stream_new_sorted(argv[arg]);
last_stream = ltrdigest_stream = gt_ltrdigest_stream_new(last_stream,
tests_to_run,
encseq,
&arguments->pbs_opts,
&arguments->ppt_opts,
#ifdef HAVE_HMMER
&arguments->pdom_opts,
#endif
err);
if (!ltrdigest_stream)
had_err = -1;
}
if (!had_err)
{
/* attach tabular output stream, if requested */
if (gt_str_length(arguments->prefix) > 0)
{
last_stream = tab_out_stream = gt_ltr_fileout_stream_new(last_stream,
tests_to_run,
encseq,
gt_str_get(arguments->prefix),
&arguments->ppt_opts,
&arguments->pbs_opts,
#ifdef HAVE_HMMER
&arguments->pdom_opts,
#endif
gt_str_get(arguments->trna_lib),
argv[arg+1],
argv[arg],
arguments->seqnamelen,
err);
#ifdef HAVE_HMMER
if (&arguments->pdom_opts.write_alignments)
gt_ltr_fileout_stream_enable_pdom_alignment_output(tab_out_stream);
if (&arguments->pdom_opts.write_aaseqs)
gt_ltr_fileout_stream_enable_aa_sequence_output(tab_out_stream);
#endif
}
last_stream = gff3_out_stream = gt_gff3_out_stream_new(last_stream,
arguments->outfp);
/* pull the features through the stream and free them afterwards */
had_err = gt_node_stream_pull(last_stream, err);
}
gt_node_stream_delete(gff3_out_stream);
gt_node_stream_delete(ltrdigest_stream);
if (tab_out_stream != NULL)
gt_node_stream_delete(tab_out_stream);
gt_node_stream_delete(gff3_in_stream);
gt_encseq_loader_delete(el);
gt_encseq_delete(encseq);
encseq = NULL;
gt_bioseq_delete(arguments->pbs_opts.trna_lib);
gt_logger_delete(logger);
return had_err;
}
static int bioseq_fill(GtBioseq *bs, bool recreate, GtError *err)
{
GtStr *bioseq_index_file = NULL,
*bioseq_ois_file = NULL,
*bioseq_sds_file = NULL,
*bioseq_md5_file = NULL,
*bioseq_des_file = NULL;
int had_err = 0;
GtStr *bioseq_basename;
gt_assert(!bs->encseq);
if (bs->use_stdin)
bioseq_basename = gt_str_new_cstr("stdin");
else
bioseq_basename = bs->sequence_file;
/* construct file names */
bioseq_index_file = gt_str_clone(bioseq_basename);
gt_str_append_cstr(bioseq_index_file, GT_ENCSEQFILESUFFIX);
bioseq_ois_file = gt_str_clone(bioseq_basename);
gt_str_append_cstr(bioseq_ois_file, GT_OISTABFILESUFFIX);
bioseq_sds_file = gt_str_clone(bioseq_basename);
gt_str_append_cstr(bioseq_sds_file, GT_SDSTABFILESUFFIX);
bioseq_md5_file = gt_str_clone(bioseq_basename);
gt_str_append_cstr(bioseq_md5_file, GT_MD5TABFILESUFFIX);
bioseq_des_file = gt_str_clone(bioseq_basename);
gt_str_append_cstr(bioseq_des_file, GT_DESTABFILESUFFIX);
/* construct the bioseq files if necessary */
if (recreate || bs->use_stdin ||
!gt_file_exists(gt_str_get(bioseq_index_file)) ||
!gt_file_exists(gt_str_get(bioseq_ois_file)) ||
!gt_file_exists(gt_str_get(bioseq_sds_file)) ||
!gt_file_exists(gt_str_get(bioseq_md5_file)) ||
!gt_file_exists(gt_str_get(bioseq_des_file)) ||
gt_file_is_newer(gt_str_get(bs->sequence_file),
gt_str_get(bioseq_index_file))) {
had_err = construct_bioseq_files(bs, bioseq_basename, err);
}
if (!had_err) {
GtEncseqLoader *el = gt_encseq_loader_new();
gt_encseq_loader_disable_autosupport(el);
gt_encseq_loader_require_lossless_support(el);
gt_encseq_loader_require_description_support(el);
gt_encseq_loader_require_md5_support(el);
gt_encseq_loader_require_multiseq_support(el);
bs->encseq = gt_encseq_loader_load(el, gt_str_get(bioseq_basename), err);
if (bs->encseq == NULL) {
had_err = -1;
gt_assert(gt_error_is_set(err));
}
gt_encseq_loader_delete(el);
}
if (!had_err) {
gt_assert(bs->encseq);
}
/* free */
if (bs->use_stdin)
gt_str_delete(bioseq_basename);
gt_str_delete(bioseq_index_file);
gt_str_delete(bioseq_ois_file);
gt_str_delete(bioseq_md5_file);
gt_str_delete(bioseq_sds_file);
gt_str_delete(bioseq_des_file);
return had_err;
}
static void* gt_feature_index_unit_test_query(void *data)
{
GtFeatureIndexTestShared *shm = (GtFeatureIndexTestShared*) data;
GtRange rng;
GtError *err = shm->err;
GtUword i;
int had_err = 0;
GtArray *arr, *arr_ref;
gt_mutex_lock(shm->mutex);
if (gt_error_is_set(shm->err)) {
gt_mutex_unlock(shm->mutex);
return NULL;
}
gt_mutex_unlock(shm->mutex);
arr = gt_array_new(sizeof (GtFeatureNode*));
arr_ref = gt_array_new(sizeof (GtFeatureNode*));
rng.start = random() % (GT_FI_TEST_END - GT_FI_TEST_QUERY_WIDTH);
rng.end = rng.start + random() % (GT_FI_TEST_QUERY_WIDTH);
/* get reference set by linear search */
gt_mutex_lock(shm->mutex);
for (i=0; i<GT_FI_TEST_FEATURES_PER_THREAD * gt_jobs; i++) {
GtRange rng2;
GtFeatureNode *fn;
fn = *(GtFeatureNode**) gt_array_get(shm->nodes, i);
rng2 = gt_genome_node_get_range((GtGenomeNode*) fn);
if (gt_range_overlap(&rng, &rng2)) {
gt_array_add(arr_ref, fn);
}
}
gt_mutex_unlock(shm->mutex);
/* query feature index */
gt_feature_index_get_features_for_range(shm->fi, arr, GT_FI_TEST_SEQID, &rng,
err);
/* result size must be equal */
if (gt_array_size(arr) != gt_array_size(arr_ref))
had_err = -1;
/* nodes must be the same (note that we should not rely on ptr equality) */
if (!had_err) {
gt_array_sort(arr_ref, cmp_range_start);
gt_array_sort(arr , cmp_range_start);
for (i=0;i<gt_array_size(arr);i++) {
if (had_err)
break;
if (!gt_feature_node_is_similar(*(GtFeatureNode**) gt_array_get(arr, i),
*(GtFeatureNode**)
gt_array_get(arr_ref, i))) {
had_err = -1;
}
}
}
if (had_err) {
gt_mutex_lock(shm->mutex);
shm->error_count++;
gt_mutex_unlock(shm->mutex);
}
gt_array_delete(arr);
gt_array_delete(arr_ref);
return NULL;
}
int gt_canvas_cairo_visit_element(GtCanvas *canvas, GtElement *elem,
GtError *err)
{
int had_err = 0, arrow_status = ARROW_NONE;
GtRange elem_range = gt_element_get_range(elem);
GtDrawingRange draw_range;
double elem_start = GT_UNDEF_DOUBLE,
elem_width = GT_UNDEF_DOUBLE,
stroke_width = STROKE_WIDTH_DEFAULT,
bar_height = BAR_HEIGHT_DEFAULT,
arrow_width = ARROW_WIDTH_DEFAULT;
GtColor elem_color, grey, fill_color;
const char *type;
GtStyleQueryStatus rval;
GtStr *style;
GtStrand strand = gt_element_get_strand(elem);
gt_assert(canvas && elem);
/* This shouldn't happen. */
if (!gt_range_overlap(&elem_range, &canvas->pvt->viewrange))
return -1;
type = gt_element_get_type(elem);
grey.red = grey.green = grey.blue = .85;
grey.alpha = 0.5;
/* get default or image-wide bar height */
if (gt_style_get_num(canvas->pvt->sty, "format", "bar_height", &bar_height,
NULL, err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
/* try to get type-specific bar height */
if (gt_style_get_num_with_track(canvas->pvt->sty, type, "bar_height",
&bar_height,
gt_element_get_node_ref(elem),
gt_track_get_title(canvas->pvt->current_track),
err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
/* get default or image-wide arrow width */
if (gt_style_get_num(canvas->pvt->sty, "format", "arrow_width", &arrow_width,
NULL, err)== GT_STYLE_QUERY_ERROR) {
return -1;
}
/* try to get type-specific arrow width */
if (gt_style_get_num_with_track(canvas->pvt->sty, type, "arrow_width",
&arrow_width,
gt_element_get_node_ref(elem),
gt_track_get_title(canvas->pvt->current_track),
err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if ((strand == GT_STRAND_REVERSE || strand == GT_STRAND_BOTH)
/*&& delem == gt_dlist_first(elems)*/)
arrow_status = ARROW_LEFT;
if ((strand == GT_STRAND_FORWARD || strand == GT_STRAND_BOTH)
/*&& gt_dlistelem_next(delem) == NULL*/)
arrow_status = (arrow_status == ARROW_LEFT ? ARROW_BOTH : ARROW_RIGHT);
gt_log_log("processing element from %lu to %lu, strand %d\n",
elem_range.start, elem_range.end, (int) strand);
draw_range = gt_coords_calc_generic_range(elem_range, canvas->pvt->viewrange);
draw_range.start *= (canvas->pvt->width-2*canvas->pvt->margins);
draw_range.end *= (canvas->pvt->width-2*canvas->pvt->margins);
elem_start = draw_range.start + canvas->pvt->margins;
elem_width = draw_range.end - draw_range.start;
gt_assert(elem_start != GT_UNDEF_DOUBLE && elem_width != GT_UNDEF_DOUBLE);
if (gt_element_is_marked(elem)) {
if (gt_style_get_color_with_track(canvas->pvt->sty, type, "stroke_marked",
&elem_color, gt_element_get_node_ref(elem),
gt_track_get_title(canvas->pvt->current_track),
err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if (gt_style_get_num_with_track(canvas->pvt->sty, "format",
"stroke_marked_width",
&stroke_width, gt_element_get_node_ref(elem),
gt_track_get_title(canvas->pvt->current_track),
err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
}
else {
if (gt_style_get_color_with_track(canvas->pvt->sty, type, "stroke",
&elem_color,
gt_element_get_node_ref(elem),
gt_track_get_title(canvas->pvt->current_track),
err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if (gt_style_get_num_with_track(canvas->pvt->sty, "format", "stroke_width",
&stroke_width,
gt_element_get_node_ref(elem),
gt_track_get_title(canvas->pvt->current_track),
err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if (gt_style_get_num_with_track(canvas->pvt->sty, type, "stroke_width",
&stroke_width,
gt_element_get_node_ref(elem),
gt_track_get_title(canvas->pvt->current_track),
err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
}
if (gt_style_get_color_with_track(canvas->pvt->sty, type, "fill",
&fill_color,
gt_element_get_node_ref(elem),
gt_track_get_title(canvas->pvt->current_track),
err) == GT_STYLE_QUERY_ERROR) {
return -1;
}
if (canvas->pvt->bt &&
gt_double_smaller_double(draw_range.end-draw_range.start, 1.1))
{
if ((unsigned long) draw_range.start > gt_bittab_size(canvas->pvt->bt))
return had_err;
if (gt_bittab_bit_is_set(canvas->pvt->bt, (unsigned long) draw_range.start))
return had_err;
gt_graphics_draw_vertical_line(canvas->pvt->g,
elem_start,
canvas->pvt->y - bar_height/2,
elem_color,
bar_height,
stroke_width);
gt_bittab_set_bit(canvas->pvt->bt, (unsigned long) draw_range.start);
}
/* register coordinates in GtImageInfo object if available */
if (canvas->pvt->ii)
{
GtRecMap *rm = gt_rec_map_new(elem_start, canvas->pvt->y - bar_height/2,
elem_start+elem_width,
canvas->pvt->y+bar_height/2,
(GtFeatureNode*)
gt_element_get_node_ref(elem));
gt_image_info_add_rec_map(canvas->pvt->ii, rm);
}
if (canvas->pvt->bt && draw_range.end-draw_range.start <= 1.1)
{
return had_err;
}
gt_log_log("drawing element from %f to %f, arrow status: %d",
draw_range.start, draw_range.end, arrow_status);
/* draw each element according to style set in the style */
style = gt_str_new();
rval = gt_style_get_str_with_track(canvas->pvt->sty, type, "style", style,
gt_element_get_node_ref(elem),
gt_track_get_title(canvas->pvt->current_track),
err);
switch (rval) {
case GT_STYLE_QUERY_NOT_SET:
gt_str_set(style, "box"); /* default style */
break;
case GT_STYLE_QUERY_ERROR:
gt_str_delete(style);
gt_assert(gt_error_is_set(err));
return -1;
default:
break;
}
if (strcmp(gt_str_get(style), "box") == 0)
{
gt_graphics_draw_box(canvas->pvt->g,
elem_start,
canvas->pvt->y - bar_height/2,
elem_width,
bar_height,
fill_color,
arrow_status,
arrow_width,
stroke_width,
elem_color,
false);
}
else if (strcmp(gt_str_get(style), "rectangle") == 0)
{
gt_graphics_draw_box(canvas->pvt->g,
elem_start,
canvas->pvt->y - bar_height/2,
elem_width,
bar_height,
fill_color,
ARROW_NONE,
arrow_width,
stroke_width,
elem_color,
false);
}
else if (strcmp(gt_str_get(style), "caret") == 0)
{
gt_graphics_draw_caret(canvas->pvt->g,
elem_start,
canvas->pvt->y - bar_height/2,
elem_width,
bar_height,
ARROW_NONE,
arrow_width,
stroke_width,
elem_color);
}
else if (strcmp(gt_str_get(style), "dashes") == 0)
{
gt_graphics_draw_dashes(canvas->pvt->g,
elem_start,
canvas->pvt->y - bar_height/2,
elem_width,
bar_height,
arrow_status,
arrow_width,
stroke_width,
elem_color);
}
else if (strcmp(gt_str_get(style), "line") == 0)
{
gt_graphics_draw_horizontal_line(canvas->pvt->g,
elem_start,
canvas->pvt->y - bar_height/2,
elem_color,
elem_width,
1.0);
}
else
{
gt_graphics_draw_box(canvas->pvt->g,
elem_start,
canvas->pvt->y - bar_height/2,
elem_width,
bar_height,
fill_color,
arrow_status,
arrow_width,
stroke_width,
elem_color,
false);
}
gt_str_delete(style);
/* draw arrowheads at clipped margins */
if (draw_range.clip == CLIPPED_LEFT || draw_range.clip == CLIPPED_BOTH)
gt_graphics_draw_arrowhead(canvas->pvt->g,
canvas->pvt->margins - 10,
canvas->pvt->y - 4,
grey,
ARROW_LEFT);
if (draw_range.clip == CLIPPED_RIGHT || draw_range.clip == CLIPPED_BOTH)
gt_graphics_draw_arrowhead(canvas->pvt->g,
canvas->pvt->width-canvas->pvt->margins + 10,
canvas->pvt->y - 4,
grey,
ARROW_RIGHT);
return had_err;
}
static int gt_ltrdigest_runner(GT_UNUSED int argc, const char **argv,
int parsed_args, void *tool_arguments,
GtError *err)
{
GtLTRdigestOptions *arguments = tool_arguments;
GtNodeStream *gff3_in_stream = NULL,
*gff3_out_stream = NULL,
*pdom_stream = NULL,
*ppt_stream = NULL,
*pbs_stream = NULL,
*tab_out_stream = NULL,
*sa_stream = NULL,
*last_stream = NULL;
int had_err = 0,
tests_to_run = 0,
arg = parsed_args;
GtRegionMapping *rmap = NULL;
GtPdomModelSet *ms = NULL;
gt_error_check(err);
gt_assert(arguments);
/* determine and open sequence source */
if (gt_seqid2file_option_used(arguments->s2fi)) {
/* create region mapping */
rmap = gt_seqid2file_region_mapping_new(arguments->s2fi, err);
if (!rmap)
had_err = -1;
} else {
GtEncseqLoader *el;
GtEncseq *encseq;
/* no new-style sequence source option given, fall back to legacy syntax */
if (argc < 3) {
gt_error_set(err, "missing mandatory argument(s)");
had_err = -1;
}
if (!had_err) {
el = gt_encseq_loader_new();
gt_encseq_loader_disable_autosupport(el);
gt_encseq_loader_require_md5_support(el);
gt_encseq_loader_require_description_support(el);
encseq = gt_encseq_loader_load(el, argv[argc-1], err);
/* XXX: clip off terminal argument */
gt_free((char*) argv[argc-1]);
argv[argc-1] = NULL;
argc--;
gt_encseq_loader_delete(el);
if (!encseq)
had_err = -1;
else {
rmap = gt_region_mapping_new_encseq_seqno(encseq);
gt_encseq_delete(encseq);
}
}
}
gt_assert(had_err || rmap);
/* Always search for PPT. */
tests_to_run |= GT_LTRDIGEST_RUN_PPT;
/* Open tRNA library if given. */
if (!had_err && arguments->trna_lib
&& gt_str_length(arguments->trna_lib) > 0)
{
tests_to_run |= GT_LTRDIGEST_RUN_PBS;
arguments->trna_lib_bs = gt_bioseq_new(gt_str_get(arguments->trna_lib),
err);
if (gt_error_is_set(err))
had_err = -1;
}
/* Set HMMER cutoffs. */
if (!had_err && gt_str_array_size(arguments->hmm_files) > 0)
{
tests_to_run |= GT_LTRDIGEST_RUN_PDOM;
if (!strcmp(gt_str_get(arguments->cutoffs), "GA")) {
arguments->cutoff = GT_PHMM_CUTOFF_GA;
} else if (!strcmp(gt_str_get(arguments->cutoffs), "TC")) {
arguments->cutoff = GT_PHMM_CUTOFF_TC;
} else if (!strcmp(gt_str_get(arguments->cutoffs), "NONE")) {
arguments->cutoff = GT_PHMM_CUTOFF_NONE;
} else {
gt_error_set(err, "invalid cutoff setting!");
had_err = -1;
}
}
if (!had_err) {
last_stream = gff3_in_stream = gt_gff3_in_stream_new_sorted(argv[arg]);
}
if (!had_err && gt_str_array_size(arguments->hmm_files) > 0) {
GtNodeVisitor *pdom_v;
ms = gt_pdom_model_set_new(arguments->hmm_files, err);
if (ms != NULL) {
pdom_v = gt_ltrdigest_pdom_visitor_new(ms, arguments->evalue_cutoff,
arguments->chain_max_gap_length,
arguments->cutoff, rmap, err);
if (pdom_v == NULL)
had_err = -1;
if (!had_err) {
gt_ltrdigest_pdom_visitor_set_source_tag((GtLTRdigestPdomVisitor*)
pdom_v,
GT_LTRDIGEST_TAG);
if (arguments->output_all_chains)
gt_ltrdigest_pdom_visitor_output_all_chains((GtLTRdigestPdomVisitor*)
pdom_v);
last_stream = pdom_stream = gt_visitor_stream_new(last_stream, pdom_v);
}
} else had_err = -1;
}
if (!had_err && arguments->trna_lib_bs) {
GtNodeVisitor *pbs_v;
pbs_v = gt_ltrdigest_pbs_visitor_new(rmap, arguments->pbs_radius,
arguments->max_edist,
arguments->alilen,
arguments->offsetlen,
arguments->trnaoffsetlen,
arguments->ali_score_match,
arguments->ali_score_mismatch,
arguments->ali_score_insertion,
arguments->ali_score_deletion,
arguments->trna_lib_bs, err);
if (pbs_v != NULL)
last_stream = pbs_stream = gt_visitor_stream_new(last_stream, pbs_v);
else
had_err = -1;
}
if (!had_err) {
GtNodeVisitor *ppt_v;
ppt_v = gt_ltrdigest_ppt_visitor_new(rmap, arguments->ppt_len,
arguments->ubox_len,
arguments->ppt_pyrimidine_prob,
arguments->ppt_purine_prob,
arguments->bkg_a_prob,
arguments->bkg_g_prob,
arguments->bkg_t_prob,
arguments->bkg_c_prob,
arguments->ubox_u_prob,
arguments->ppt_radius,
arguments->max_ubox_dist, err);
if (ppt_v != NULL)
last_stream = ppt_stream = gt_visitor_stream_new(last_stream, ppt_v);
else
had_err = -1;
}
if (!had_err) {
GtNodeVisitor *sa_v;
sa_v = gt_ltrdigest_strand_assign_visitor_new();
gt_assert(sa_v);
last_stream = sa_stream = gt_visitor_stream_new(last_stream, sa_v);
}
if (!had_err)
{
/* attach tabular output stream, if requested */
if (gt_str_length(arguments->prefix) > 0)
{
last_stream = tab_out_stream = gt_ltrdigest_file_out_stream_new(
last_stream,
tests_to_run,
rmap,
gt_str_get(arguments->prefix),
arguments->seqnamelen,
err);
if (!tab_out_stream)
had_err = -1;
if (!had_err && arguments->print_metadata)
{
had_err = gt_ltrdigest_file_out_stream_write_metadata(
(GtLTRdigestFileOutStream*)
tab_out_stream,
tests_to_run,
gt_str_get(arguments->trna_lib),
argv[arg],
arguments->ppt_len,
arguments->ubox_len,
arguments->ppt_radius,
arguments->alilen,
arguments->max_edist,
arguments->offsetlen,
arguments->trnaoffsetlen,
arguments->pbs_radius,
arguments->hmm_files,
arguments->chain_max_gap_length,
arguments->evalue_cutoff,
err);
}
if (!had_err)
{
if (arguments->write_alignments)
gt_ltrdigest_file_out_stream_enable_pdom_alignment_output(
tab_out_stream);
if (arguments->write_aaseqs)
gt_ltrdigest_file_out_stream_enable_aa_sequence_output(
tab_out_stream);
}
}
last_stream = gff3_out_stream = gt_gff3_out_stream_new(last_stream,
arguments->outfp);
/* pull the features through the stream and free them afterwards */
had_err = gt_node_stream_pull(last_stream, err);
}
gt_pdom_model_set_delete(ms);
gt_node_stream_delete(gff3_out_stream);
gt_node_stream_delete(ppt_stream);
gt_node_stream_delete(pbs_stream);
gt_node_stream_delete(sa_stream);
gt_node_stream_delete(pdom_stream);
gt_node_stream_delete(tab_out_stream);
gt_node_stream_delete(gff3_in_stream);
gt_bioseq_delete(arguments->trna_lib_bs);
gt_region_mapping_delete(rmap);
return had_err;
}
GtStrArray* agn_seq_intersection(GtFeatureIndex *refrfeats,
GtFeatureIndex *predfeats, AgnLogger *logger)
{
// Fetch seqids from reference and prediction annotations
GtError *e = gt_error_new();
GtStrArray *refrseqids = gt_feature_index_get_seqids(refrfeats, e);
if(gt_error_is_set(e))
{
agn_logger_log_error(logger, "error fetching seqids for reference: %s",
gt_error_get(e));
gt_error_unset(e);
}
GtStrArray *predseqids = gt_feature_index_get_seqids(predfeats, e);
if(gt_error_is_set(e))
{
agn_logger_log_error(logger, "error fetching seqids for prediction: %s",
gt_error_get(e));
gt_error_unset(e);
}
gt_error_delete(e);
if(agn_logger_has_error(logger))
{
gt_str_array_delete(refrseqids);
gt_str_array_delete(predseqids);
return NULL;
}
GtStrArray *seqids = agn_gt_str_array_intersection(refrseqids, predseqids);
// Print reference sequences with no prediction annotations
GtUword i, j;
for(i = 0; i < gt_str_array_size(refrseqids); i++)
{
const char *refrseq = gt_str_array_get(refrseqids, i);
int matches = 0;
for(j = 0; j < gt_str_array_size(seqids); j++)
{
const char *seq = gt_str_array_get(seqids, j);
if(strcmp(refrseq, seq) == 0)
matches++;
}
if(matches == 0)
{
agn_logger_log_warning(logger, "no prediction annotations found for "
"sequence '%s'", refrseq);
}
}
// Print prediction sequences with no reference annotations
for(i = 0; i < gt_str_array_size(predseqids); i++)
{
const char *predseq = gt_str_array_get(predseqids, i);
int matches = 0;
for(j = 0; j < gt_str_array_size(seqids); j++)
{
const char *seq = gt_str_array_get(seqids, j);
if(strcmp(predseq, seq) == 0)
matches++;
}
if(matches == 0)
{
agn_logger_log_warning(logger, "no reference annotations found for "
"sequence '%s'", predseq);
}
}
if(gt_str_array_size(seqids) == 0)
{
agn_logger_log_error(logger, "no sequences in common between reference and "
"prediction");
}
gt_str_array_delete(refrseqids);
gt_str_array_delete(predseqids);
return seqids;
}
static int hcr_write_seqs(FILE *fp, GtHcrEncoder *hcr_enc, GtError *err)
{
int had_err = 0, seqit_err;
GtUword bits_to_write = 0,
len,
read_counter = 0,
page_counter = 0,
bits_left_in_page,
cur_read = 0;
GtWord filepos;
GtSeqIterator *seqit;
const GtUchar *seq,
*qual;
char *desc;
GtBitOutStream *bitstream;
gt_error_check(err);
gt_assert(hcr_enc->seq_encoder->sampling);
gt_safe_assign(bits_left_in_page, (hcr_enc->pagesize * 8));
gt_xfseek(fp, hcr_enc->seq_encoder->start_of_encoding, SEEK_SET);
bitstream = gt_bitoutstream_new(fp);
seqit = gt_seq_iterator_fastq_new(hcr_enc->files, err);
if (!seqit) {
gt_assert(gt_error_is_set(err));
had_err = -1;
}
if (!had_err) {
gt_seq_iterator_set_quality_buffer(seqit, &qual);
gt_seq_iterator_set_symbolmap(seqit,
gt_alphabet_symbolmap(hcr_enc->seq_encoder->alpha));
hcr_enc->seq_encoder->total_num_of_symbols = 0;
while (!had_err &&
(seqit_err = gt_seq_iterator_next(seqit,
&seq,
&len,
&desc, err)) == 1) {
/* count the bits */
bits_to_write = hcr_write_seq(hcr_enc->seq_encoder, seq, qual, len,
bitstream, true);
/* check if a new sample has to be added */
if (gt_sampling_is_next_element_sample(hcr_enc->seq_encoder->sampling,
page_counter,
read_counter,
bits_to_write,
bits_left_in_page)) {
gt_bitoutstream_flush_advance(bitstream);
filepos = gt_bitoutstream_pos(bitstream);
if (filepos < 0) {
had_err = -1;
gt_error_set(err, "error by ftell: %s", strerror(errno));
}
else {
gt_sampling_add_sample(hcr_enc->seq_encoder->sampling,
(size_t) filepos,
cur_read);
read_counter = 0;
page_counter = 0;
gt_safe_assign(bits_left_in_page, (hcr_enc->pagesize * 8));
}
}
if (!had_err) {
/* do the writing */
bits_to_write = hcr_write_seq(hcr_enc->seq_encoder,
seq, qual, len, bitstream, false);
/* update counter for sampling */
while (bits_left_in_page < bits_to_write) {
page_counter++;
bits_to_write -= bits_left_in_page;
gt_safe_assign(bits_left_in_page, (hcr_enc->pagesize * 8));
}
bits_left_in_page -= bits_to_write;
/* always set first page as written */
if (page_counter == 0)
page_counter++;
read_counter++;
hcr_enc->seq_encoder->total_num_of_symbols += len;
cur_read++;
}
}
gt_assert(hcr_enc->num_of_reads == cur_read);
if (!had_err && seqit_err) {
had_err = seqit_err;
gt_assert(gt_error_is_set(err));
}
}
if (!had_err) {
gt_bitoutstream_flush(bitstream);
filepos = gt_bitoutstream_pos(bitstream);
if (filepos < 0) {
had_err = -1;
gt_error_set(err, "error by ftell: %s", strerror(errno));
}
else {
hcr_enc->seq_encoder->startofsamplingtab = filepos;
gt_log_log("start of samplingtab: "GT_WU"",
hcr_enc->seq_encoder->startofsamplingtab);
if (hcr_enc->seq_encoder->sampling != NULL)
gt_sampling_write(hcr_enc->seq_encoder->sampling, fp);
}
}
gt_bitoutstream_delete(bitstream);
gt_seq_iterator_delete(seqit);
return had_err;
}
int gt_hcr_decoder_decode(GtHcrDecoder *hcr_dec, GtUword readnum,
char *seq, char *qual, GtStr *desc, GtError *err)
{
int had_err = 0;
GtUword nearestsample = 0,
reads_to_read = 0,
idx,
current_read = hcr_dec->seq_dec->cur_read ;
size_t startofnearestsample = 0;
GtSampling *sampling;
HcrHuffDataIterator *data_iter;
GtHuffmanDecoder *huff_dec;
gt_error_check(err);
gt_assert(hcr_dec);
gt_assert(readnum < hcr_dec->seq_dec->num_of_reads);
gt_assert(seq != NULL && qual != NULL);
if (current_read == readnum)
had_err = hcr_next_seq_qual(hcr_dec->seq_dec, seq, qual, err) == -1 ?
-1 : 0;
else {
sampling = hcr_dec->seq_dec->sampling;
data_iter = hcr_dec->seq_dec->data_iter;
huff_dec = hcr_dec->seq_dec->huff_dec;
if (sampling != NULL) {
gt_sampling_get_page(sampling,
readnum,
&nearestsample,
&startofnearestsample);
/* nearestsample <= cur_read < readnum: current sample is the right one */
if (nearestsample <= current_read && current_read <= readnum)
reads_to_read = readnum - current_read;
else { /* reset decoder to new sample */
reset_data_iterator_to_pos(data_iter, startofnearestsample);
had_err = gt_huffman_decoder_get_new_mem_chunk(huff_dec, err);
reads_to_read = readnum - nearestsample;
hcr_dec->seq_dec->cur_read = nearestsample;
}
gt_log_log("reads to read: "GT_WU", nearest sample: "GT_WU"",
reads_to_read,nearestsample);
gt_log_log("start of nearest: "GT_WU"", (GtUword) startofnearestsample);
}
else {
if (current_read <= readnum)
reads_to_read = readnum - current_read;
else {
reset_data_iterator_to_start(data_iter);
had_err = gt_huffman_decoder_get_new_mem_chunk(huff_dec, err);
reads_to_read = readnum;
hcr_dec->seq_dec->cur_read = 0;
}
}
for (idx = 0; !had_err && idx < reads_to_read; idx++)
had_err = hcr_next_seq_qual(hcr_dec->seq_dec, seq,qual, err) == -1 ?
-1 : 0;
if (!had_err)
had_err = hcr_next_seq_qual(hcr_dec->seq_dec, seq, qual, err) == -1 ?
-1 : 0;
}
if (had_err)
gt_assert(gt_error_is_set(err));
if (!had_err && hcr_dec->encdesc != NULL)
had_err = gt_encdesc_decode(hcr_dec->encdesc, readnum, desc, err);
if (had_err)
gt_assert(gt_error_is_set(err));
return had_err;
}
int main(int argc, char *argv[])
{
const char *style_file, *png_file, *gff3_file;
char *seqid;
GtStyle *style;
GtBioseq *bioseq;
GtFeatureIndex *feature_index;
GtRange range;
GtDiagram *diagram;
GtLayout *layout;
GtCanvas *canvas;
GtCustomTrack *custom;
GtUword height, windowsize;
GtError *err;
if (argc != 9) {
fprintf(stderr, "Usage: %s style_file PNG_file GFF3_file Seq_file seqid"
" start end windowsize\n",
argv[0]);
return EXIT_FAILURE;
}
style_file = argv[1];
png_file = argv[2];
gff3_file = argv[3];
/* initialize */
gt_lib_init();
/* create error object */
err = gt_error_new();
/* create style */
if (!(style = gt_style_new(err)))
handle_error(err);
/* load style file */
if (gt_style_load_file(style, style_file, err))
handle_error(err);
/* create feature index */
feature_index = gt_feature_index_memory_new();
/* add GFF3 file to index */
if (gt_feature_index_add_gff3file(feature_index, gff3_file, err))
handle_error(err);
/* create diagram for first sequence ID in feature index */
seqid = argv[5];
if (gt_feature_index_get_range_for_seqid(feature_index, &range, seqid, err))
handle_error(err);
sscanf(argv[6], "%lu", &range.start);
sscanf(argv[7], "%lu", &range.end);
sscanf(argv[8], "%lu", &windowsize);
diagram = gt_diagram_new(feature_index, seqid, &range, style, err);
if (gt_error_is_set(err))
handle_error(err);
/* load sequence for GC plot */
bioseq = gt_bioseq_new(argv[4], err);
if (gt_error_is_set(err))
handle_error(err);
/* create custom track with GC plot for first sequence in file,
window size 1000, 40px height and average line at 16.5% */
custom = gt_custom_track_gc_content_new(gt_bioseq_get_sequence(bioseq, 0),
gt_bioseq_get_sequence_length(bioseq,
0),
windowsize,
70,
0.165,
true);
gt_diagram_add_custom_track(diagram, custom);
/* create layout with given width, determine resulting image height */
layout = gt_layout_new(diagram, 600, style, err);
if (gt_error_is_set(err))
handle_error(err);
if (gt_layout_get_height(layout, &height, err))
handle_error(err);
/* create PNG canvas */
canvas = gt_canvas_cairo_file_new(style, GT_GRAPHICS_PNG, 600, height,
NULL, err);
if (!canvas)
handle_error(err);
/* sketch layout on canvas */
if (gt_layout_sketch(layout, canvas, err))
handle_error(err);
/* write canvas to file */
if (gt_canvas_cairo_file_to_file((GtCanvasCairoFile*) canvas, png_file, err))
handle_error(err);
/* free */
gt_custom_track_delete(custom);
gt_bioseq_delete(bioseq);
gt_canvas_delete(canvas);
gt_layout_delete(layout);
gt_diagram_delete(diagram);
gt_feature_index_delete(feature_index);
gt_style_delete(style);
gt_error_delete(err);
/* perform static data cleanup */
gt_lib_clean();
return EXIT_SUCCESS;
}
static int hcr_next_seq_qual(GtHcrSeqDecoder *seq_dec, char *seq, char *qual,
GtError *err)
{
enum state {
HCR_ERROR = -1,
END,
SUCCESS
};
unsigned char base;
GtUword i,
nearestsample,
*symbol;
size_t startofnearestsample = 0;
enum state status = END;
FastqFileInfo cur_read;
FastqFileInfo *fileinfo = NULL;
if (seq_dec->cur_read <= seq_dec->num_of_reads) {
status = SUCCESS;
if (seq_dec->symbols == NULL)
seq_dec->symbols = gt_array_new(sizeof (GtUword));
else
gt_array_reset(seq_dec->symbols);
cur_read.readnum = seq_dec->cur_read;
gt_log_log("cur_read: "GT_WU"",seq_dec->cur_read);
fileinfo = (FastqFileInfo *)gt_rbtree_next_key(seq_dec->file_info_rbt,
&cur_read,
hcr_cmp_FastqFileInfo,
NULL);
gt_assert(fileinfo);
/* reset huffman_decoder if next read is sampled */
if (gt_sampling_get_next_elementnum(seq_dec->sampling) ==
seq_dec->cur_read) {
gt_log_log("reset because sampled read is next");
(void) gt_sampling_get_next_sample(seq_dec->sampling,
&nearestsample,
&startofnearestsample);
reset_data_iterator_to_pos(seq_dec->data_iter, startofnearestsample);
(void) gt_huffman_decoder_get_new_mem_chunk(seq_dec->huff_dec, err);
if (gt_error_is_set(err))
status = HCR_ERROR;
}
if (status != HCR_ERROR) {
int ret;
ret = gt_huffman_decoder_next(seq_dec->huff_dec, seq_dec->symbols,
fileinfo->readlength, err);
if (ret != 1)
status = HCR_ERROR;
if (ret == 0)
gt_error_set(err, "reached end of file");
}
if (qual || seq) {
gt_log_log("set strings");
for (i = 0; i < gt_array_size(seq_dec->symbols); i++) {
symbol = (GtUword*) gt_array_get(seq_dec->symbols, i);
if (qual != NULL)
qual[i] = get_qual_from_symbol(seq_dec, *symbol);
if (seq != NULL) {
base = get_base_from_symbol(seq_dec, *symbol);
seq[i] = (char)toupper(gt_alphabet_decode(seq_dec->alpha,
(GtUchar) base));
}
}
if (qual != NULL)
qual[gt_array_size(seq_dec->symbols)] = '\0';
if (seq != NULL)
seq[gt_array_size(seq_dec->symbols)] = '\0';
}
seq_dec->cur_read++;
}
return (int) status;
}
int gt_block_unit_test(GtError *err)
{
GtRange r1, r2, r_temp, b_range;
GtStrand s;
GtGenomeNode *gn1, *gn2;
GtElement *e1, *e2;
double height;
GtBlock *b;
GtStr *seqid, *caption1, *caption2;
int had_err = 0;
GtStyle *sty;
GtError *testerr;
gt_error_check(err);
seqid = gt_str_new_cstr("seqid");
caption1 = gt_str_new_cstr("foo");
caption2 = gt_str_new_cstr("bar");
testerr = gt_error_new();
r1.start = 10UL;
r1.end = 50UL;
r2.start = 40UL;
r2.end = 50UL;
gn1 = gt_feature_node_new(seqid, gt_ft_gene, r1.start, r1.end,
GT_STRAND_FORWARD);
gn2 = gt_feature_node_new(seqid, gt_ft_exon, r2.start, r2.end,
GT_STRAND_FORWARD);
e1 = gt_element_new((GtFeatureNode*) gn1);
e2 = gt_element_new((GtFeatureNode*) gn2);
b = gt_block_new();
/* test gt_block_insert_elements */
gt_ensure((0UL == gt_block_get_size(b)));
gt_block_insert_element(b, (GtFeatureNode*) gn1);
gt_ensure((1UL == gt_block_get_size(b)));
gt_block_insert_element(b, (GtFeatureNode*) gn2);
gt_ensure((2UL == gt_block_get_size(b)));
/* test gt_block_set_range & gt_block_get_range */
r_temp = gt_range_join(&r1, &r2);
gt_block_set_range(b, r_temp);
b_range = gt_block_get_range(b);
gt_ensure((0 == gt_range_compare(&b_range, &r_temp)));
gt_ensure((1 == gt_range_compare(&r2, &r_temp)));
/* tests gt_block_set_caption & gt_block_get_caption */
gt_block_set_caption(b, caption1);
gt_ensure((0 == gt_str_cmp(gt_block_get_caption(b), caption1)));
gt_ensure((0 != gt_str_cmp(gt_block_get_caption(b), caption2)));
/* tests gt_block_set_strand & gt_block_get_range */
s = gt_block_get_strand(b);
gt_ensure((GT_STRAND_UNKNOWN == s));
gt_block_set_strand(b, GT_STRAND_FORWARD);
s = gt_block_get_strand(b);
gt_ensure((GT_STRAND_FORWARD == s));
/* test gt_block_get_max_height() */
sty = gt_style_new(err);
gt_ensure(gt_block_get_max_height(b, &height, sty, err) == 0);
gt_ensure(!gt_error_is_set(testerr));
gt_ensure(height == BAR_HEIGHT_DEFAULT);
gt_style_set_num(sty, "exon", "bar_height", 42);
gt_ensure(gt_block_get_max_height(b, &height, sty, err) == 0);
gt_ensure(!gt_error_is_set(testerr));
gt_ensure(height == 42);
gt_style_set_num(sty, "gene", "bar_height", 23);
gt_ensure(gt_block_get_max_height(b, &height, sty, err) == 0);
gt_ensure(!gt_error_is_set(testerr));
gt_ensure(height == 42);
gt_style_unset(sty, "exon", "bar_height");
gt_ensure(gt_block_get_max_height(b, &height, sty, err) == 0);
gt_ensure(!gt_error_is_set(testerr));
gt_ensure(height == 23);
gt_str_delete(caption2);
gt_str_delete(seqid);
gt_element_delete(e1);
gt_element_delete(e2);
gt_block_delete(b);
gt_style_delete(sty);
gt_error_delete(testerr);
gt_genome_node_delete(gn1);
gt_genome_node_delete(gn2);
return had_err;
}
int gt_track_unit_test(GtError *err)
{
int had_err = 0;
GtBlock *b[4];
GtRange r[4];
GtTrack *track;
GtGenomeNode *parent[4], *gn[4];
GtStr *title;
double height, tmp;
GtStyle *sty;
unsigned long i;
GtLineBreaker *lb;
double t_rest = 0,
l_rest = 0;
gt_error_check(err);
title = gt_str_new_cstr("test");
r[0].start=100UL;
r[0].end=1000UL;
r[1].start=1001UL;
r[1].end=1500UL;
r[2].start=700UL;
r[2].end=1200UL;
r[3].start=10UL;
r[3].end=200UL;
for (i=0; i<4; i++)
{
parent[i] = gt_feature_node_new(title, gt_ft_gene, r[i].start, r[i].end,
GT_STRAND_FORWARD);
gn[i] = gt_feature_node_new(title, gt_ft_exon, r[i].start, r[i].end,
GT_STRAND_FORWARD);
gt_feature_node_add_child((GtFeatureNode*) parent[i],
(GtFeatureNode*) gn[i]);
gt_feature_node_add_attribute((GtFeatureNode*) parent[i], GT_GFF_NAME,
"parent");
gt_feature_node_add_attribute((GtFeatureNode*) gn[i], GT_GFF_NAME, "child");
}
for (i=0; i<4; i++)
{
b[i] = gt_block_new();
gt_block_set_range(b[i], r[i]);
gt_block_insert_element(b[i], (GtFeatureNode*) parent[i]);
gt_block_insert_element(b[i], (GtFeatureNode*) gn[i]);
}
lb = gt_line_breaker_bases_new();
sty = gt_style_new(err);
if (gt_style_get_num(sty, "format", "track_caption_font_size", &tmp,
NULL, err) == GT_STYLE_QUERY_NOT_SET) {
tmp = TEXT_SIZE_DEFAULT;
}
t_rest += tmp;
if (gt_style_get_num(sty, "format", "track_caption_space", &tmp,
NULL, err) == GT_STYLE_QUERY_NOT_SET) {
tmp = CAPTION_BAR_SPACE_DEFAULT;
}
t_rest += tmp;
if (gt_style_get_num(sty, "format", "track_vspace", &tmp,
NULL, err) == GT_STYLE_QUERY_NOT_SET) {
tmp = TRACK_VSPACE_DEFAULT;
}
t_rest += tmp;
if (gt_style_get_num(sty, "format", "bar_vspace", &l_rest,
NULL, err) == GT_STYLE_QUERY_NOT_SET) {
l_rest = BAR_VSPACE_DEFAULT;
}
track = gt_track_new(title, GT_UNDEF_ULONG, true, lb);
gt_ensure(had_err, track);
gt_ensure(had_err, gt_track_get_title(track) == title);
gt_ensure(had_err, gt_track_get_number_of_lines(track) == 0);
gt_ensure(had_err, gt_track_get_height(track, &height, sty, err) == 0);
gt_ensure(had_err, height == t_rest);
gt_ensure(had_err, !gt_error_is_set(err));
gt_ensure(had_err, gt_track_insert_block(track, b[0], err) == 0);
gt_ensure(had_err, !gt_error_is_set(err));
gt_ensure(had_err, gt_track_get_number_of_lines(track) == 1);
gt_ensure(had_err, gt_track_get_height(track, &height, sty, err) == 0);
gt_ensure(had_err, height == t_rest + l_rest + BAR_HEIGHT_DEFAULT);
gt_ensure(had_err, !gt_error_is_set(err));
gt_ensure(had_err, gt_track_insert_block(track, b[1], err) == 0);
gt_ensure(had_err, !gt_error_is_set(err));
gt_ensure(had_err, gt_track_get_number_of_lines(track) == 1);
gt_ensure(had_err, gt_track_get_height(track, &height, sty, err) == 0);
gt_ensure(had_err, height == t_rest + l_rest + BAR_HEIGHT_DEFAULT);
gt_ensure(had_err, !gt_error_is_set(err));
gt_ensure(had_err, gt_track_insert_block(track, b[2], err) == 0);
gt_ensure(had_err, !gt_error_is_set(err));
gt_ensure(had_err, gt_track_get_number_of_lines(track) == 2);
gt_ensure(had_err, gt_track_insert_block(track, b[3], err) == 0);
gt_ensure(had_err, !gt_error_is_set(err));
gt_ensure(had_err, gt_track_get_number_of_lines(track) == 2);
gt_ensure(had_err, gt_track_get_height(track, &height, sty, err) == 0);
gt_ensure(had_err, height == t_rest + 2*(l_rest + BAR_HEIGHT_DEFAULT));
gt_ensure(had_err, !gt_error_is_set(err));
gt_style_set_num(sty, "exon", "bar_height", 42);
gt_ensure(had_err, gt_track_get_height(track, &height, sty, err) == 0);
gt_ensure(had_err, height == t_rest + 2*(l_rest+42));
gt_ensure(had_err, !gt_error_is_set(err));
gt_style_set_num(sty, "gene", "bar_height", 23);
gt_ensure(had_err, gt_track_get_height(track, &height, sty, err) == 0);
gt_ensure(had_err, height == t_rest + 2*(l_rest+42));
gt_ensure(had_err, !gt_error_is_set(err));
gt_style_unset(sty, "exon", "bar_height");
gt_ensure(had_err, gt_track_get_height(track, &height, sty, err) == 0);
gt_ensure(had_err, height == t_rest + 2*(l_rest+23));
gt_ensure(had_err, !gt_error_is_set(err));
gt_style_unset(sty, "gene", "bar_height");
gt_style_set_num(sty, "format", "bar_height", 99);
gt_ensure(had_err, gt_track_get_height(track, &height, sty, err) == 0);
gt_ensure(had_err, height == t_rest + 2*(l_rest+99));
gt_ensure(had_err, !gt_error_is_set(err));
gt_ensure(had_err, gt_track_get_number_of_discarded_blocks(track) == 0);
gt_track_delete(track);
gt_str_delete(title);
gt_style_delete(sty);
for (i=0; i<4; i++)
{
gt_block_delete(b[i]);
gt_genome_node_delete(parent[i]);
}
return had_err;
}
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;
}
int gt_translator_unit_test(GtError *err)
{
int had_err = 0;
GtTranslatorStatus test_errnum;
GtTranslator *tr;
GtCodonIterator *ci;
GtError *test_err;
GtStrArray *codons, *invalidcodons;
const char *seq = "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGT"
"GGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGT"
"TACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG";
const char *no_startcodon = "AAAAAAAAAATCATCTCCCCATTTTTTT";
const char *invalidseq = "ZAGCTTTTCATTCTGACTGCAAATATGTCTCTGTGT";
const char *invalidseq2 = "AGCTTTTCATTCTGACZTGCAAATATGTCTCTGTGT";
char translated;
unsigned int frame;
GtUword pos = 0;
GtStr *protein[3];
gt_error_check(err);
test_err = gt_error_new();
ci = gt_codon_iterator_simple_new(seq, (GtUword) strlen(seq), test_err);
tr = gt_translator_new(ci);
protein[0] = gt_str_new();
protein[1] = gt_str_new();
protein[2] = gt_str_new();
codons = gt_str_array_new();
gt_str_array_add_cstr(codons, "ACG");
gt_str_array_add_cstr(codons, "ACT");
invalidcodons = gt_str_array_new();
gt_str_array_add_cstr(invalidcodons, "ACG");
gt_str_array_add_cstr(invalidcodons, "AC");
/* do 3-frame translation */
gt_error_unset(test_err);
test_errnum = gt_translator_next(tr, &translated, &frame, test_err);
while (!test_errnum && translated) {
gt_str_append_char(protein[frame], translated);
test_errnum = gt_translator_next(tr, &translated, &frame, test_err);
gt_ensure(
test_errnum != GT_TRANSLATOR_ERROR && !gt_error_is_set(test_err));
}
gt_ensure(
test_errnum == GT_TRANSLATOR_END && !gt_error_is_set(test_err));
/* check 3-frame translation */
gt_ensure(strcmp(gt_str_get(protein[0]),
"SFSF*LQRAICLCVD*KKSV**QLLNWLPAVSKLKFY*LR") == 0);
gt_ensure(strcmp(gt_str_get(protein[1]),
"AFHSDCNGQYVSVWIKKRVSDSSF*TGYLP*VN*NFIDL") == 0);
gt_ensure(strcmp(gt_str_get(protein[2]),
"LFILTATGNMSLCGLKKECLIAASELVTCRE*IKILLT*") == 0);
/* find start codon -- positive */
gt_error_unset(test_err);
gt_codon_iterator_rewind(ci);
test_errnum = gt_translator_find_startcodon(tr, &pos, test_err);
gt_ensure(!test_errnum && !gt_error_is_set(test_err));
gt_ensure(pos == 11UL);
/* find stop codon -- positive */
gt_error_unset(test_err);
gt_codon_iterator_rewind(ci);
test_errnum = gt_translator_find_stopcodon(tr, &pos, test_err);
gt_ensure(!test_errnum && !gt_error_is_set(test_err));
gt_ensure(pos == 12UL);
/* find arbitrary codons -- positive */
gt_error_unset(test_err);
gt_codon_iterator_rewind(ci);
test_errnum = gt_translator_find_codon(tr, codons, &pos, test_err);
gt_ensure(!test_errnum && !gt_error_is_set(test_err));
gt_ensure(pos == 14UL);
/* find arbitrary codons -- negative (invalid codons) */
gt_error_unset(test_err);
gt_codon_iterator_rewind(ci);
test_errnum = gt_translator_find_codon(tr, invalidcodons, &pos, test_err);
gt_ensure(
test_errnum == GT_TRANSLATOR_ERROR && gt_error_is_set(test_err));
gt_error_unset(test_err);
gt_codon_iterator_delete(ci);
ci = gt_codon_iterator_simple_new(invalidseq,
(GtUword) strlen(invalidseq),
test_err);
gt_ensure(ci && !gt_error_is_set(test_err));
gt_translator_reset(tr, ci);
/* check translation of sequence with invalid beginning */
test_errnum = gt_translator_next(tr, &translated, &frame, test_err);
gt_ensure(test_errnum && gt_error_is_set(test_err));
/* check translation of sequence with invalid character within */
gt_error_unset(test_err);
gt_codon_iterator_delete(ci);
ci = gt_codon_iterator_simple_new(invalidseq2,
(GtUword) strlen(invalidseq2),
test_err);
gt_ensure(ci && !gt_error_is_set(test_err));
gt_translator_reset(tr, ci);
test_errnum = gt_translator_next(tr, &translated, &frame, test_err);
while (!test_errnum && translated) {
gt_str_append_char(protein[frame], translated);
test_errnum = gt_translator_next(tr, &translated, &frame, test_err);
}
gt_ensure(
test_errnum == GT_TRANSLATOR_ERROR && gt_error_is_set(test_err));
/* find start codon -- fail */
gt_error_unset(test_err);
gt_codon_iterator_delete(ci);
ci = gt_codon_iterator_simple_new(no_startcodon,
(GtUword) strlen(no_startcodon),
test_err);
gt_ensure(ci && !gt_error_is_set(test_err));
gt_translator_reset(tr, ci);
test_errnum = gt_translator_find_startcodon(tr, &pos, test_err);
gt_ensure(
test_errnum == GT_TRANSLATOR_END && !gt_error_is_set(test_err));
/* find stop codon -- fail */
gt_error_unset(test_err);
gt_codon_iterator_rewind(ci);
test_errnum = gt_translator_find_stopcodon(tr, &pos, test_err);
gt_ensure(
test_errnum == GT_TRANSLATOR_END && !gt_error_is_set(test_err));
/* find arbitrary codons -- negative (none there) */
gt_error_unset(test_err);
gt_codon_iterator_rewind(ci);
test_errnum = gt_translator_find_codon(tr, codons, &pos, test_err);
gt_ensure(
test_errnum == GT_TRANSLATOR_END && !gt_error_is_set(test_err));
gt_codon_iterator_delete(ci);
gt_translator_delete(tr);
gt_str_delete(protein[0]);
gt_str_delete(protein[1]);
gt_str_delete(protein[2]);
gt_str_array_delete(codons);
gt_str_array_delete(invalidcodons);
gt_error_delete(test_err);
return had_err;
}
static int gt_readjoiner_cnttest_runner(GT_UNUSED int argc,
GT_UNUSED const char **argv, GT_UNUSED int parsed_args,
void *tool_arguments, GT_UNUSED GtError *err)
{
GtReadjoinerCnttestArguments *arguments = tool_arguments;
GtEncseqLoader *el = NULL;
GtEncseq *reads = NULL;
GtBitsequence *bits = NULL;
GtUword nofreads;
int had_err = 0;
gt_error_check(err);
gt_assert(arguments);
if (arguments->test == GT_READJOINER_CNTTEST_SHOWLIST)
{
GtStr *fn = NULL;
fn = gt_str_clone(arguments->readset);
gt_str_append_cstr(fn, GT_READJOINER_SUFFIX_CNTLIST);
had_err = gt_cntlist_parse(gt_str_get(fn), true, &bits, &nofreads, err);
gt_str_delete(fn);
}
else if (arguments->test == GT_READJOINER_CNTTEST_BRUTEFORCE ||
arguments->test == GT_READJOINER_CNTTEST_KMP)
{
el = gt_encseq_loader_new();
gt_encseq_loader_drop_description_support(el);
gt_encseq_loader_disable_autosupport(el);
if (!arguments->singlestrand)
gt_encseq_loader_mirror(el);
reads = gt_encseq_loader_load(el, gt_str_get(arguments->readset), err);
if (reads == NULL)
had_err = -1;
else
{
gt_rdj_pairwise_exact(GT_OVLFIND_CNT, reads, !arguments->singlestrand,
false, arguments->test == GT_READJOINER_CNTTEST_KMP, 1UL, true,
NULL, NULL, false, NULL, &bits, &nofreads);
}
gt_encseq_delete(reads);
gt_encseq_loader_delete(el);
}
else if (arguments->test == GT_READJOINER_CNTTEST_ESA)
{
Sequentialsuffixarrayreader *ssar = NULL;
GtUword readlength = 0, firstrevcompl = 0;
GtLogger *verbose_logger = gt_logger_new(arguments->verbose,
GT_LOGGER_DEFLT_PREFIX, stderr);
ssar = gt_newSequentialsuffixarrayreaderfromfile(gt_str_get(
arguments->readset), SARR_LCPTAB | SARR_SUFTAB | SARR_SSPTAB,
true, verbose_logger, err);
if (gt_error_is_set(err))
had_err = -1;
else
{
nofreads = gt_encseq_num_of_sequences(ssar->encseq);
if (!arguments->singlestrand)
{
nofreads = GT_DIV2(nofreads);
firstrevcompl = nofreads;
}
GT_INITBITTAB(bits, nofreads);
if (!arguments->singlestrand)
if (gt_encseq_accesstype_get(ssar->encseq) == GT_ACCESS_TYPE_EQUALLENGTH)
readlength = gt_encseq_seqlength(ssar->encseq, 0);
(void)gt_contfind_bottomup(ssar, false, bits, arguments->singlestrand ? 0
: firstrevcompl, readlength);
}
if (ssar != NULL)
gt_freeSequentialsuffixarrayreader(&ssar);
gt_logger_delete(verbose_logger);
}
else
{
gt_assert(false);
}
if (!had_err)
had_err = gt_cntlist_show(bits, nofreads, NULL, false, err);
gt_free(bits);
return had_err;
}