void gt_consensus_sa(const void *set_of_sas, unsigned long number_of_sas,
size_t size_of_sa, GetGenomicRangeFunc get_genomic_range,
GetStrandFunc get_strand, GetExonsFunc get_exons,
ProcessSpliceFormFunc process_splice_form, void *userdata)
{
ConsensusSA csa;
gt_assert(set_of_sas && number_of_sas && size_of_sa);
gt_assert(get_genomic_range && get_strand && get_exons);
gt_assert(set_of_sas_is_sorted(set_of_sas, number_of_sas, size_of_sa,
get_genomic_range));
gt_log_log("-from %lu", get_genomic_range(set_of_sas).start);
gt_log_log("csa number_of_sas=%lu", number_of_sas);
/* init */
csa.set_of_sas = set_of_sas;
csa.number_of_sas = number_of_sas;
csa.size_of_sa = size_of_sa;
csa.get_genomic_range = get_genomic_range;
csa.get_strand = get_strand;
csa.get_exons = get_exons;
csa.process_splice_form = process_splice_form;
csa.userdata = userdata;
/* computation */
compute_csas(&csa);
gt_log_log("csa finished");
}
/**
* @param alphabet ownership of alphabet is with the newly produced
* sequence object if return value is not 0
*/
static int
initBWTSeqFromEncSeqIdx(BWTSeq *bwtSeq, struct encIdxSeq *seqIdx,
MRAEnc *alphabet, GtUword *counts,
enum rangeSortMode *rangeSort,
const enum rangeSortMode *defaultRangeSort)
{
size_t alphabetSize;
Symbol bwtTerminatorFlat;
EISHint hint;
gt_assert(bwtSeq && seqIdx);
bwtSeq->alphabet = alphabet;
alphabetSize = gt_MRAEncGetSize(alphabet);
if (!alphabetSize)
/* weird error, shouldn't happen, but I prefer error return to
* segfault in case someone tampered with the input */
return 0;
/* FIXME: this should probably be handled in chardef.h to have a
* unique mapping */
/* FIXME: this assumes there is exactly two ranges */
gt_MRAEncAddSymbolToRange(alphabet, bwtTerminatorSym, 1);
gt_assert(gt_MRAEncGetSize(alphabet) == alphabetSize + 1);
alphabetSize = gt_MRAEncGetSize(alphabet);
bwtSeq->bwtTerminatorFallback = bwtTerminatorFlat
= MRAEncMapSymbol(alphabet, UNDEFBWTCHAR);
bwtSeq->bwtTerminatorFallbackRange = 1;
bwtSeq->count = counts;
bwtSeq->rangeSort = rangeSort;
bwtSeq->seqIdx = seqIdx;
bwtSeq->alphabetSize = alphabetSize;
bwtSeq->hint = hint = newEISHint(seqIdx);
{
Symbol i;
GtUword len = EISLength(seqIdx), *count = bwtSeq->count;
count[0] = 0;
for (i = 0; i < bwtTerminatorFlat; ++i)
count[i + 1] = count[i]
+ EISSymTransformedRank(seqIdx, i, len, hint);
/* handle character which the terminator has been mapped to specially */
count[i + 1] = count[i]
+ EISSymTransformedRank(seqIdx, i, len, hint) - 1;
gt_assert(count[i + 1] >= count[i]);
/* now we can finish the rest of the symbols */
for (i += 2; i < alphabetSize; ++i)
count[i] = count[i - 1]
+ EISSymTransformedRank(seqIdx, i - 1, len, hint);
/* and finally place the 1-count for the terminator */
count[i] = count[i - 1] + 1;
#ifdef EIS_DEBUG
gt_log_log("count[alphabetSize]="GT_WU", len="GT_WU"",count[alphabetSize],
len);
for (i = 0; i <= alphabetSize; ++i)
gt_log_log("count[%u]="GT_WU"", (unsigned)i, count[i]);
#endif
gt_assert(count[alphabetSize] == len);
}
gt_BWTSeqInitLocateHandling(bwtSeq, defaultRangeSort);
return 1;
}
static void log_fragments(GtFragment *fragments, unsigned long num_of_fragments)
{
unsigned long i;
gt_log_log("show chaining fragments");
for (i = 0; i < num_of_fragments; i++) {
GtFragment *frag = fragments + i;
gt_log_log("#%lu: s1=%lu, s1=%lu, l1=%lu, s2=%lu, e2=%lu, l2=%lu, w=%lu", i,
frag->startpos1, frag->endpos1, frag->endpos1 - frag->startpos1 + 1,
frag->startpos2, frag->endpos2, frag->endpos2 - frag->startpos2 + 1,
frag->weight);
}
}
/*call makeblastdb with given path to <dbfile>*/
static inline int gt_condenser_search_create_blastdb(const char* dbfile,
const char *dbtype,
GtError *err) {
int had_err = 0,
pipe_status;
GtStr *call = gt_str_new_cstr("makeblastdb -dbtype ");
char *call_str;
FILE* fpipe;
gt_str_append_cstr(call, dbtype);
gt_str_append_cstr(call, " -in ");
gt_str_append_cstr(call, dbfile);
call_str = gt_str_get(call);
gt_log_log("executed call: %s", call_str);
if ((fpipe = popen(call_str, "r")) == NULL) {
gt_error_set(err, "Could not open pipe to call makeblastdb");
had_err = -1;
}
if (!had_err) {
char *newline = NULL;
char line[BUFSIZ + 1];
line[BUFSIZ] = '\0';
while (fgets(line, (int) BUFSIZ, fpipe) != NULL) {
if ((newline = strrchr(line, '\n')) != NULL) {
*newline = '\0';
newline = NULL;
}
gt_log_log("%.*s", BUFSIZ, line);
}
}
gt_str_delete(call);
if (!had_err) {
pipe_status = pclose(fpipe);
if (pipe_status != 0) {
had_err = -1;
if (errno == ECHILD)
gt_error_set(err, "Error calling makeblastdb.");
#ifndef _WIN32
else if (WEXITSTATUS(pipe_status) == 127)
gt_error_set(err, "shell returned 127, makeblastdb not installed?");
else
gt_error_set(err, "makeblastdb error, returned %d",
WEXITSTATUS(pipe_status));
#endif
}
}
return had_err;
}
static bool gt_encseq2spm_kmersize(GtEncseq2spmArguments *arguments,
unsigned int *kmersize, GtError *err)
{
bool haserr = false;
gt_assert(kmersize != NULL);
if (arguments->forcek > 0)
{
*kmersize = arguments->forcek;
if (*kmersize > arguments->minmatchlength)
{
gt_error_set(err,"argument %u to option -forcek > l",
*kmersize);
haserr = true;
}
else if (*kmersize > (unsigned int)GT_UNITSIN2BITENC)
{
gt_error_set(err,
"argument %u to option -forcek > %u (machine word size/2)",
*kmersize, (unsigned int)GT_UNITSIN2BITENC);
haserr = true;
}
}
else
{
*kmersize = MIN((unsigned int) GT_UNITSIN2BITENC,
arguments->minmatchlength);
}
gt_log_log("kmersize=%u", *kmersize);
gt_assert(*kmersize > 0);
return haserr;
}
static int add_to_parent(GtDiagram *d, GtFeatureNode *node,
GtFeatureNode *parent, GtError *err)
{
GtBlock *block = NULL;
NodeInfoElement *par_ni, *ni;
gt_assert(d && node);
if (!parent)
return 0;
par_ni = nodeinfo_get(d, parent);
ni = nodeinfo_get(d, node);
gt_log_log("adding %s to parent %p", gt_feature_node_get_type(node), parent);
ni->parent = parent;
block = nodeinfo_find_block(par_ni,
gt_feature_node_get_type(node),
parent);
if (!block) {
block = gt_block_new_from_node(parent);
gt_block_set_type(block, gt_feature_node_get_type(node));
if (assign_block_caption(d, node, parent, block, err) < 0) {
gt_block_delete(block);
return -1;
}
nodeinfo_add_block(par_ni,
gt_feature_node_get_type((GtFeatureNode*) node),
parent,
block);
}
gt_assert(block);
gt_block_insert_element(block, node);
return 0;
}
void gt_Sfxmappedrange_usetmp(GtSfxmappedrange *sfxmappedrange,
const GtStr *tmpfilename,
void **usedptrptr,
GtUword numofentries,
bool writable)
{
gt_assert(sfxmappedrange != NULL);
sfxmappedrange->ptr = NULL;
/*gt_assert(usedptrptr != NULL && *usedptrptr == NULL);*/
sfxmappedrange->usedptrptr = usedptrptr;
sfxmappedrange->filename = gt_str_clone(tmpfilename);
sfxmappedrange->writable = writable;
if (sfxmappedrange->type == GtSfxGtBitsequence)
{
sfxmappedrange->numofunits = GT_NUMOFINTSFORBITS(numofentries);
} else
{
sfxmappedrange->numofunits = (size_t) numofentries;
}
gt_log_log("use file %s for table %s ("GT_WU" units of "GT_WU" bytes)",
gt_str_get(sfxmappedrange->filename),
gt_str_get(sfxmappedrange->tablename),
(GtUword) sfxmappedrange->numofunits,
(GtUword) sfxmappedrange->sizeofunit);
gt_free(*sfxmappedrange->usedptrptr);
*sfxmappedrange->usedptrptr = NULL;
}
void *gt_Sfxmappedrange_map_entire(GtSfxmappedrange *sfxmappedrange,
GtError *err)
{
size_t mappedsize;
gt_assert(sfxmappedrange != NULL);
sfxmappedrange->entire = gt_fa_mmap_read(gt_str_get(sfxmappedrange->filename),
&mappedsize,err);
if (sfxmappedrange->entire == NULL)
{
return NULL;
}
if (mappedsize != gt_Sfxmappedrange_size_entire(sfxmappedrange))
{
gt_error_set(err,
"map file %s: mapped size = "GT_WU" != "
GT_WU" = expected size",
gt_str_get(sfxmappedrange->filename), (GtUword) mappedsize,
(GtUword) gt_Sfxmappedrange_size_entire(sfxmappedrange));
gt_fa_xmunmap(sfxmappedrange->entire);
sfxmappedrange->entire = NULL;
return NULL;
}
gt_log_log("map %s completely ("GT_WU" units of size %u)",
gt_str_get(sfxmappedrange->tablename),
(GtUword) sfxmappedrange->numofunits,
(unsigned int) sfxmappedrange->sizeofunit);
return sfxmappedrange->entire;
}
static int gt_xrf_abbr_parse_tree_blank_line(GtIO *xrf_abbr_file, GtError *err)
{
int had_err;
gt_error_check(err);
gt_log_log("blank");
had_err = gt_io_expect(xrf_abbr_file, XRF_BLANK_CHAR, err);
while (!had_err) {
char cc = gt_io_peek(xrf_abbr_file);
if (cc == XRF_COMMENT_CHAR)
return gt_xrf_abbr_parse_tree_comment_line(xrf_abbr_file, err);
else if (cc == GT_CARRIAGE_RETURN) {
gt_io_next(xrf_abbr_file);
if (gt_io_peek(xrf_abbr_file) == GT_END_OF_LINE)
gt_io_next(xrf_abbr_file);
break;
}
else if ((cc == GT_END_OF_LINE) || (cc == GT_END_OF_FILE)) {
gt_io_next(xrf_abbr_file);
break;
}
else
had_err = gt_io_expect(xrf_abbr_file, XRF_BLANK_CHAR, err);
}
return had_err;
}
static int gt_xrf_abbr_parse_tree_comment_line(GtIO *xrf_abbr_file,
GtError *err)
{
int had_err;
gt_error_check(err);
gt_log_log("comment");
had_err = gt_io_expect(xrf_abbr_file, XRF_COMMENT_CHAR, err);
while (!had_err) {
switch (gt_io_peek(xrf_abbr_file)) {
case GT_CARRIAGE_RETURN:
gt_io_next(xrf_abbr_file);
if (gt_io_peek(xrf_abbr_file) == GT_END_OF_LINE)
gt_io_next(xrf_abbr_file);
return had_err;
case GT_END_OF_LINE:
gt_io_next(xrf_abbr_file);
/*@fallthrough@*/
case GT_END_OF_FILE:
return had_err;
default:
gt_io_next(xrf_abbr_file);
}
}
return had_err;
}
extern void
BWTSeqInitLocateHandling(BWTSeq *bwtSeq,
const enum rangeSortMode *defaultRangeSort)
{
struct encIdxSeq *seqIdx;
struct locateHeader locHeader;
gt_assert(bwtSeq);
seqIdx = bwtSeq->seqIdx;
if (!readLocateInfoHeader(seqIdx, &locHeader)
|| !locHeader.locateInterval)
{
gt_log_log("Index does not contain locate information.\n"
"Localization of matches will not be supported!");
bwtSeq->locateSampleInterval = 0;
bwtSeq->featureToggles = BWTBaseFeatures;
}
else
{
bwtSeq->locateSampleInterval = locHeader.locateInterval;
bwtSeq->rot0Pos = locHeader.rot0Pos;
/* FIXME: this really deserves its own header */
bwtSeq->featureToggles = locHeader.featureToggles;
if (readRankSortHeader(seqIdx, &bwtSeq->bitsPerOrigRank,
bwtSeq->alphabet, bwtSeq->rangeSort))
;
else
{
AlphabetRangeID numRanges = MRAEncGetNumRanges(bwtSeq->alphabet);
bwtSeq->bitsPerOrigRank = 0;
memcpy(bwtSeq->rangeSort, defaultRangeSort,
numRanges * sizeof (defaultRangeSort[0]));
}
}
}
static void gt_firstcodes_updatemax(GtFirstcodesspacelog *fcsl)
{
if (fcsl->workspace + fcsl->splitspace > fcsl->spacepeak)
{
fcsl->spacepeak = fcsl->workspace + fcsl->splitspace;
gt_log_log("update spacepeak to %.2f MB",
GT_MEGABYTES(fcsl->spacepeak));
}
}
int gt_cntlist_parse(const char *filename, bool alloc_cntlist,
GtBitsequence **cntlist, GtUword *nofreads, GtError *err)
{
int c, retval = 0;
FILE *infp;
gt_log_log("parse contained reads list file: %s", filename);
infp = gt_fa_fopen(filename, "rb", err);
if (infp == NULL)
return -1;
c = gt_xfgetc(infp);
switch (c)
{
case EOF:
gt_error_set(err, "%s: unexpected end of file", filename);
retval = 1;
break;
case GT_CNTLIST_BIN_HEADER:
gt_log_log("contained reads list format: BIN");
retval = gt_cntlist_parse_bin(infp, alloc_cntlist, cntlist, nofreads,
err);
break;
case GT_CNTLIST_BIT_HEADER:
gt_log_log("contained reads list format: BIT");
retval = gt_cntlist_parse_bit(infp, alloc_cntlist, cntlist, nofreads,
err);
break;
case GT_CNTLIST_ASCII_HEADER:
gt_xungetc(c, infp);
gt_log_log("contained reads list format: ASCII");
retval = gt_cntlist_parse_ascii(infp, alloc_cntlist, cntlist, nofreads,
err);
break;
default:
gt_error_set(err, "%s: unrecognized format", filename);
retval = 1;
break;
}
gt_fa_fclose(infp);
return retval;
}
static int gt_compreads_decompress_benchmark(GtHcrDecoder *hcrd,
unsigned long amount,
GtTimer *timer,
GtError *err) {
char qual[BUFSIZ] = {0},
seq[BUFSIZ] = {0};
int had_err = 0;
unsigned long rand,
max_rand = gt_hcr_decoder_num_of_reads(hcrd) - 1,
count;
GtStr *timer_comment = gt_str_new_cstr("extracting ");
GtStr *desc = gt_str_new();
gt_str_append_ulong(timer_comment, amount);
gt_str_append_cstr(timer_comment, " reads of ");
gt_str_append_ulong(timer_comment, max_rand + 1);
gt_str_append_cstr(timer_comment, "!");
if (timer == NULL) {
timer = gt_timer_new_with_progress_description("extract random reads");
gt_timer_start(timer);
}
else {
gt_timer_show_progress(timer, "extract random reads", stdout);
}
gt_log_log("%s",gt_str_get(timer_comment));
for (count = 0; count < amount; count++) {
if (!had_err) {
rand = gt_rand_max(max_rand);
gt_log_log("get read: %lu", rand);
had_err = gt_hcr_decoder_decode(hcrd, rand, seq, qual, desc, err);
gt_log_log("%s",gt_str_get(desc));
gt_log_log("%s",seq);
gt_log_log("%s",qual);
}
}
gt_str_delete(timer_comment);
gt_str_delete(desc);
if (!gt_showtime_enabled())
gt_timer_delete(timer);
return had_err;
}
FILE *gt_blast_process_call_run(GtBlastProcessCall *call, GtError *err)
{
int had_err = 0;
#ifndef _WIN32
int errcode;
#endif
FILE *blastout = NULL,
*installcheck = NULL;
gt_assert(call->query && call->db);
installcheck = popen(call->version_call, "r");
if (installcheck == NULL) {
gt_error_set(err, "Could not open pipe to run %s: %s",
call->version_call, strerror(errno));
had_err = -1;
}
/* this assures that we get the output if debugging is set, and also we
prevent BROKEN_PIPE error if pclose(3) is called before the version call
exits */
if (!had_err) {
char *newline = NULL;
char line[BUFSIZ + 1];
line[BUFSIZ] = '\0';
while (fgets(line, (int) BUFSIZ, installcheck) != NULL) {
if ((newline = strrchr(line, '\n')) != NULL) {
*newline = '\0';
newline = NULL;
}
gt_log_log("%.*s", BUFSIZ, line);
}
}
if (!had_err) {
#ifndef _WIN32
errcode = pclose(installcheck);
if ((call->all && WEXITSTATUS(errcode) != 1) ||
errcode != 0) {
if (errno == ECHILD)
gt_error_set(err, "Error calling %s.", call->version_call);
else if (WEXITSTATUS(errcode) == 127)
gt_error_set(err, "shell returned 127, BLAST not installed?");
else
gt_error_set(err, "%s error, returned %d",
call->version_call, WEXITSTATUS(errcode));
had_err = -1;
}
#endif
}
if (!had_err) {
blastout = popen(gt_str_get(call->str), "r");
if (blastout == NULL) {
gt_error_set(err, "Could not open pipe to run BLAST process: %s",
strerror(errno));
}
}
return blastout;
}
static void add_recursive(GtDiagram *d, GtFeatureNode *node,
GtFeatureNode* parent,
GtFeatureNode *original_node)
{
NodeInfoElement *ni;
GtFeatureNode *rep = GT_UNDEF_REPR;
gt_assert(d && node && original_node);
if (!parent) return;
ni = nodeinfo_get(d, node);
if (gt_feature_node_is_multi(original_node)) {
rep = gt_feature_node_get_multi_representative(original_node);
}
/* end of recursion, insert into target block */
if (parent == node) {
GtBlock *block ;
block = nodeinfo_find_block(ni,
gt_feature_node_get_type(node),
rep);
if (!block) {
block = gt_block_new_from_node(node);
nodeinfo_add_block(ni,
gt_feature_node_get_type(node),
rep,
block);
}
gt_block_insert_element(block, original_node);
gt_log_log("add %s to target %s", gt_feature_node_get_type(original_node),
gt_block_get_type(block));
}
else
{
/* not at target type block yet, set up reverse entry and follow */
NodeInfoElement *parent_ni;
/* set up reverse entry */
ni->parent = parent;
parent_ni = gt_hashmap_get(d->nodeinfo, parent);
if (parent_ni) {
gt_log_log("recursion: %s -> %s", gt_feature_node_get_type(node),
gt_feature_node_get_type(parent));
add_recursive(d, parent, parent_ni->parent, original_node);
}
}
}
int gt_hcr_encoder_encode(GtHcrEncoder *hcr_enc, const char *name,
GtTimer *timer, GtError *err)
{
int had_err = 0;
GtStr *name1;
gt_error_check(err);
if (timer != NULL)
gt_timer_show_progress(timer, "write encoding", stdout);
if (hcr_enc->encdesc_encoder != NULL) {
GtCstrIterator *cstr_iterator = gt_fasta_header_iterator_new(hcr_enc->files,
err);
had_err = gt_encdesc_encoder_encode(hcr_enc->encdesc_encoder,
cstr_iterator, name, err);
gt_cstr_iterator_delete(cstr_iterator);
}
if (!had_err)
had_err = hcr_write_seq_qual_data(name, hcr_enc, timer, err);
if (!had_err && gt_log_enabled()) {
name1 = gt_str_new_cstr(name);
gt_str_append_cstr(name1, HCRFILESUFFIX);
gt_log_log("sequences with qualities encoding overview:");
gt_log_log("**>");
if (hcr_enc->page_sampling)
gt_log_log("applied sampling technique: sampling every " GT_WU
"th page",
hcr_enc->sampling_rate);
else if (hcr_enc->regular_sampling)
gt_log_log("applied sampling technique: sampling every " GT_WU
"th read",
hcr_enc->sampling_rate);
else
gt_log_log("applied sampling technique: none");
gt_log_log("total number of encoded nucleotide sequences with qualities: "
GT_WU, hcr_enc->num_of_reads);
gt_log_log("total number of encoded nucleotides: " GT_LLU,
hcr_enc->seq_encoder->total_num_of_symbols);
gt_log_log("bits per nucleotide encoding: %f",
(gt_file_estimate_size(gt_str_get(name1)) * 8.0) /
hcr_enc->seq_encoder->total_num_of_symbols);
gt_log_log("<**");
gt_str_delete(name1);
}
return had_err;
}
static void gt_ltrdigest_pdom_visitor_chainproc(GtChain *c, GtFragment *f,
GT_UNUSED unsigned long nof_frags,
GT_UNUSED unsigned long gap_length,
void *data)
{
unsigned long i,
*chainno = (unsigned long*) data;
gt_log_log("resulting chain has %ld GtFragments, score %ld",
gt_chain_size(c),
gt_chain_get_score(c));
for (i = 0; i < gt_chain_size(c); i++) {
GtFragment frag;
frag = f[gt_chain_get_fragnum(c, i)];
gt_log_log("(%lu %lu) (%lu %lu)", frag.startpos1, frag.endpos1,
frag.startpos2, frag.endpos2);
gt_array_add(((GtHMMERSingleHit*) frag.data)->chains, *chainno);
}
(*chainno)++;
gt_log_log("\n");
}
static int add_to_current(GtDiagram *d, GtFeatureNode *node,
GtFeatureNode *parent, GtError *err)
{
GtBlock *block;
NodeInfoElement *ni;
GtStyleQueryStatus rval;
GtStr *caption = NULL;
bool status = true;
const char *nnid_p = NULL,
*nnid_n = NULL,
*nodetype;
gt_assert(d && node);
nodetype = gt_feature_node_get_type(node);
if (get_caption_display_status(d, nodetype, &status, err) < 0) {
return -1;
}
/* Get nodeinfo element and set itself as parent */
ni = nodeinfo_get(d, node);
gt_log_log("adding %s to self", nodetype);
ni->parent = node;
/* create new GtBlock tuple and add to node info */
block = gt_block_new_from_node(node);
caption = gt_str_new();
rval = gt_style_get_str(d->style,
nodetype, "block_caption",
caption, node, err);
if (rval == GT_STYLE_QUERY_ERROR) {
gt_str_delete(caption);
gt_block_delete(block);
return -1;
} else if (rval == GT_STYLE_QUERY_NOT_SET) {
nnid_p = get_node_name_or_id(parent);
nnid_n = get_node_name_or_id(node);
if ((nnid_p || nnid_n) && status)
{
if (parent) {
if (nnid_p && gt_feature_node_has_children(parent))
gt_str_append_cstr(caption, nnid_p);
else
gt_str_append_cstr(caption, "-");
gt_str_append_cstr(caption, "/");
}
if (nnid_n)
gt_str_append_cstr(caption, nnid_n);
} else {
gt_str_delete(caption);
caption = NULL;
}
}
gt_block_set_caption(block, caption);
gt_block_insert_element(block, node);
nodeinfo_add_block(ni, gt_feature_node_get_type(node), GT_UNDEF_REPR, block);
return 0;
}
static void reset_data_iterator_to_pos(HcrHuffDataIterator *data_iter,
size_t pos)
{
gt_assert(data_iter);
gt_assert(pos < data_iter->end);
gt_assert(data_iter->start <= pos);
gt_fa_xmunmap(data_iter->data);
gt_log_log("reset to pos: "GT_WU"", (GtUword) pos);
data_iter->data = NULL;
data_iter->pos = pos;
}
static void gt_ltrdigest_pdom_visitor_chainproc(GtChain *c, GtFragment *f,
GT_UNUSED GtUword nof_frags,
GT_UNUSED GtUword gap_length,
void *data)
{
GtUword i,
*chainno = (GtUword*) data;
gt_log_log("resulting chain has "GT_WD" GtFragments, score "GT_WD"",
gt_chain_size(c),
gt_chain_get_score(c));
for (i = 0; i < gt_chain_size(c); i++) {
GtFragment frag;
frag = f[gt_chain_get_fragnum(c, i)];
gt_log_log("("GT_WU" "GT_WU") ("GT_WU" "GT_WU")", frag.startpos1,
frag.endpos1, frag.startpos2, frag.endpos2);
gt_array_add(((GtHMMERSingleHit*) frag.data)->chains, *chainno);
}
(*chainno)++;
gt_log_log("\n");
}
static void reset_data_iterator_to_pos(HcrHuffDataIterator *data_iter,
size_t pos)
{
gt_assert(data_iter);
gt_assert(pos < data_iter->end);
gt_assert(data_iter->start <= pos);
gt_fa_xmunmap(data_iter->data);
gt_log_log("reset to pos: %lu", (unsigned long) pos);
data_iter->data = NULL;
data_iter->pos = pos;
}
static inline void gt_readjoiner_assembly_show_current_space(const char *label)
{
GtUword m, f;
if (gt_ma_bookkeeping_enabled())
{
m = gt_ma_get_space_current();
f = gt_fa_get_space_current();
gt_log_log("used space %s: %.2f MB (ma: %.2f MB; fa: %.2f MB)",
label == NULL ? "" : label, GT_MEGABYTES(m + f), GT_MEGABYTES(m),
GT_MEGABYTES(f));
}
}
static bool gt_xrf_abbr_parse_tree_ignored_line(GtIO *xrf_abbr_file,
GtError *err)
{
gt_error_check(err);
gt_log_log("ignored");
if (gt_io_peek(xrf_abbr_file) == XRF_BLANK_CHAR)
return gt_xrf_abbr_parse_tree_blank_line(xrf_abbr_file, err);
if (gt_io_peek(xrf_abbr_file) == XRF_COMMENT_CHAR)
return gt_xrf_abbr_parse_tree_comment_line(xrf_abbr_file, err);
gt_io_next(xrf_abbr_file);
return false;
}
static int gt_ltrdigest_pdom_visitor_process_hit(GT_UNUSED void *key, void *val,
void *data,
GT_UNUSED GtError *err)
{
GtHMMERModelHit *mh = (GtHMMERModelHit*) val;
GtLTRdigestPdomVisitor *lv = (GtLTRdigestPdomVisitor*) data;
const char *mdl = (const char*) key;
GtArray *hits = NULL;
GtUword nof_hits;
GtFragment *frags;
if (gt_double_compare(mh->best_fwd, mh->best_rev) <= 0)
hits = mh->fwd_hits;
else
hits = mh->rev_hits;
gt_assert(hits);
nof_hits = gt_array_size(hits);
if (nof_hits == 0) return 0;
if (nof_hits > 1UL) {
GtUword i, chainno;
frags = gt_malloc((size_t) nof_hits * sizeof (GtFragment));
for (i = 0; i < nof_hits; i++) {
GtHMMERSingleHit *h = *(GtHMMERSingleHit**) gt_array_get(hits, i);
gt_assert(h);
frags[i].startpos1 = h->hmmfrom;
frags[i].endpos1 = h->hmmto;
frags[i].startpos2 = h->alifrom;
frags[i].endpos2 = h->alito;
frags[i].weight = (GtWord) (h->alito - h->alifrom + 1) * h->score;
frags[i].data = h;
}
qsort(frags, (size_t) nof_hits, sizeof (GtFragment),
gt_ltrdigest_pdom_visitor_fragcmp);
gt_log_log("%s: chaining "GT_WU" frags", mdl, nof_hits);
gt_globalchaining_max(frags, nof_hits,
(GtUword) lv->chain_max_gap_length,
gt_ltrdigest_pdom_visitor_chainproc, &chainno);
gt_free(frags);
for (i = 0; i < nof_hits; i++) {
GtHMMERSingleHit *h = *(GtHMMERSingleHit**) gt_array_get(hits, i);
(void) gt_ltrdigest_pdom_visitor_attach_hit(lv, mh, h);
}
} else {
GtUword chainno = 0UL;
GtHMMERSingleHit *h = *(GtHMMERSingleHit**) gt_array_get(hits, 0);
gt_array_add(h->chains, chainno);
(void) gt_ltrdigest_pdom_visitor_attach_hit(lv, mh, h);
}
return 0;
}
static void numeric_field_check_distri_dependence(DescField *field,
bool *needs_delta_dist,
bool *needs_value_dist)
{
field->use_hc = false;
if (field->use_delta_coding) {
if (!field->is_delta_cons &&
field->delta_values_size <= GT_ENCDESC_MAX_NUM_VAL_HUF) {
*needs_delta_dist = true;
field->use_hc = true;
gt_log_log("delta_values_size: "GT_WU"", field->delta_values_size);
}
}
else {
if (!field->is_value_cons && field->num_values_size > 0 &&
field->num_values_size <= GT_ENCDESC_MAX_NUM_VAL_HUF) {
*needs_value_dist = true;
field->use_hc = true;
gt_log_log("num_values_size: "GT_WU"", field->num_values_size);
}
}
}
static void pbs_attach_results_to_gff3(GtPBSResults *results,
GtLTRElement *element,
GtStrand *canonical_strand,
GtStr *tag)
{
GtRange pbs_range;
GtGenomeNode *gf;
unsigned long i = 0;
char buffer[BUFSIZ];
GtPBSHit* hit = gt_pbs_results_get_ranked_hit(results, i++);
if (*canonical_strand == GT_STRAND_UNKNOWN)
*canonical_strand = gt_pbs_hit_get_strand(hit);
else
{
/* do we have to satisfy a strand constraint?
* then find best-scoring PBS on the given canonical strand */
while (gt_pbs_hit_get_strand(hit) != *canonical_strand
&& i < gt_pbs_results_get_number_of_hits(results))
{
gt_log_log("dropping PBS because of nonconsistent strand: %s\n",
gt_feature_node_get_attribute(element->mainnode, "ID"));
hit = gt_pbs_results_get_ranked_hit(results, i++);
}
/* if there is none, do not report a PBS */
if (gt_pbs_hit_get_strand(hit) != *canonical_strand)
return;
}
pbs_range = gt_pbs_hit_get_coords(hit);
pbs_range.start++; pbs_range.end++; /* GFF3 is 1-based */
gf = gt_feature_node_new(gt_genome_node_get_seqid((GtGenomeNode*)
element->mainnode),
GT_PBS_TYPE,
pbs_range.start,
pbs_range.end,
gt_pbs_hit_get_strand(hit));
gt_feature_node_set_source((GtFeatureNode*) gf, tag);
gt_feature_node_set_score((GtFeatureNode*) gf,
(float) gt_pbs_hit_get_score(hit));
if (gt_pbs_hit_get_trna(hit) != NULL) {
gt_feature_node_add_attribute((GtFeatureNode*) gf, "trna",
gt_pbs_hit_get_trna(hit));
}
gt_feature_node_set_strand(element->mainnode, gt_pbs_hit_get_strand(hit));
(void) snprintf(buffer, BUFSIZ-1, "%lu", gt_pbs_hit_get_tstart(hit));
gt_feature_node_add_attribute((GtFeatureNode*) gf, "trnaoffset", buffer);
(void) snprintf(buffer, BUFSIZ-1, "%lu", gt_pbs_hit_get_offset(hit));
gt_feature_node_add_attribute((GtFeatureNode*) gf, "pbsoffset", buffer);
(void) snprintf(buffer, BUFSIZ-1, "%lu", gt_pbs_hit_get_edist(hit));
gt_feature_node_add_attribute((GtFeatureNode*) gf, "edist", buffer);
gt_feature_node_add_child(element->mainnode, (GtFeatureNode*) gf);
}
static int hmmsearch_call_coarse_search(GtCondenseq* ces,
char *hmmsearch_path,
char *table_filename,
char *hmm_filename,
GtLogger *logger,
GtError *err) {
int had_err = 0;
char **hmmargs = NULL,
*hmmenv[] = { NULL };
GtStr *coarse_fas = gt_condenseq_unique_fasta_file(ces);
GtSafePipe *pipe = NULL;
gt_assert(coarse_fas != NULL);
/* Array has to end with NULL */
hmmargs = gt_calloc((size_t) 8, sizeof (*hmmargs));
hmmargs[0] = hmmsearch_path;
hmmargs[1] = gt_cstr_dup("--noali");
hmmargs[2] = gt_cstr_dup("--notextw");
hmmargs[3] = gt_cstr_dup("--domtblout");
hmmargs[4] = table_filename;
hmmargs[5] = hmm_filename;
hmmargs[6] = gt_str_get(coarse_fas);
gt_logger_log(logger, "calling: %s", hmmsearch_path);
pipe = gt_safe_popen(hmmsearch_path, hmmargs, hmmenv, err);
if (pipe == NULL)
had_err = -1;
gt_free(hmmargs[1]);
gt_free(hmmargs[2]);
gt_free(hmmargs[3]);
gt_free(hmmargs);
gt_str_delete(coarse_fas);
/* pipe test for splint */
if (!had_err && pipe != NULL) {
if (gt_log_enabled()) {
GtStr *line = gt_str_new();
while (gt_str_read_next_line(line, pipe->read_fd) == 0) {
gt_log_log("%s", gt_str_get(line));
gt_str_reset(line);
}
gt_str_delete(line);
}
(void) gt_safe_pclose(pipe);
}
return had_err;
}
void gt_Sfxmappedrange_delete(GtSfxmappedrange *sfxmappedrange)
{
if (sfxmappedrange == NULL)
{
return;
}
gt_log_log("delete table %s",gt_str_get(sfxmappedrange->tablename));
gt_fa_xmunmap(sfxmappedrange->ptr);
sfxmappedrange->ptr = NULL;
gt_fa_xmunmap(sfxmappedrange->entire);
sfxmappedrange->entire = NULL;
if (sfxmappedrange->usedptrptr != NULL)
{
*sfxmappedrange->usedptrptr = NULL;
}
if (sfxmappedrange->filename != NULL)
{
gt_log_log("remove \"%s\"",gt_str_get(sfxmappedrange->filename));
gt_xunlink(gt_str_get(sfxmappedrange->filename));
}
gt_str_delete(sfxmappedrange->tablename);
gt_str_delete(sfxmappedrange->filename);
gt_free(sfxmappedrange);
}
static int gt_xrf_abbr_parse_tree_tag_line(GtIO *xrf_abbr_file, GtStr *tag,
GtStr *value, GtError *err)
{
int had_err = 0;
gt_error_check(err);
gt_log_log("tag");
gt_assert(xrf_abbr_file && tag && value);
do {
had_err = gt_xrf_abbr_parse_tree_proc_any_char(xrf_abbr_file, tag,
false, err);
} while (!had_err && gt_xrf_abbr_parse_tree_any_char(xrf_abbr_file, false));
if (!had_err)
had_err = gt_io_expect(xrf_abbr_file, XRF_SEPARATOR_CHAR, err);
while (!had_err && gt_io_peek(xrf_abbr_file) == XRF_BLANK_CHAR)
gt_io_next(xrf_abbr_file);
if (!had_err) {
do {
had_err = gt_xrf_abbr_parse_tree_proc_any_char(xrf_abbr_file, value,
true, err);
} while (!had_err && gt_xrf_abbr_parse_tree_any_char(xrf_abbr_file, true));
}
if (!had_err) {
if (gt_io_peek(xrf_abbr_file) == XRF_COMMENT_CHAR)
had_err = gt_xrf_abbr_parse_tree_comment_line(xrf_abbr_file, err);
else
had_err = gt_io_expect(xrf_abbr_file, GT_END_OF_LINE, err);
}
if (!had_err && !gt_xrf_abbr_parse_tree_valid_label(gt_str_get(tag))) {
gt_warning("file \"%s\": line "GT_WU": unknown label \"%s\"",
gt_io_get_filename(xrf_abbr_file),
gt_io_get_line_number(xrf_abbr_file),
gt_str_get(tag));
}
gt_log_log("parsed line %s/%s", gt_str_get(tag), gt_str_get(value));
return had_err;
}
