static void buildPositionRemap(unsigned int* remap, unsigned int* wedge, const float* vertex_positions_data, size_t vertex_count, size_t vertex_positions_stride, meshopt_Allocator& allocator)
{
PositionHasher hasher = {vertex_positions_data, vertex_positions_stride / sizeof(float)};
size_t table_size = hashBuckets2(vertex_count);
unsigned int* table = allocator.allocate<unsigned int>(table_size);
memset(table, -1, table_size * sizeof(unsigned int));
// build forward remap: for each vertex, which other (canonical) vertex does it map to?
// we use position equivalence for this, and remap vertices to other existing vertices
for (size_t i = 0; i < vertex_count; ++i)
{
unsigned int index = unsigned(i);
unsigned int* entry = hashLookup2(table, table_size, hasher, index, ~0u);
if (*entry == ~0u)
*entry = index;
remap[index] = *entry;
}
// build wedge table: for each vertex, which other vertex is the next wedge that also maps to the same vertex?
// entries in table form a (cyclic) wedge loop per vertex; for manifold vertices, wedge[i] == remap[i] == i
for (size_t i = 0; i < vertex_count; ++i)
wedge[i] = unsigned(i);
for (size_t i = 0; i < vertex_count; ++i)
if (remap[i] != i)
{
unsigned int r = remap[i];
wedge[i] = wedge[r];
wedge[r] = unsigned(i);
}
}
void loadGeneToMotif(struct sqlConnection *conn, char *fileName, char *table,
struct hash *geneToModuleHash, struct hash *moduleAndMotifHash,
struct hash *motifHash, struct hash *positionsHash,
char *regionTable)
/* Load file which is a big matrix with genes for rows and motifs for
* columns. There is a semicolon-separated list of numbers in the matrix
* where a gene has the motif, and an empty (tab separated) field
* where there is no motif. The numbers are relative to the
* region associated with the gene in the positionsHash.
* Only load bits of this where motif actually occurs in module associated
* with gene. */
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *line;
FILE *f = hgCreateTabFile(tmpDir, table);
char *motifNames[32*1024], *row[32*1024];
int motifCount, rowSize, i;
char *gene, *module;
int geneCount = 0, total = 0;
struct dyString *dy = dyStringNew(512);
struct genomePos *motifPosList = NULL, *motifPosForGene;
struct genomePos *regionPosList = NULL, *regionPos;
/* Read first line, which is labels. */
if (!lineFileNextReal(lf, &line))
errAbort("Empty file %s", fileName);
subChar(line, ' ', '_');
motifCount = chopLine(line, motifNames);
if (motifCount >= ArraySize(motifNames))
errAbort("Too many motifs line 1 of %s", fileName);
lineFileExpectAtLeast(lf, 2, motifCount);
motifNames[0] = NULL;
for (i=1; i<motifCount; ++i)
{
char name[64];
motifNames[i] = cloneString(fixMotifName(motifNames[i],name,sizeof(name)));
if (!hashLookup(motifHash, motifNames[i]))
errAbort("Motif %s is in %s but not modules_motifs.gxm",
motifNames[i], fileName);
}
/* Read subsequent lines. */
while ((rowSize = lineFileChopTab(lf, row)) != 0)
{
lineFileExpectWords(lf, motifCount, rowSize);
gene = row[0];
module = hashFindVal(geneToModuleHash, gene);
if (module == NULL)
{
warn("WARNING: Gene %s in line %d of %s but not module_assignments.tab",
gene, lf->lineIx, lf->fileName);
continue;
}
regionPos = NULL;
for (i=1; i<rowSize; ++i)
{
if (row[i][0] != 0)
{
if (hashLookup2(moduleAndMotifHash, module, motifNames[i]))
{
regionPos = hashFindVal(positionsHash, gene);
if (regionPos == NULL)
{
warn("WARNING: %s in %s but not gene_positions.tab",
gene, fileName);
i = rowSize; continue;
}
motifPosForGene = convertMotifPos(row[i], regionPos,
hashMustFindVal(motifHash, motifNames[i]), lf);
motifPosList = slCat(motifPosForGene, motifPosList);
++total;
}
}
}
if (regionPos != NULL)
{
slAddHead(®ionPosList, regionPos);
}
++geneCount;
}
lineFileClose(&lf);
/* Output sorted table of all motif hits. */
{
struct genomePos *pos;
slSort(&motifPosList, genomePosCmp);
for (pos = motifPosList; pos != NULL; pos = pos->next)
{
int start = pos->start;
int end = pos->end;
if (start < 0) start = 0;
fprintf(f, "%d\t", binFromRange(start, end));
fprintf(f, "%s\t", pos->chrom);
fprintf(f, "%d\t%d\t", start, end);
fprintf(f, "%s\t", pos->motif);
fprintf(f, "%d\t", pos->score);
fprintf(f, "%c\t", pos->strand);
fprintf(f, "%s\n", pos->name);
}
dyStringPrintf(dy,
"CREATE TABLE %s (\n"
" bin smallInt unsigned not null,\n"
" chrom varChar(255) not null,\n"
" chromStart int not null,\n"
" chromEnd int not null,\n"
" name varchar(255) not null,\n"
" score int not null,\n"
" strand char(1) not null,\n"
" gene varchar(255) not null,\n"
" #Indices\n"
" INDEX(gene(12)),\n"
" INDEX(name(16)),\n"
" INDEX(chrom(8),bin)\n"
")\n", table);
sqlRemakeTable(conn, table, dy->string);
verbose(1, "%d genes, %d motifs, %d motifs in genes\n",
geneCount, motifCount-1, total);
hgLoadTabFile(conn, tmpDir, table, &f);
// hgRemoveTabFile(tmpDir, table);
verbose(1, "Loaded %s table\n", table);
slFreeList(&motifPosList);
}
/* Now output sorted table of upstream regions. */
{
FILE *f = hgCreateTabFile(tmpDir, regionTable);
struct genomePos *pos;
dyStringClear(dy);
dyStringPrintf(dy,
"CREATE TABLE %s (\n"
" bin smallInt unsigned not null,\n"
" chrom varChar(255) not null,\n"
" chromStart int not null,\n"
" chromEnd int not null,\n"
" name varchar(255) not null,\n"
" score int not null,\n"
" strand char(1) not null,\n"
" #Indices\n"
" INDEX(name(16)),\n"
" INDEX(chrom(8),bin)\n"
")\n", regionTable);
sqlRemakeTable(conn, regionTable, dy->string);
slSort(®ionPosList, genomePosCmp);
for (pos = regionPosList; pos != NULL; pos = pos->next)
{
int start = pos->start;
int end = pos->end;
if (start < 0) start = 0;
fprintf(f, "%d\t", binFromRange(start, end));
fprintf(f, "%s\t", pos->chrom);
fprintf(f, "%d\t%d\t", start, end);
fprintf(f, "%s\t", pos->name);
fprintf(f, "%d\t", pos->score);
fprintf(f, "%c\n", pos->strand);
}
hgLoadTabFile(conn, tmpDir, regionTable, &f);
// hgRemoveTabFile(tmpDir, regionTable);
}
}
