// Return value: 0 if all PBWTs finished, otherwise the current position is returned
static int pbwt_reader_next(pbwt_reader_t *reader, int nshared)
{
int i, min_pos = INT_MAX;
char *min_als = NULL;
// advance all readers, first looking at coordinates only
for (i=0; i<reader->n; i++)
{
PBWT *p = reader->pbwt[i];
int j = reader->cpos[i];
if ( j>=p->N ) continue; // no more sites in this pbwt
Site *site = arrp(p->sites, j, Site);
char *als = dictName(variationDict, site->varD);
// assuming:
// - one chromosome only (no checking sequence name)
// - sorted alleles (strcmp() on als)
while ( j < p->N && site->x <= reader->mpos && (!reader->mals || strcmp(als,reader->mals)<=0) )
{
site = arrp(p->sites, j, Site);
als = dictName(variationDict, site->varD);
reader->cpos[i] = j++;
}
if ( reader->cpos[i]+1 >= p->N && site->x == reader->mpos && (!reader->mals || !strcmp(als,reader->mals)) )
{
// this pbwt is positioned on the last site which has been read before
reader->cpos[i] = p->N;
continue;
}
if ( reader->cpos[i] < p->N && site->x < min_pos )
{
min_pos = site->x;
min_als = als;
}
if ( site->x==min_pos && (!min_als || strcmp(als,min_als)<0) ) min_als = als;
}
if ( min_pos==INT_MAX )
{
reader->mpos = 0;
reader->mals = NULL;
}
else
{
reader->mpos = min_pos;
reader->mals = min_als;
}
return reader->mpos;
}
void test() {
// Процедура для тестирования на "утечки" памяти
QString dictName("счета");
for (int i = 0; i < 50; i++) { // 50 раз откроем, закроем справочник
Dictionaries* dicts = TApplication::exemplar()->getDictionaries();
dicts->addDictionary(dictName);
Dictionary* dict = dicts->getDictionary(dictName); // Откроем справочник и подсправочники 1-го уровня
if (dict != 0) {
dicts->removeDictionary(dictName);
}
}
}
int DB::qt_metacall(QMetaObject::Call _c, int _id, void **_a)
{
_id = QObject::qt_metacall(_c, _id, _a);
if (_id < 0)
return _id;
if (_c == QMetaObject::InvokeMetaMethod) {
switch (_id) {
case 0: dbChanged(); break;
case 1: { bool _r = addRow((*reinterpret_cast< QString(*)>(_a[1])),(*reinterpret_cast< QString(*)>(_a[2])),(*reinterpret_cast< QString(*)>(_a[3])));
if (_a[0]) *reinterpret_cast< bool*>(_a[0]) = _r; } break;
case 2: { QString _r = dictName((*reinterpret_cast< QString(*)>(_a[1])));
if (_a[0]) *reinterpret_cast< QString*>(_a[0]) = _r; } break;
case 3: removeRow((*reinterpret_cast< QString(*)>(_a[1]))); break;
default: ;
}
_id -= 4;
}
return _id;
}
int main(int argc, char *argv[])
{
# include "addRegionOption.H"
# include "addLoadFunctionPlugins.H"
argList::validOptions.insert("overwrite", "");
argList::validOptions.insert("expression","expression to write");
argList::validOptions.insert("dictExt","Extension to the dictionary");
argList::validOptions.insert("relative", "");
argList::validOptions.insert("allowFunctionObjects","");
# include "setRootCase.H"
printSwakVersion();
# include "createTime.H"
Foam::instantList timeDirs = Foam::timeSelector::select0(runTime, args);
# include "createNamedMesh.H"
# include "loadFunctionPlugins.H"
if(!args.options().found("allowFunctionObjects")) {
runTime.functionObjects().off();
} else {
runTime.functionObjects().start();
}
const word oldInstance = mesh.pointsInstance();
bool overwrite = args.optionFound("overwrite");
bool relative = false;
pointField newPoints;
if (!overwrite)
{
runTime++;
}
if(args.optionFound("expression")) {
if(args.optionFound("dictExt")) {
FatalErrorIn(args.executable())
<< "Can't specify 'dictExt' and 'expression' at the same time"
<< endl
<< exit(FatalError);
}
relative=args.optionFound("relative");
exprString expression(
args.options()["expression"],
dictionary::null
);
FieldValueExpressionDriver driver(
runTime.timeName(),
runTime,
mesh
);
// no clearVariables needed here
driver.parse(expression);
if(!driver.resultIsTyp<pointVectorField>()) {
FatalErrorIn(args.executable())
<< "Expression " << expression
<< " does not evaluate to a pointVectorField but a "
<< driver.typ()
<< endl
<< exit(FatalError);
}
newPoints=driver.getResult<pointVectorField>().internalField();
} else {
Info << "Dictionary mode" << nl << endl;
if(args.optionFound("relative")) {
FatalErrorIn(args.executable())
<< "Option 'relative' not allowed in dictionary-mode"
<< endl
<< exit(FatalError);
}
word dictName("funkyWarpMeshDict");
if(args.optionFound("dictExt")) {
dictName+="."+word(args.options()["dictExt"]);
}
IOdictionary warpDict
(
IOobject
(
dictName,
runTime.system(),
mesh,
IOobject::MUST_READ,
IOobject::NO_WRITE
)
);
const word mode(warpDict.lookup("mode"));
if(mode=="set") {
relative=readBool(warpDict.lookup("relative"));
exprString expression(
warpDict.lookup("expression"),
warpDict
);
FieldValueExpressionDriver driver(
runTime.timeName(),
runTime,
mesh
);
driver.readVariablesAndTables(warpDict);
driver.clearVariables();
driver.parse(expression);
if(!driver.resultIsTyp<pointVectorField>()) {
FatalErrorIn(args.executable())
<< "Expression " << expression
<< " does not evaluate to a pointVectorField but a "
<< driver.typ()
<< endl
<< exit(FatalError);
}
newPoints=driver.getResult<pointVectorField>().internalField();
} else if (mode=="move") {
notImplemented(args.executable()+" mode: move");
} else {
FatalErrorIn(args.executable())
<< "Possible values for 'mode' are 'set' or 'move'"
<< endl
<< exit(FatalError);
}
}
if(relative) {
newPoints += mesh.points();
}
mesh.movePoints(newPoints);
// Write mesh
if (overwrite)
{
mesh.setInstance(oldInstance);
}
Info << nl << "Writing polyMesh to time " << runTime.timeName() << endl;
IOstream::defaultPrecision(15);
// Bypass runTime write (since only writes at outputTime)
if
(
!runTime.objectRegistry::writeObject
(
runTime.writeFormat(),
IOstream::currentVersion,
runTime.writeCompression()
#ifdef FOAM_REGIOOBJECT_WRITEOBJECT_WITH_VALID
,true
#endif
)
)
{
FatalErrorIn(args.executable())
<< "Failed writing polyMesh."
<< exit(FatalError);
}
// Write points goes here
// Write fields
runTime.write();
Info << "End\n" << endl;
Info << nl << "Now run 'checkMesh' before you do anything else"
<< nl << endl;
return 0;
}
PBWT *pbwtMerge(const char **fnames, int nfiles)
{
pbwt_reader_t *reader = pbwt_reader_init(fnames, nfiles);
int nhaps = 0, i;
for (i=0; i<nfiles; i++) nhaps += reader->pbwt[i]->M;
PBWT *out_pbwt = pbwtCreate(nhaps, 0);
PbwtCursor *cursor = pbwtNakedCursorCreate(nhaps, 0);
uchar *yseq = myalloc(nhaps, uchar);
out_pbwt->yz = arrayCreate (1<<20, uchar) ;
out_pbwt->sites = arrayReCreate(out_pbwt->sites, reader->pbwt[0]->N, Site);
out_pbwt->chrom = strdup(reader->pbwt[0]->chrom);
int pos, j;
while ( (pos=pbwt_reader_next(reader, nfiles)) )
{
// Merge only records shared by all files
for (i=0; i<nfiles; i++)
{
PBWT *p = reader->pbwt[i];
Site *site = arrp(p->sites, reader->cpos[i], Site);
// Both position and alleles must match. This requires that the records are sorted by alleles.
if ( site->x!=pos ) break;
char *als = dictName(variationDict, site->varD);
if ( strcmp(als,reader->mals) ) break;
}
if ( i!=nfiles )
{
// intersection: skip records which are not present in all files
for (i=0; i<nfiles; i++)
{
PBWT *p = reader->pbwt[i];
Site *site = arrp(p->sites, reader->cpos[i], Site);
if ( site->x!=pos ) continue;
char *als = dictName(variationDict, site->varD);
if ( strcmp(als,reader->mals) ) continue;
PbwtCursor *c = reader->cursor[i];
reader->unpacked[i] += unpack3(arrp(p->yz,reader->unpacked[i],uchar), p->M, c->y, 0);
pbwtCursorForwardsA(c);
}
continue;
}
// read and merge
int ihap = 0;
for (i=0; i<nfiles; i++)
{
PbwtCursor *c = reader->cursor[i];
PBWT *p = reader->pbwt[i];
Site *site = arrp(p->sites, reader->cpos[i], Site);
reader->unpacked[i] += unpack3(arrp(p->yz,reader->unpacked[i],uchar), p->M, c->y, 0);
for (j=0; j<p->M; j++) yseq[ihap + c->a[j]] = c->y[j];
pbwtCursorForwardsA(c);
ihap += p->M;
}
// pack merged haplotypes
for (j=0; j<nhaps; j++)
cursor->y[j] = yseq[cursor->a[j]];
pack3arrayAdd(cursor->y, out_pbwt->M, out_pbwt->yz);
pbwtCursorForwardsA(cursor);
// insert new site
arrayExtend(out_pbwt->sites, out_pbwt->N+1);
Site *site = arrayp(out_pbwt->sites, out_pbwt->N, Site);
site->x = pos;
dictAdd(variationDict, reader->mals, &site->varD);
out_pbwt->N++;
}
pbwtCursorToAFend (cursor, out_pbwt) ;
free(yseq);
pbwtCursorDestroy(cursor);
pbwt_reader_destroy(reader);
return out_pbwt;
}
