void
placeContainsUsingAllOverlaps(UnitigVector &unitigs,
bool withMatesToNonContained,
bool withMatesToUnambiguousContain) {
#if 0
for (uint32 fid=1; fid<FI->numFragments()+1; fid++) {
ufNode frag;
if (Unitig::fragIn(fid) > 0)
// Fragment placed already.
continue;
frag.ident = fid;
placeFragUsingOverlaps(frag, ovlStoreUniq, ovlStoreRept);
}
#endif
}
void
placeUnplacedUsingAllOverlaps(UnitigVector &unitigs,
const char *prefix) {
uint32 fiLimit = FI->numFragments();
uint32 numThreads = omp_get_max_threads();
uint32 blockSize = (fiLimit < 100 * numThreads) ? numThreads : fiLimit / 99;
uint32 *placedTig = new uint32 [FI->numFragments() + 1];
SeqInterval *placedPos = new SeqInterval [FI->numFragments() + 1];
memset(placedTig, 0, sizeof(uint32) * (FI->numFragments() + 1));
memset(placedPos, 0, sizeof(SeqInterval) * (FI->numFragments() + 1));
// Just some logging. Count the number of reads we try to place.
uint32 nToPlaceContained = 0;
uint32 nToPlace = 0;
uint32 nPlacedContained = 0;
uint32 nPlaced = 0;
uint32 nFailedContained = 0;
uint32 nFailed = 0;
for (uint32 fid=1; fid<FI->numFragments()+1; fid++)
if (Unitig::fragIn(fid) == 0)
if (OG->isContained(fid))
nToPlaceContained++;
else
nToPlace++;
writeLog("placeContains()-- placing %u contained and %u unplaced reads, with %d threads.\n",
nToPlaceContained, nToPlace, numThreads);
// Do the placing!
#pragma omp parallel for schedule(dynamic, blockSize)
for (uint32 fid=1; fid<FI->numFragments()+1; fid++) {
bool enableLog = true;
if (Unitig::fragIn(fid) > 0)
continue;
// Place the read.
vector<overlapPlacement> placements;
placeFragUsingOverlaps(unitigs, AS_MAX_ERATE, NULL, fid, placements);
// Search the placements for the highest expected identity placement using all overlaps in the unitig.
uint32 b = UINT32_MAX;
for (uint32 i=0; i<placements.size(); i++) {
Unitig *tig = unitigs[placements[i].tigID];
if (placements[i].fCoverage < 0.99) // Ignore partially placed reads.
continue;
if (tig->ufpath.size() == 1) // Ignore placements in singletons.
continue;
uint32 bgn = (placements[i].position.bgn < placements[i].position.end) ? placements[i].position.bgn : placements[i].position.end;
uint32 end = (placements[i].position.bgn < placements[i].position.end) ? placements[i].position.end : placements[i].position.bgn;
double erate = placements[i].errors / placements[i].aligned;
if (tig->overlapConsistentWithTig(5.0, bgn, end, erate) < 0.5) {
if ((enableLog == true) && (logFileFlagSet(LOG_PLACE_UNPLACED)))
writeLog("frag %8u tested tig %6u (%6u reads) at %8u-%8u (cov %7.5f erate %6.4f) - HIGH ERROR\n",
fid, placements[i].tigID, tig->ufpath.size(), placements[i].position.bgn, placements[i].position.end, placements[i].fCoverage, erate);
continue;
}
if ((enableLog == true) && (logFileFlagSet(LOG_PLACE_UNPLACED)))
writeLog("frag %8u tested tig %6u (%6u reads) at %8u-%8u (cov %7.5f erate %6.4f)\n",
fid, placements[i].tigID, tig->ufpath.size(), placements[i].position.bgn, placements[i].position.end, placements[i].fCoverage, erate);
if ((b == UINT32_MAX) ||
(placements[i].errors / placements[i].aligned < placements[b].errors / placements[b].aligned))
b = i;
}
// If we didn't find a best, b will be invalid; set positions for adding to a new tig.
// If we did, save both the position it was placed at, and the tigID it was placed in.
if (b == UINT32_MAX) {
if ((enableLog == true) && (logFileFlagSet(LOG_PLACE_UNPLACED)))
writeLog("frag %8u remains unplaced\n", fid);
placedPos[fid].bgn = 0;
placedPos[fid].end = FI->fragmentLength(fid);
}
else {
if ((enableLog == true) && (logFileFlagSet(LOG_PLACE_UNPLACED)))
writeLog("frag %8u placed tig %6u (%6u reads) at %8u-%8u (cov %7.5f erate %6.4f)\n",
fid, placements[b].tigID, unitigs[placements[b].tigID]->ufpath.size(),
placements[b].position.bgn, placements[b].position.end,
placements[b].fCoverage,
placements[b].errors / placements[b].aligned);
placedTig[fid] = placements[b].tigID;
placedPos[fid] = placements[b].position;
}
}
// All reads placed, now just dump them in their correct tigs.
for (uint32 fid=1; fid<FI->numFragments()+1; fid++) {
Unitig *tig = NULL;
ufNode frg;
if (Unitig::fragIn(fid) > 0)
continue;
// If not placed, dump it in a new unitig. Well, not anymore. These reads were not placed in
// any tig initially, were not allowed to seed a tig, and now, could find no place to go.
// They're garbage. Plus, it screws up the logging above because we don't know the new tig ID
// until now.
if (placedTig[fid] == 0) {
if (OG->isContained(fid))
nFailedContained++;
else
nFailed++;
//tig = unitigs.newUnitig(false);
}
// Otherwise, it was placed somewhere, grab the tig.
else {
if (OG->isContained(fid))
nPlacedContained++;
else
nPlaced++;
tig = unitigs[placedTig[fid]];
}
// Regardless, add it to the tig. Logging for this is above.
if (tig) {
frg.ident = fid;
frg.contained = 0;
frg.parent = 0;
frg.ahang = 0;
frg.bhang = 0;
frg.position = placedPos[fid];
tig->addFrag(frg, 0, false);
}
}
// Cleanup.
delete [] placedPos;
delete [] placedTig;
writeLog("placeContains()-- Placed %u contained reads and %u unplaced reads.\n", nPlacedContained, nPlaced);
writeLog("placeContains()-- Failed to place %u contained reads (too high error suspected) and %u unplaced reads (lack of overlaps suspected).\n", nFailedContained, nFailed);
// But wait! All the tigs need to be sorted. Well, not really _all_, but the hard ones to sort
// are big, and those quite likely had reads added to them, so it's really not worth the effort
// of tracking which ones need sorting, since the ones that don't need it are trivial to sort.
for (uint32 ti=1; ti<unitigs.size(); ti++) {
Unitig *utg = unitigs[ti];
if (utg)
utg->sort();
}
}