void
reportUnitigs(UnitigVector &unitigs, const char *prefix, const char *name) {
if (logFileFlagSet(LOG_INTERMEDIATE_UNITIGS) == 0)
return;
uint32 numFragsT = 0;
uint32 numFragsP = 0;
uint64 utgLen = 0;
// Compute average frags per partition.
for (uint32 ti=0; ti<unitigs.size(); ti++) {
Unitig *utg = unitigs[ti];
if (utg == NULL)
continue;
numFragsT += utg->ufpath.size();
if (utg->ufpath.size() > 2)
utgLen += utg->getLength();
}
if (utgLen < 16 * 1024 * 1024)
numFragsP = numFragsT / 7;
else if (utgLen < 64 * 1024 * 1024)
numFragsP = numFragsT / 63;
else
numFragsP = numFragsT / 127;
char tigStorePath[FILENAME_MAX];
sprintf(tigStorePath, "%s.%03u.%s.tigStore", prefix, logFileOrder, name);
// Failing to do this results in consensus running about 40 times slower. Three hours instead of
// five minutes.
setParentAndHang(unitigs);
writeUnitigsToStore(unitigs, tigStorePath, tigStorePath, numFragsP, false);
}
void
reportUnitigs(UnitigVector &unitigs, const char *prefix, const char *name, uint64 genomeSize) {
// Generate n50. Assumes unitigs have been 'classified' already.
vector<uint32> unassembledLength;
vector<uint32> bubbleLength;
vector<uint32> repeatLength;
vector<uint32> circularLength;
vector<uint32> contigLength;
for (uint32 ti=0; ti<unitigs.size(); ti++) {
Unitig *utg = unitigs[ti];
if (utg == NULL)
continue;
if (utg->_isUnassembled) {
unassembledLength.push_back(utg->getLength());
}
else if (utg->_isBubble) {
bubbleLength.push_back(utg->getLength());
}
else if (utg->_isRepeat) {
repeatLength.push_back(utg->getLength());
}
else if (utg->_isCircular) {
circularLength.push_back(utg->getLength());
}
else {
contigLength.push_back(utg->getLength());
}
}
char N[FILENAME_MAX];
sprintf(N, "%s.sizes", getLogFilePrefix());
errno = 0;
FILE *F = fopen(N, "w");
if (errno == 0) {
reportN50(F, unassembledLength, "UNASSEMBLED", genomeSize);
reportN50(F, bubbleLength, "BUBBLE", genomeSize);
reportN50(F, repeatLength, "REPEAT", genomeSize);
reportN50(F, circularLength, "CIRCULAR", genomeSize);
reportN50(F, contigLength, "CONTIGS", genomeSize);
fclose(F);
}
if (logFileFlagSet(LOG_INTERMEDIATE_UNITIGS) == 0)
return;
// Dump to an intermediate store.
char tigStorePath[FILENAME_MAX];
sprintf(tigStorePath, "%s.tigStore", getLogFilePrefix());
fprintf(stderr, "Creating intermediate tigStore '%s'\n", tigStorePath);
uint32 numFragsT = 0;
uint32 numFragsP = 0;
uint64 utgLen = 0;
// Compute average frags per partition.
for (uint32 ti=0; ti<unitigs.size(); ti++) {
Unitig *utg = unitigs[ti];
if (utg == NULL)
continue;
numFragsT += utg->ufpath.size();
if (utg->ufpath.size() > 2)
utgLen += utg->getLength();
}
if (utgLen < 16 * 1024 * 1024)
numFragsP = numFragsT / 7;
else if (utgLen < 64 * 1024 * 1024)
numFragsP = numFragsT / 63;
else
numFragsP = numFragsT / 127;
// Dump the unitigs to an intermediate store.
setParentAndHang(unitigs);
writeUnitigsToStore(unitigs, tigStorePath, tigStorePath, numFragsP, false);
}
