ChunkGraph::ChunkGraph(set<uint32> *restrict) {
_maxFragment = 0;
_restrict = restrict;
for (set<uint32>::iterator it=_restrict->begin(); it != _restrict->end(); it++)
_idMap[*it] = _maxFragment++;
_pathLen = new uint32 [_maxFragment * 2 + 2];
_chunkLength = new ChunkLength [_maxFragment];
_chunkLengthIter = 0;
memset(_pathLen, 0, sizeof(uint32) * (_maxFragment * 2 + 2));
memset(_chunkLength, 0, sizeof(ChunkLength) * (_maxFragment));
for (set<uint32>::iterator it=_restrict->begin(); it != _restrict->end(); it++) {
uint32 fid = *it; // Actual fragment ID
uint32 fit = _idMap[fid]; // Local array index
if (OG->isContained(fid))
continue;
_chunkLength[fit].fragId = fid;
_chunkLength[fit].cnt = (countFullWidth(FragmentEnd(fid, false)) +
countFullWidth(FragmentEnd(fid, true)));
}
delete [] _pathLen;
_pathLen = NULL;
std::sort(_chunkLength, _chunkLength + _maxFragment);
}
ChunkGraph::ChunkGraph(const char *output_prefix) {
setLogFile(output_prefix, "ChunkGraph");
_maxFragment = FI->numFragments();
_pathLen = new uint32 [_maxFragment * 2 + 2];
_chunkLength = new ChunkLength [_maxFragment];
_chunkLengthIter = 0;
memset(_pathLen, 0, sizeof(uint32) * (_maxFragment * 2 + 2));
memset(_chunkLength, 0, sizeof(ChunkLength) * (_maxFragment));
for (uint32 fid=1; fid <= _maxFragment; fid++) {
if (OG->isContained(fid))
continue;
_chunkLength[fid-1].fragId = fid;
_chunkLength[fid-1].cnt = (countFullWidth(FragmentEnd(fid, false)) +
countFullWidth(FragmentEnd(fid, true)));
}
delete [] _pathLen;
_pathLen = NULL;
std::sort(_chunkLength, _chunkLength + _maxFragment);
}
ChunkGraph::ChunkGraph(const char *output_prefix) {
setLogFile(output_prefix, "ChunkGraph");
_maxFragment = FI->numFragments();
_restrict = NULL;
_pathLen = new uint32 [_maxFragment * 2 + 2];
_chunkLength = new ChunkLength [_maxFragment];
_chunkLengthIter = 0;
memset(_pathLen, 0, sizeof(uint32) * (_maxFragment * 2 + 2));
memset(_chunkLength, 0, sizeof(ChunkLength) * (_maxFragment));
for (uint32 fid=1; fid <= _maxFragment; fid++) {
if (OG->isContained(fid))
continue;
if (OG->isSuspicious(fid))
// Fragment is suspicious. We won't seed a BOG from it, and populateUnitig will make only a
// singleton.
continue;
_chunkLength[fid-1].fragId = fid;
_chunkLength[fid-1].cnt = (countFullWidth(FragmentEnd(fid, false)) +
countFullWidth(FragmentEnd(fid, true)));
}
delete [] _pathLen;
_pathLen = NULL;
std::sort(_chunkLength, _chunkLength + _maxFragment);
}
ChunkGraph::ChunkGraph(const char *output_prefix) {
setLogFile(output_prefix, "ChunkGraph");
_maxFragment = FI->numFragments();
_restrict = NULL;
_pathLen = new uint32 [_maxFragment * 2 + 2];
_chunkLength = new ChunkLength [_maxFragment];
_chunkLengthIter = 0;
memset(_pathLen, 0, sizeof(uint32) * (_maxFragment * 2 + 2));
memset(_chunkLength, 0, sizeof(ChunkLength) * (_maxFragment));
for (uint32 fid=1; fid <= _maxFragment; fid++) {
if (OG->isContained(fid)) {
if (logFileFlagSet(LOG_CHUNK_GRAPH))
writeLog("read %u contained\n", fid);
continue;
}
if (OG->isSuspicious(fid)) {
if (logFileFlagSet(LOG_CHUNK_GRAPH))
writeLog("read %u suspicious\n", fid);
continue;
}
uint32 l5 = countFullWidth(FragmentEnd(fid, false));
uint32 l3 = countFullWidth(FragmentEnd(fid, true));
_chunkLength[fid-1].fragId = fid;
_chunkLength[fid-1].cnt = l5 + l3;
}
delete [] _pathLen;
_pathLen = NULL;
std::sort(_chunkLength, _chunkLength + _maxFragment);
}
