void prepareGraphForLocalCorrections(Graph * argGraph)
{
IDnum nodes = nodeCount(argGraph);
IDnum index;
//Setting global params
graph = argGraph;
WORDLENGTH = getWordLength(graph);;
// Done with global params
velvetLog("Preparing to correct graph with cutoff %f\n",
MAXDIVERGENCE);
// Allocating memory
times = mallocOrExit(2 * nodes + 1, Time);
previous = mallocOrExit(2 * nodes + 1, Node *);
dheapNodes = mallocOrExit(2 * nodes + 1, DFibHeapNode *);
dheap = newDFibHeap();
fastSequence = newTightString(MAXREADLENGTH);
slowSequence = newTightString(MAXREADLENGTH);
for (index = 0; index < (2 * nodeCount(graph) + 1); index++) {
times[index] = -1;
dheapNodes[index] = NULL;
previous[index] = NULL;
}
Fmatrix = callocOrExit(MAXREADLENGTH + 1, double *);
for (index = 0; index < MAXREADLENGTH + 1; index++)
Fmatrix[index] = callocOrExit(MAXREADLENGTH + 1, double);
//Done with memory
}
static TightString *readPositivePassageMarker(PassageMarkerI marker,
TightString ** seqs,
int WORDLENGTH)
{
Coordinate index;
Nucleotide nucleotide;
TightString *tString =
seqs[getPassageMarkerSequenceID(marker) - 1];
TightString *res = newTightString(getPassageMarkerLength(marker));
for (index = 0; index < getLength(tString); index++) {
nucleotide =
getNucleotide(getPassageMarkerStart(marker) + index +
WORDLENGTH - 1, tString);
writeNucleotideAtPosition(nucleotide, index, res);
}
return res;
}
static TightString *readNegativePassageMarker(PassageMarkerI marker,
TightString ** seqs)
{
Coordinate index;
Nucleotide nucleotide;
TightString *tString =
seqs[getAbsolutePassMarkerSeqID(marker) - 1];
TightString *res = newTightString(getPassageMarkerLength(marker));
for (index = 0; index < getPassageMarkerLength(marker); index++) {
nucleotide =
getNucleotide(getPassageMarkerStart(marker) - index,
tString);
#ifndef COLOR
writeNucleotideAtPosition(3 - nucleotide, index, res);
#else
writeNucleotideAtPosition(nucleotide, index, res);
#endif
}
return res;
}
