Graph *importPreGraph(char *preGraphFilename, ReadSet * reads, char * roadmapFilename,
boolean readTracking, short int accelerationBits)
{
boolean double_strand = false;
Graph *graph = readPreGraphFile(preGraphFilename, &double_strand);
Coordinate referenceMappingCount = 0;
IDnum referenceCount = 0;
if (nodeCount(graph) == 0)
return graph;
// If necessary compile reference -> node
ReferenceMapping * referenceMappings = computeReferenceMappings(preGraphFilename, reads, &referenceMappingCount, &referenceCount);
// Node -> reference maps
NodeMask * nodeMasks = computeNodeMasks(referenceMappings, referenceMappingCount, graph);
// Map k-mers to nodes
KmerOccurenceTable *kmerTable =
referenceGraphKmers(preGraphFilename, accelerationBits, graph, double_strand, nodeMasks, referenceMappingCount);
free(nodeMasks);
// Map sequences -> kmers -> nodes
fillUpGraph(reads, kmerTable, graph, readTracking, double_strand, referenceMappings, referenceMappingCount, referenceCount, roadmapFilename);
free(referenceMappings);
return graph;
}
Graph *importPreGraph(char *preGraphFilename, ReadSet * reads,
boolean readTracking, short int accelerationBits)
{
boolean double_strand = false;
Graph *graph = readPreGraphFile(preGraphFilename, &double_strand);
KmerOccurenceTable *kmerOccurences =
referenceGraphKmers(preGraphFilename, accelerationBits, graph, double_strand);
fillUpGraph(reads, kmerOccurences, graph, readTracking, double_strand);
return graph;
}