static inline vector<const AlignmentColumn*>
getPredecessorColumns(BoostGraph& g,
Vertex v,
const AlignmentColumnMap& alignmentColumnForVertex)
{
vector<const AlignmentColumn*> predecessorColumns;
const AlignmentColumn* predCol;
foreach (Edge e, in_edges(v, g))
{
Vertex u = source(e, g);
predCol = alignmentColumnForVertex.at(u);
assert(predCol != NULL);
predecessorColumns.push_back(predCol);
}
void PoaGraphImpl::tracebackAndThread(std::string sequence,
const AlignmentColumnMap& alignmentColumnForVertex,
AlignMode alignMode, std::vector<Vertex>* outputPath)
{
const int I = sequence.length();
// perform traceback from (I,$), threading the new sequence into
// the graph as we go.
int i = I;
const AlignmentColumn* curCol;
VD v = null_vertex, forkVertex = null_vertex;
VD u = exitVertex_;
VD startSpanVertex;
VD endSpanVertex = alignmentColumnForVertex.at(exitVertex_)->PreviousVertex[I];
if (outputPath) {
outputPath->resize(I);
std::fill(outputPath->begin(), outputPath->end(), (size_t)-1);
}
#define READPOS (i - 1)
#define VERTEX_ON_PATH(readPos, v) \
if (outputPath) { \
(*outputPath)[(readPos)] = externalize(v); \
}
while (!(u == enterVertex_ && i == 0)) {
// u -> v
// u: current vertex
// v: vertex last visited in traceback (could be == u)
// forkVertex: the vertex that will be the target of a new edge
Vertex uExt = this->externalize(u); // DEBUGGING
Vertex vExt = this->externalize(v); // DEBUGGING
curCol = alignmentColumnForVertex.at(u);
assert(curCol != NULL);
PoaNode& curNodeInfo = vertexInfoMap_[u];
VD prevVertex = curCol->PreviousVertex[i];
MoveType reachingMove = curCol->ReachingMove[i];
if (reachingMove == StartMove) {
assert(v != null_vertex);
if (forkVertex == null_vertex) {
forkVertex = v;
}
// In local model thread read bases, adjusting i (should stop at 0)
while (i > 0) {
assert(alignMode == AlignMode::LOCAL);
VD newForkVertex = addVertex(sequence[READPOS]);
add_edge(newForkVertex, forkVertex, g_);
VERTEX_ON_PATH(READPOS, newForkVertex);
forkVertex = newForkVertex;
i--;
}
} else if (reachingMove == EndMove) {
assert(forkVertex == null_vertex && u == exitVertex_ && v == null_vertex);
forkVertex = exitVertex_;
if (alignMode == AlignMode::LOCAL) {
// Find the row # we are coming from, walk
// back to there, threading read bases onto
// graph via forkVertex, adjusting i.
const AlignmentColumn* prevCol = alignmentColumnForVertex.at(prevVertex);
int prevRow = ArgMax(prevCol->Score);
while (i > static_cast<int>(prevRow)) {
VD newForkVertex = addVertex(sequence[READPOS]);
add_edge(newForkVertex, forkVertex, g_);
VERTEX_ON_PATH(READPOS, newForkVertex);
forkVertex = newForkVertex;
i--;
}
}
} else if (reachingMove == MatchMove) {
VERTEX_ON_PATH(READPOS, u);
// if there is an extant forkVertex, join it
if (forkVertex != null_vertex) {
add_edge(u, forkVertex, g_);
forkVertex = null_vertex;
}
// add to existing node
curNodeInfo.Reads++;
i--;
} else if (reachingMove == DeleteMove) {
if (forkVertex == null_vertex) {
forkVertex = v;
}
} else if (reachingMove == ExtraMove || reachingMove == MismatchMove) {
// begin a new arc with this read base
VD newForkVertex = addVertex(sequence[READPOS]);
if (forkVertex == null_vertex) {
forkVertex = v;
}
add_edge(newForkVertex, forkVertex, g_);
VERTEX_ON_PATH(READPOS, newForkVertex);
forkVertex = newForkVertex;
i--;
} else {
throw std::runtime_error("unreachable");
}
v = u;
u = prevVertex;
}
startSpanVertex = v;
// if there is an extant forkVertex, join it to enterVertex
if (forkVertex != null_vertex) {
add_edge(enterVertex_, forkVertex, g_);
startSpanVertex = forkVertex;
forkVertex = null_vertex;
}
if (startSpanVertex != exitVertex_) {
tagSpan(startSpanVertex, endSpanVertex);
}
// all filled in?
assert(outputPath == NULL ||
std::find(outputPath->begin(), outputPath->end(), ((size_t)-1)) == outputPath->end());
#undef READPOS
#undef VERTEX_ON_PATH
}
