void PoaGraphImpl::threadFirstRead(std::string sequence, std::vector<Vertex>* outputPath)
{
// first sequence in the alignment
VD u = null_vertex, v;
VD startSpanVertex = null_vertex, endSpanVertex;
int readPos = 0;
if (outputPath) {
outputPath->clear();
}
for (const char base : sequence) {
v = addVertex(base);
if (outputPath) {
outputPath->push_back(externalize(v));
}
if (readPos == 0) {
add_edge(enterVertex_, v, g_);
startSpanVertex = v;
} else {
add_edge(u, v, g_);
}
u = v;
readPos++;
}
assert(startSpanVertex != null_vertex);
assert(u != null_vertex);
endSpanVertex = u;
add_edge(u, exitVertex_, g_); // terminus -> $
tagSpan(startSpanVertex, endSpanVertex);
}
static int do_interned_pushv(yrc_str_t* str, const char* data, size_t sz) {
size_t current;
int i, j;
int newsz;
current = interned_size(str);
newsz = current + sz;
if (newsz >= kInternedSize) {
return externalize(str, data, current, sz);
}
str->interned.flag = 1 | (newsz << 1);
memcpy(str->interned.data, data, sz);
return 0;
}