//TODO: translate this
void haplo_d::initialize_skeleton(thread_t& t, pair<int,int> interval, cross_section& prevAs, xg::XG& graph) {
rectangle rect;
int new_height;
int last_height = prevAs.S[0].J;
bool add_rectangle;
bool add_A;
//TODO: fix this
int width = 0;
for(int i = interval.first; i <= interval.second; i++) {
// Count the number of base pairs since the last entry or exit node
width += graph.node_length(t[i-1].node_id);
new_height = graph.node_height(t[i]);
if(cs.back().S.size() != 0) {
if(i == interval.first) {
prevAs.S[0];
} else {
rect = cs.back().S[0];
}
rect.J = rect.get_next_J(t[i],graph); // step this strip forward
// Did any threads leave?
if(last_height > rect.J) {
add_A = 1;
}
// Are there any threads here which didn't come from the previous node?
if(rect.J < new_height) {
add_rectangle = 1;
add_A = 1;
}
// This is an entry or exit node, add a cross-section to the vector of
// cross-sections (which corresponds to the "A" set in the theory doc)
if(add_A) {
cs.back().width = width;
width = 0;
cs.push_back(cross_section(new_height,i,t[i]));
} else {
// This isn't a node where anything leaves or joins, let's skip over it
cs.back().bridge.push_back(t[i]);
for (size_t a = 0; a < cs.back().S.size(); a++) {
cs.back().S[a].extend(t[i],graph);
}
}
// This is an entry node; we also need a new rectangle corresponding to the
// new strip. We need to do this *before* we populate since cross_sections
// arrange rectangles newest -> oldest
// NB that add_rectangle implies add_A
if(add_rectangle) {
rectangle new_rect;
new_rect.extend(t[i],graph);
new_rect.J = new_height;
cs.back().height = new_rect.J;
cs.back().S.push_back(new_rect);
cs.back().S.back().I = new_rect.J - rect.J;
}
if(add_A) {
int b = cs.size()-1;
if(rect.J > 0) {
cs[b].S.push_back(rect);
cs[b].S.back().prev = 0;
cs[b-1].S[0].next = cs[b].S.size()-1;
}
}
last_height = new_height;
add_A = 0;
add_rectangle = 0;
} else {
cs.back().width = width;
width = 0;
cs.push_back(cross_section(new_height,i,t[i]));
if(new_height > 0) {
rectangle new_rect;
new_rect.extend(t[i],graph);
new_rect.J = new_height;
cs.back().height = new_rect.J;
cs.back().S.push_back(new_rect);
cs.back().S.back().I = new_rect.J - rect.J;
}
}
}
if(cs.size() == 1) {
cs.back().width = width;
}
cs.back().width += graph.node_length(t.back().node_id) - 1;
for(int i = 0; i < cs.size(); i++) {
tot_width += cs[i].width;
}
}
PathIndex::PathIndex(const Path& path, const xg::XG& index) {
// Trace the given path in the given XG graph, collecting sequence
// We're going to build the sequence string
std::stringstream seq_stream;
// What base are we at in the path?
size_t path_base = 0;
// What was the last rank? Ranks must always go up.
int64_t last_rank = -1;
for (size_t i = 0; i < path.mapping_size(); i++) {
auto& mapping = path.mapping(i);
if (!by_id.count(mapping.position().node_id())) {
// This is the first time we have visited this node in the path.
// Add in a mapping.
by_id[mapping.position().node_id()] =
std::make_pair(path_base, mapping.position().is_reverse());
#ifdef debug
#pragma omp critical (cerr)
std::cerr << "Node " << mapping.position().node_id() << " rank " << mapping.rank()
<< " starts at base " << path_base << " with "
<< index.node_sequence(mapping.position().node_id()) << std::endl;
#endif
// Make sure ranks are monotonically increasing along the path, or
// unset.
assert(mapping.rank() > last_rank || (mapping.rank() == 0 && last_rank == 0));
last_rank = mapping.rank();
}
// Say that this node appears here along the reference in this
// orientation.
by_start[path_base] = NodeSide(mapping.position().node_id(), mapping.position().is_reverse());
// Remember that occurrence by node ID.
node_occurrences[mapping.position().node_id()].push_back(by_start.find(path_base));
// Find the node's sequence
std::string node_sequence = index.node_sequence(mapping.position().node_id());
while(path_base == 0 && node_sequence.size() > 0 &&
(node_sequence[0] != 'A' && node_sequence[0] != 'T' && node_sequence[0] != 'C' &&
node_sequence[0] != 'G' && node_sequence[0] != 'N')) {
// If the path leads with invalid characters (like "X"), throw them
// out when computing path positions.
// TODO: this is a hack to deal with the debruijn-brca1-k63 graph,
// which leads with an X.
#pragma omp critical (cerr)
std::cerr << "Warning: dropping invalid leading character "
<< node_sequence[0] << " from node " << mapping.position().node_id()
<< std::endl;
node_sequence.erase(node_sequence.begin());
}
if (mapping.position().is_reverse()) {
// Put the reverse sequence in the path
seq_stream << reverse_complement(node_sequence);
} else {
// Put the forward sequence in the path
seq_stream << node_sequence;
}
// Whether we found the right place for this node in the reference or
// not, we still need to advance along the reference path. We assume the
// whole node (except any leading bogus characters) is included in the
// path (since it sort of has to be, syntactically, unless it's the
// first or last node).
path_base += node_sequence.size();
// TODO: handle leading bogus characters in calls on the first node.
}
// Record the length of the last mapping's node, since there's no next mapping to work it out from
last_node_length = path.mapping_size() > 0 ?
index.node_length(path.mapping(path.mapping_size() - 1).position().node_id()) :
0;
// Create the actual reference sequence we will use
sequence = seq_stream.str();
#ifdef debug
// Announce progress.
#pragma omp critical (cerr)
std::cerr << "Traced " << path_base << " bp path." << std::endl;
if (sequence.size() < 100) {
#pragma omp critical (cerr)
std::cerr << "Sequence: " << sequence << std::endl;
}
#endif
}