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#ifndef GFAIO_H
#define GFAIO_H 1
#include "Common/IOUtil.h"
#include "Graph/Properties.h"
#include <boost/graph/graph_traits.hpp>
#include <cassert>
#include <cstdlib>
#include <iostream>
#include <string>
using boost::graph_traits;
struct Distance;
struct DistanceEst;
/** Write a graph in GFA format. */
template <typename Graph>
std::ostream& write_gfa1(std::ostream& out, Graph& g)
{
typedef typename graph_traits<Graph>::edge_descriptor E;
typedef typename graph_traits<Graph>::edge_iterator Eit;
typedef typename graph_traits<Graph>::vertex_descriptor V;
typedef typename graph_traits<Graph>::vertex_iterator Vit;
typedef typename vertex_bundle_type<Graph>::type VP;
out << "H\tVN:Z:1.0\n";
assert(out);
std::pair<Vit, Vit> vrange = vertices(g);
for (Vit uit = vrange.first; uit != vrange.second; ++uit, ++uit) {
V u = *uit;
if (get(vertex_removed, g, u))
continue;
const VP& vp = g[u];
out << "S\t" << get(vertex_contig_name, g, u)
<< "\t*\tLN:i:" << vp.length;
if (vp.coverage > 0)
out << "\tKC:i:" << vp.coverage;
out << '\n';
}
std::pair<Eit, Eit> erange = edges(g);
for (Eit eit = erange.first; eit != erange.second; ++eit) {
E e = *eit;
V u = source(e, g);
V v = target(e, g);
if (get(vertex_removed, g, u))
continue;
// Output only the canonical edge.
if (u > get(vertex_complement, g, v))
continue;
int distance = g[e].distance;
out << 'L'
<< '\t' << get(vertex_contig_name, g, u)
<< '\t' << (get(vertex_sense, g, u) ? '-' : '+')
<< '\t' << get(vertex_contig_name, g, v)
<< '\t' << (get(vertex_sense, g, v) ? '-' : '+');
if (distance <= 0)
out << '\t' << -distance << "M\n";
else
out << "\t*\n";
assert(out);
}
return out;
}
/** Write a GFA 2 overlap edge. */
template <typename Graph>
std::ostream& write_gfa2_edge(std::ostream& out, const Graph& g,
typename graph_traits<Graph>::edge_iterator eit)
{
typedef typename graph_traits<Graph>::edge_descriptor E;
typedef typename graph_traits<Graph>::vertex_descriptor V;
E e = *eit;
V u = source(e, g);
V v = target(e, g);
int distance = get(edge_bundle, g, eit).distance;
assert(distance <= 0);
unsigned overlap = -distance;
unsigned ulen = g[u].length;
unsigned vlen = g[v].length;
bool usense = get(vertex_sense, g, u);
bool vsense = get(vertex_sense, g, v);
unsigned ustart = usense ? 0 : ulen - overlap;
unsigned uend = usense ? overlap : ulen;
unsigned vstart = !vsense ? 0 : vlen - overlap;
unsigned vend = !vsense ? overlap : vlen;
out << "E\t*"
<< '\t' << get(vertex_name, g, u)
<< '\t' << get(vertex_name, g, v);
out << '\t' << ustart;
if (ustart == ulen)
out << '$';
out << '\t' << uend;
if (uend == ulen)
out << '$';
out << '\t' << vstart;
if (vstart == vlen)
out << '$';
out << '\t' << vend;
if (vend == vlen)
out << '$';
out << '\t' << overlap << 'M' << "\n";
assert(out);
return out;
}
/** Write GFA 2 gap edge. */
template <typename Graph>
std::ostream& write_gfa2_gap(std::ostream& out, const Graph& g,
typename graph_traits<Graph>::edge_iterator eit)
{
typedef typename graph_traits<Graph>::edge_descriptor E;
typedef typename graph_traits<Graph>::vertex_descriptor V;
E e = *eit;
V u = source(e, g);
V v = target(e, g);
return out << "G\t*"
<< '\t' << get(vertex_name, g, u)
<< '\t' << get(vertex_name, g, v)
<< '\t' << get(edge_bundle, g, eit)
<< '\n';
}
/** Write GFA 2 overlap edges. */
template <typename Graph>
std::ostream& write_gfa2_edges(std::ostream& out, const Graph& g,
const Distance*)
{
typedef typename graph_traits<Graph>::edge_iterator Eit;
typedef typename graph_traits<Graph>::edge_descriptor E;
typedef typename graph_traits<Graph>::vertex_descriptor V;
std::pair<Eit, Eit> erange = edges(g);
for (Eit eit = erange.first; eit != erange.second; ++eit) {
E e = *eit;
V u = source(e, g);
V v = target(e, g);
if (get(vertex_removed, g, u))
continue;
// Output only the canonical edge.
if (u > get(vertex_complement, g, v))
continue;
assert(!get(vertex_removed, g, v));
write_gfa2_edge(out, g, eit);
}
return out;
}
/** Write GFA 2 overlap and gap edges. */
template <typename Graph>
std::ostream& write_gfa2_edges(std::ostream& out, const Graph& g,
const DistanceEst*)
{
typedef typename graph_traits<Graph>::edge_descriptor E;
typedef typename graph_traits<Graph>::edge_iterator Eit;
typedef typename graph_traits<Graph>::vertex_descriptor V;
typedef typename edge_bundle_type<Graph>::type EP;
std::pair<Eit, Eit> erange = edges(g);
for (Eit eit = erange.first; eit != erange.second; ++eit) {
E e = *eit;
V u = source(e, g);
V v = target(e, g);
if (get(vertex_removed, g, u))
continue;
// Output only the canonical edge.
if (u > get(vertex_complement, g, v))
continue;
assert(!get(vertex_removed, g, v));
const EP& ep = get(edge_bundle, g, eit);
if (ep.stdDev > 0)
write_gfa2_gap(out, g, eit);
else
write_gfa2_edge(out, g, eit);
}
return out;
}
/** Write a graph in GFA 2 format. */
template <typename Graph>
std::ostream& write_gfa2(std::ostream& out, Graph& g)
{
typedef typename graph_traits<Graph>::vertex_descriptor V;
typedef typename graph_traits<Graph>::vertex_iterator Vit;
typedef typename vertex_bundle_type<Graph>::type VP;
typedef typename edge_bundle_type<Graph>::type EP;
out << "H\tVN:Z:2.0\n";
assert(out);
std::pair<Vit, Vit> vrange = vertices(g);
for (Vit uit = vrange.first; uit != vrange.second; ++uit, ++uit) {
V u = *uit;
if (get(vertex_removed, g, u))
continue;
const VP& vp = g[u];
out << "S\t" << get(vertex_contig_name, g, u)
<< '\t' << vp.length << "\t*";
if (vp.coverage > 0)
out << "\tKC:i:" << vp.coverage;
out << '\n';
}
return write_gfa2_edges(out, g, (EP*)NULL);
}
/** Read a graph in GFA format. */
template <typename Graph, typename BetterEP>
std::istream& read_gfa(std::istream& in, Graph& g, BetterEP betterEP)
{
assert(in);
typedef typename graph_traits<Graph>::vertex_descriptor V;
typedef typename vertex_property<Graph>::type VP;
typedef typename graph_traits<Graph>::edge_descriptor E;
typedef typename edge_property<Graph>::type EP;
// Add vertices if this graph is empty.
bool addVertices = num_vertices(g) == 0;
while (in && in.peek() != EOF) {
switch (in.peek()) {
case 'H':
in >> expect("H\tVN:Z:");
if (in.peek() == '1')
in >> expect("1.0\n");
else
in >> expect("2.0\n");
assert(in);
break;
case 'S': {
std::string uname;
in >> expect("S\t") >> uname >> expect("\t");
assert(in);
std::string seq;
unsigned length = 0;
if (isdigit(in.peek())) {
// GFA 2
in >> length >> seq;
assert(in);
} else {
// GFA 1
in >> seq;
assert(in);
assert(!seq.empty());
if (seq == "*") {
in >> expect(" LN:i:") >> length;
assert(in);
} else
length = seq.size();
}
unsigned coverage = 0;
if (in.peek() == '\t' && in.get() == '\t' && in.peek() == 'K') {
in >> expect("KC:i:") >> coverage;
assert(in);
}
in >> Ignore('\n');
assert(in);
if (addVertices) {
VP vp;
put(vertex_length, vp, length);
put(vertex_coverage, vp, coverage);
V u = add_vertex(vp, g);
put(vertex_name, g, u, uname);
} else {
V u = find_vertex(uname, false, g);
assert(get(vertex_index, g, u) < num_vertices(g));
(void)u;
}
break;
}
case 'L': {
std::string uname, vname;
char usense, vsense;
int overlap;
in >> expect("L\t")
>> uname >> usense
>> vname >> vsense >> std::ws;
if (in.peek() == '*') {
in.get();
overlap = -1;
} else {
in >> overlap >> expect("M");
}
in >> Ignore('\n');
assert(in);
assert(!uname.empty());
assert(!vname.empty());
assert(usense == '+' || usense == '-');
assert(vsense == '+' || vsense == '-');
V u = find_vertex(uname, usense == '-', g);
V v = find_vertex(vname, vsense == '-', g);
if (overlap >= 0) {
int d = -overlap;
EP ep(d);
add_edge(u, v, ep, g);
} else
add_edge(u, v, g);
break;
}
case 'E': {
std::string ename, uname, vname;
in >> expect("E\t") >> ename >> uname >> vname;
assert(in);
unsigned ustart, uend, vstart, vend;
in >> ustart >> Skip('$')
>> uend >> Skip('$')
>> vstart >> Skip('$')
>> vend >> Skip('$')
>> Ignore('\n');
assert(in);
unsigned ulength = uend - ustart;
unsigned vlength = vend - vstart;
if (ulength != vlength) {
std::cerr << "error: alignment contains gaps: " << ename << '\t' << uname << '\t' << vname << '\n';
exit(EXIT_FAILURE);
}
V u = find_vertex(uname, g);
V v = find_vertex(vname, g);
int d = -ulength;
EP ep(d);
add_edge(u, v, ep, g);
break;
}
case 'G': {
std::string ename, uname, vname;
in >> expect("G\t") >> ename >> uname >> vname;
assert(in);
EP ep;
in >> ep >> Ignore('\n');
assert(in);
V u = find_vertex(uname, g);
V v = find_vertex(vname, g);
E e;
bool found;
boost::tie(e, found) = edge(u, v, g);
if (found) {
// Parallel edge
EP& ref = g[e];
ref = betterEP(ref, ep);
} else
add_edge(u, v, ep, g);
break;
}
case '#': // comment
case 'C': // GFA1 containment
case 'F': // GFA2 fragment
case 'O': // GFA2 ordered path
case 'P': // GFA1 path
case 'U': // GFA2 unordered set
in >> Ignore('\n');
break;
default: {
std::string s;
in >> s >> Ignore('\n');
std::cerr << "warning: unknown record type: `" << s << "'\n";
}
}
}
assert(in.eof());
return in;
}
#endif
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