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#ifndef FASTA_INDEX_H
#define FASTA_INDEX_H 1
#include "IOUtil.h"
#include <boost/tuple/tuple.hpp>
#include <algorithm>
#include <cassert>
#include <fstream>
#include <iterator> // for ostream_iterator
#include <string>
#include <vector>
/** A record of an indexed FASTA file. */
struct FAIRecord
{
size_t offset;
size_t size;
std::string id;
FAIRecord() : offset(0), size(0) { }
FAIRecord(size_t offset, size_t size, const std::string& id)
: offset(offset), size(size), id(id) { }
friend std::ostream& operator<<(std::ostream& out,
const FAIRecord& o)
{
return out << o.id << '\t' << o.size << '\t' << o.offset
<< '\t' << o.size << '\t' << o.size + 1;
}
friend std::istream& operator>>(std::istream& in,
FAIRecord& o)
{
size_t lineLen, lineBinLen;
in >> o.id >> o.size >> o.offset >> lineLen >> lineBinLen;
if (!in)
return in;
assert(o.size == lineLen || lineLen == lineBinLen);
return in >> Ignore('\n');
}
};
/** An indexed FASTA (fai) file. */
class FastaIndex
{
typedef std::vector<FAIRecord> Data;
struct CompareOffset
{
/** Used with upper_bound. */
bool operator()(size_t a, const FAIRecord& b) const
{
return a < b.offset;
}
};
public:
typedef boost::tuple<const FAIRecord&, size_t> SeqPos;
/** Return the number of contigs. */
size_t size() { return m_data.size(); }
/** Return the size of the FASTA file. */
size_t fileSize() const
{
assert(!m_data.empty());
return m_data.back().offset + m_data.back().size + 1;
}
typedef Data::const_iterator const_iterator;
const_iterator begin() const { return m_data.begin(); }
const_iterator end() const { return m_data.end(); }
/** Index the specified FASTA file. */
void index(const std::string& path)
{
m_data.clear();
std::ifstream in(path.c_str());
assert_good(in, path);
char c;
for (std::string id;
in >> c && in >> id && in >> Ignore('\n');) {
assert(c == '>');
assert(!id.empty());
std::streampos offset = in.tellg();
assert(offset > 0);
in >> Ignore('\n');
size_t n = in.gcount();
assert(n > 0);
m_data.push_back(FAIRecord(offset, n - 1, id));
}
assert(in.eof());
}
/** Translate a file offset to a sequence:position coordinate. */
SeqPos operator[](size_t offset) const
{
Data::const_iterator it = std::upper_bound(
m_data.begin(), m_data.end(),
offset, CompareOffset());
assert(it != m_data.begin());
--it;
assert(it != m_data.end());
assert(it->offset <= offset);
assert(offset < it->offset + it->size);
return SeqPos(*it, offset - it->offset);
}
/** Write FASTA headers to the specified seekable stream. */
void writeFASTAHeaders(std::ostream& out) const
{
assert(out);
if (!out.seekp(0))
return;
for (Data::const_iterator it = m_data.begin();
it != m_data.end(); ++it) {
out << '>' << it->id << ' ';
assert(it->offset > 0);
if (!out.seekp(it->offset - 1))
break;
out << '\n';
if (!out.seekp(it->offset + it->size))
break;
out << '\n';
}
}
/** Write this index to a stream in SAM format. */
void writeSAMHeader(std::ostream& out) const
{
for (Data::const_iterator it = m_data.begin();
it != m_data.end(); ++it)
out << "@SQ\tSN:" << it->id
<< "\tLN:" << it->size << '\n';
}
/** Write this index to a stream. */
friend std::ostream& operator<<(std::ostream& out,
const FastaIndex& o)
{
std::copy(o.m_data.begin(), o.m_data.end(),
std::ostream_iterator<FAIRecord>(out, "\n"));
return out;
}
/** Read a FASTA index from a stream. */
friend std::istream& operator>>(std::istream& in,
FastaIndex& o)
{
assert(in.good());
o.m_data.clear();
// Count the number of records.
if (in.seekg(0, std::ios::beg)) {
size_t n = 0;
while (in)
if (in.get() == '\n')
n++;
o.m_data.reserve(n);
in.clear();
in.seekg(0, std::ios::beg);
assert(in.good());
} else
in.clear();
// Read the records.
for (FAIRecord rec; in >> rec;) {
if (!o.m_data.empty())
assert(rec.offset > o.m_data.back().offset);
o.m_data.push_back(rec);
}
assert(in.eof());
assert(!o.m_data.empty());
return in;
}
private:
Data m_data;
};
#endif
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