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#ifndef FASTAREADER_H
#define FASTAREADER_H 1
#include "Common/Sequence.h"
#include "Common/StringUtil.h" // for chomp
#include <cassert>
#include <cstdlib> // for exit
#include <fstream>
#include <istream>
#include <limits> // for numeric_limits
#include <ostream>
/** Read a FASTA, FASTQ, export, qseq or SAM file. */
class FastaReader {
public:
enum {
/** Fold lower-case characters to upper-case. */
FOLD_CASE = 0, NO_FOLD_CASE = 1,
/** Convert to standard quality. */
NO_CONVERT_QUALITY = 0, CONVERT_QUALITY = 2,
};
bool flagFoldCase() { return ~m_flags & NO_FOLD_CASE; }
bool flagConvertQual() { return m_flags & CONVERT_QUALITY; }
FastaReader(const char* path, int flags, int len = 0);
~FastaReader()
{
if (!m_in.eof()) {
std::string line;
getline(line);
die() << "expected end-of-file near\n"
<< line << '\n';
exit(EXIT_FAILURE);
}
}
Sequence read(std::string& id, std::string& comment,
char& anchor, std::string& qual);
/** Split the fasta file into nsections and seek to the start
* of section. */
void split(unsigned section, unsigned nsections);
/** Return whether this stream is at end-of-file. */
bool eof() const { return m_in.eof(); };
/** Return true if failbit or badbit of stream is set. */
bool fail() const { return m_in.fail(); };
/** Return whether this stream is good. */
operator const void*() const { return m_in ? this : NULL; }
/** Return the next character of this stream. */
int peek() { return m_in.peek(); }
/** Interface for manipulators. */
FastaReader& operator>>(std::istream& (*f)(std::istream&))
{
f(m_in);
return *this;
}
/** Returns the number of unchaste reads. */
unsigned unchaste() const { return m_unchaste; }
FastaReader& operator >>(Sequence& seq)
{
std::string id, comment, qual;
char anchor;
seq = this->read(id, comment, anchor, qual);
return *this;
}
private:
/** Read a single line. */
std::istream& getline(std::string& s)
{
if (std::getline(m_in, s)) {
chomp(s, '\r');
m_line++;
}
return m_in;
}
/** Ignore the specified number of lines. */
std::istream& ignoreLines(unsigned n)
{
for (unsigned i = 0; i < n; ++i) {
if (m_in.ignore(
std::numeric_limits<std::streamsize>::max(),
'\n'))
m_line++;
}
return m_in;
}
std::ostream& die();
bool isChaste(const std::string& s, const std::string& line);
void checkSeqQual(const std::string& s, const std::string& q);
const char* m_path;
std::ifstream m_fin;
std::istream& m_in;
/** Flags indicating parsing options. */
int m_flags;
/** Number of lines read. */
unsigned m_line;
/** Count of unchaste reads. */
unsigned m_unchaste;
/** Position of the end of the current section. */
std::streampos m_end;
/** Trim sequences to this length. 0 is unlimited. */
const int m_maxLength;
};
/** A FASTA record. */
struct FastaRecord
{
/** Identifier */
std::string id;
/** Comment following the first white-space of the header */
std::string comment;
/** Anchor base for a colour-space sequence */
char anchor;
/** The sequence */
Sequence seq;
FastaRecord() : anchor(0) { }
FastaRecord(const std::string& id, const std::string& comment,
const Sequence& seq)
: id(id), comment(comment), anchor(0), seq(seq) { }
operator Sequence() const { return seq; }
FastaRecord& operator=(const std::string& s)
{
seq = s;
return *this;
}
size_t size() const { return seq.size(); }
friend FastaReader& operator >>(FastaReader& in, FastaRecord& o)
{
std::string q;
o.seq = in.read(o.id, o.comment, o.anchor, q);
return in;
}
friend std::ostream& operator <<(std::ostream& out,
const FastaRecord& o)
{
out << '>' << o.id;
if (!o.comment.empty())
out << ' ' << o.comment;
return out << '\n' << o.seq << '\n';
}
};
/** A FASTQ record. */
struct FastqRecord : FastaRecord
{
/** Quality */
std::string qual;
FastqRecord() { }
FastqRecord(const std::string& id, const std::string& comment,
const Sequence& seq, const std::string& qual)
: FastaRecord(id, comment, seq), qual(qual)
{
assert(seq.length() == qual.length());
}
friend FastaReader& operator >>(FastaReader& in, FastqRecord& o)
{
o.seq = in.read(o.id, o.comment, o.anchor, o.qual);
return in;
}
friend std::ostream& operator <<(std::ostream& out,
const FastqRecord& o)
{
if (o.qual.empty())
return out << static_cast<const FastaRecord&>(o);
out << '@' << o.id;
if (!o.comment.empty())
out << ' ' << o.comment;
return out << '\n' << o.seq << "\n"
"+\n" << o.qual << '\n';
}
};
#endif //FASTAREADER_H
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