liboxli-dev 2.0+dfsg-10 / usr / include / oxli / read_parsers.hh

/*
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2012-2015, Michigan State University.
Copyright (C) 2015, The Regents of the University of California.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:

    * Redistributions of source code must retain the above copyright
      notice, this list of conditions and the following disclaimer.

    * Redistributions in binary form must reproduce the above
      copyright notice, this list of conditions and the following
      disclaimer in the documentation and/or other materials provided
      with the distribution.

    * Neither the name of the Michigan State University nor the names
      of its contributors may be used to endorse or promote products
      derived from this software without specific prior written
      permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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LICENSE (END)

Contact: khmer-project@idyll.org
*/
#ifndef READ_PARSERS_HH
#define READ_PARSERS_HH

#include <regex.h>
#include <stddef.h>
#include <stdint.h>
#include <cstdlib>
#include <iostream>
#include <string>
#include <utility>

#include "khmer.hh"
#include "khmer_exception.hh"

namespace khmer
{



namespace read_parsers
{

struct NoMoreReadsAvailable : public  khmer_file_exception {
    explicit NoMoreReadsAvailable(const std::string& msg) :
        khmer_file_exception(msg) {}
    NoMoreReadsAvailable() :
        khmer_file_exception("No more reads available in this stream.") {}
};

struct InvalidRead : public  khmer_value_exception {
    explicit InvalidRead(const std::string& msg) :
        khmer_value_exception(msg) {}
    InvalidRead() :
        khmer_value_exception("Invalid FASTA/Q read") {}
};

struct UnknownPairReadingMode : public  khmer_value_exception {
    explicit UnknownPairReadingMode(const std::string& msg) :
        khmer_value_exception(msg) {}
    UnknownPairReadingMode() :
        khmer_value_exception("Unknown pair reading mode supplied.") {}
};

struct InvalidReadPair : public  khmer_value_exception {
    explicit InvalidReadPair(const std::string& msg) :
        khmer_value_exception(msg) {}
    InvalidReadPair() :
        khmer_value_exception("Invalid read pair detected.") {}
};

struct Read {
    std:: string    name;
    std:: string    annotations;
    std:: string    sequence;
    std:: string    quality;
    // TODO? Add description field.

    inline void reset ( )
    {
        name.clear( );
        annotations.clear( );
        sequence.clear( );
        quality.clear( );
    }

    void write_to(std::ostream&);
};

typedef std:: pair< Read, Read >	ReadPair;

struct IParser {

    enum {
        PAIR_MODE_ALLOW_UNPAIRED = 0,
        PAIR_MODE_IGNORE_UNPAIRED,
        PAIR_MODE_ERROR_ON_UNPAIRED
    };

    static IParser * const  get_parser(
        std:: string const 	&ifile_name
    );

    IParser( );
    virtual ~IParser( );

    virtual bool		is_complete( ) = 0;

    // Note: 'get_next_read' exists for legacy reasons.
    //	     In the long term, it should be eliminated in favor of direct use of
    //	     'imprint_next_read'. A potentially costly copy-by-value happens
    //	     upon return.
    // TODO: Eliminate all calls to 'get_next_read'.
    // Or switch to C++11 w/ move constructors
    inline Read		get_next_read( )
    {
        Read the_read;
        imprint_next_read( the_read );
        return the_read;
    }
    virtual void	imprint_next_read( Read &the_read ) = 0;

    virtual void	imprint_next_read_pair(
        ReadPair &the_read_pair,
        uint8_t mode = PAIR_MODE_ERROR_ON_UNPAIRED
    );

    size_t		    get_num_reads()
    {
        return _num_reads;
    }

protected:

    size_t		_num_reads;
    bool        _have_qualities;
    regex_t		_re_read_2_nosub;
    regex_t		_re_read_1;
    regex_t		_re_read_2;

#if (0)
    void		_imprint_next_read_pair_in_allow_mode(
        ReadPair &the_read_pair
    );
#endif

    void		_imprint_next_read_pair_in_ignore_mode(
        ReadPair &the_read_pair
    );
    void		_imprint_next_read_pair_in_error_mode(
        ReadPair &the_read_pair
    );
    bool		_is_valid_read_pair(
        ReadPair &the_read_pair, regmatch_t &match_1, regmatch_t &match_2
    );

}; // struct IParser

class SeqAnParser : public IParser
{

public:
    explicit SeqAnParser( const char * filename );
    ~SeqAnParser( );

    bool is_complete( );
    void imprint_next_read(Read &the_read);

private:
    struct Handle;

    Handle* _private;

};

inline PartitionID _parse_partition_id(std::string name)
{
    PartitionID p = 0;
    const char * s = name.c_str() + name.length() - 1;
    if (!(*(s + 1) == (unsigned int) NULL)) {
        throw khmer_exception();
    }

    while(*s != '\t' && s >= name.c_str()) {
        s--;
    }

    if (*s == '\t') {
        p = (PartitionID) atoi(s + 1);
    } else {
        std::cerr << "consume_partitioned_fasta barfed on read "  << name << "\n";
        throw khmer_exception();
    }

    return p;
}



} // namespace read_parsers


} // namespace khmer


#endif // READ_PARSERS_HH

// vim: set ft=cpp sts=4 sw=4 tw=80: