dozeu_interface.cpp File Reference

#include <cstdio>
#include <assert.h>
#include <utility>
#include "dozeu_interface.hpp"
#include <dozeu/dozeu.h>

Macros
#define	DZ_FULL_LENGTH_BONUS
#define	DZ_CIGAR_OP   0x04030201
#define	_add_edit(_from_len, _to_len, _subseq)
#define	_push_mapping(_id)
#define	_push_op(_m, _op, _len)
#define	_append_op(_m, _op, _init)
#define	_flush_op(_m, _next_op)

Enumerations
enum	{ MISMATCH = 1, MATCH = 2, INS = 3, DEL = 4 }

Macro Definition Documentation

_add_edit

#define _add_edit	(		_from_len,
			_to_len,
			_subseq
	)

Value:

        { \
        Edit *e = mapping->add_edit(); \
        e->set_from_length((_from_len)); \
        e->set_to_length((_to_len)); \
        /* expect a branch dependent on a compile-time NULL will be eliminated */ \
        if((_subseq) != nullptr) { e->set_sequence((char const *)(_subseq), (size_t)(_to_len)); } \
    }

_append_op

#define _append_op	(		_m,
			_op,
			_init
	)

Value:

        { \
        if((state & 0xff) == (_op)) { state += 0x100; } \
        else { _push_op(_m, state & 0xff, state>>8); state = (_op) | ((_init)<<8); } \
    }

_flush_op

#define _flush_op	(		_m,
			_next_op
	)

Value:

        { \
        _push_op(_m, state & 0xff, state>>8); state = (_next_op); \
    }

_push_mapping

#define _push_mapping

(

_id

)

Value:

        ({ \
        handle_t n = graph.order[(_id)]; \
        Mapping *mapping = path->add_mapping(); \
        mapping->set_rank(path->mapping_size()); \
        Position *position = mapping->mutable_position(); \
        position->set_node_id(graph.graph.get_id(n)); \
        position->set_is_reverse(graph.graph.get_is_reverse(n)); \
        position->set_offset(ref_offset); ref_offset = 0; \
        mapping; \
    })

_push_op

#define _push_op	(		_m,
			_op,
			_len
	)

Value:

        { \
        query_offset += push_edit(_m, (_op), &query[query_offset], (_len)); \
    }

DZ_CIGAR_OP

#define DZ_CIGAR_OP   0x04030201

DZ_FULL_LENGTH_BONUS

#define DZ_FULL_LENGTH_BONUS

Enumeration Type Documentation

anonymous enum

anonymous enum

Enumerator
MISMATCH
MATCH
INS
DEL