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/** @file
* @brief This header contains all structures and prototypes for creating a
* mutation matrix and estimating distances trough an evolutionary model
* thereof.
*/
#pragma once
#include <stdlib.h>
/**
* This enum contains all possible mutations. The total number
* of different possible mutations is MUTCOUNTS.
*/
enum {
AtoA,
AtoC,
AtoG,
AtoT,
CtoA,
CtoC,
CtoG,
CtoT,
GtoA,
GtoC,
GtoG,
GtoT,
TtoA,
TtoC,
TtoG,
TtoT,
MUTCOUNTS
};
/** @brief The mutation matrix.
*
* We need to keep track of the different types of mutations between two
* sequences. For this the following matrix is filled.
*
* To A C G T
* From
* A ( )
* C ( )
* G ( )
* T ( )
*
* The cells are absolute counts. Together with seq_len (the query length),
* we can deduce the substitution rate and coverage.
*
* As libdivsufsort is 32 bit the sequence length is limited to (INT_MAX-1)/2.
* We can thus use the same limit for the counts.
*/
typedef struct model {
/** The absolute counts of mutation types. */
unsigned int counts[MUTCOUNTS];
/** The query length. */
unsigned int seq_len;
} model;
void model_count_equal(model *, const char *, size_t);
void model_count(model *, const char *, const char *, size_t);
model model_average(const model *, const model *);
double model_coverage(const model *);
double estimate_RAW(const model *);
double estimate_JC(const model *);
double estimate_KIMURA(const model *);
double estimate_LOGDET(const model *);
model model_bootstrap(model);
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