/*

Copyright (C) 2016,2017 BGI Research

Author: Shi Quan ([email protected])

Permission is hereby granted, free of charge, to any person obtaining a copy

of this software and associated documentation files (the "Software"), to deal

in the Software without restriction, including without limitation the rights

to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

copies of the Software, and to permit persons to whom the Software is

furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in

all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL

THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING

FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER

DEALINGS IN THE SOFTWARE.

*/

// sequence - a simple collection for handling sequences

//

#ifndef SEQUENCE_HEADER

#define SEQUENCE_HEADER

#include <stdio.h>

#include <stdlib.h>

#if defined(_MSC_VER) && !defined(__clang__)

# define inline __inline

#endif

#define C4_A 0

#define C4_C 1

#define C4_G 2

#define C4_T 3

#define C4_U 3

#define C4_N 4

#define seqarr "ACGTN"

#define revseqarr "TGCAN"

#define SEQ_COMP(a,b) (a + b == 3)

typedef char * (*func_dup_seq)(const char *, unsigned long );

extern int seq2code4(int seq);

extern char *rev_seqs(const char *dna_seqs, unsigned long n);

#define C4_Stop 0

#define C4_Phe 1

#define C4_Leu 2

#define C4_Ser 3

#define C4_Tyr 4

#define C4_Cys 5

#define C4_Trp 6

#define C4_Pro 7

#define C4_His 8

#define C4_Gln 9

#define C4_Arg 10

#define C4_Ile 11

#define C4_Met 12

#define C4_Thr 13

#define C4_Asn 14

#define C4_Lys 15

#define C4_Val 16

#define C4_Ala 17

#define C4_Asp 18

#define C4_Glu 19

#define C4_Gly 20

const static char *codon_names[] = {

"Stop", "Phe", "Leu", "Ser", "Tyr", "Cys", "Trp", "Pro", "His", "Gln",

"Arg", "Ile", "Met", "Thr", "Asn", "Lys", "Val", "Ala", "Asp", "Glu", "Gly",

};

const static char *codon_short_names[] = {

"X", "F", "L", "S", "Y", "C", "W", "P", "H", "Q",

"R", "I", "M", "T", "N", "K", "V", "A", "D", "E", "G",

};

const static int codon_matrix[4][4][4] = {

{

{ C4_Lys, C4_Asn, C4_Lys, C4_Asn, },

{ C4_Thr, C4_Thr, C4_Thr, C4_Thr, },

{ C4_Arg, C4_Ser, C4_Arg, C4_Ser, },

{ C4_Ile, C4_Ile, C4_Met, C4_Ile, },

},{

{ C4_Gln, C4_His, C4_Gln, C4_His, },

{ C4_Pro, C4_Pro, C4_Pro, C4_Pro, },

{ C4_Arg, C4_Arg, C4_Arg, C4_Arg, },

{ C4_Leu, C4_Leu, C4_Leu, C4_Leu, },

},{

{ C4_Glu, C4_Asp, C4_Glu, C4_Asp, },

{ C4_Ala, C4_Ala, C4_Ala, C4_Ala, },

{ C4_Gly, C4_Gly, C4_Gly, C4_Gly, },

{ C4_Val, C4_Val, C4_Val, C4_Val, },

},{

{ C4_Stop, C4_Tyr, C4_Stop, C4_Tyr, },

{ C4_Ser, C4_Ser, C4_Ser, C4_Ser, },

{ C4_Stop, C4_Cys, C4_Trp, C4_Cys, },

{ C4_Leu, C4_Phe, C4_Leu, C4_Phe, },

},

};

// no check the codon length for fast read

static inline int codon2aminoid(char *codon)

{

return codon_matrix[seq2code4(codon[0])][seq2code4(codon[1])][seq2code4(codon[2])];

}

// check the variants type

enum var_type {

_var_type_promoter_to_int = -1,

var_is_unknown,

var_is_reference,

var_is_intron,

var_is_noncoding,

var_is_utr5,

var_is_utr3,

var_is_synonymous,

var_is_missense,

var_is_nonsense, // stop gain

var_is_inframe_insertion,

var_is_inframe_deletion,

var_is_inframe_delins,

var_is_frameshift,

var_is_stop_lost,

var_is_stop_retained,

//var_is_splice_site,

//var_is_splice_donor,

//var_is_splice_acceptor,

var_is_complex,

var_is_no_call,

};

enum var_type_splice {

var_is_not_splice = 0,

var_is_splice_site,

var_is_splice_donor,

var_is_splice_acceptor,

};

static inline const char *var_type_string(enum var_type type)

{

static const char* vartypes[21] = {

"Unknown",

"Reference",

"Intron",

"Noncoding",

"Utr5",

"Utr3",

"Synonymous",

"Missense",

"Nonsense",

"InframeInsertion",

"InframeDeletion",

"InframeDelins",

"Frameshift",

"StopLost",

"StopRetained",

//"SpliceSite",

//"SpliceDonor",

//"SpliceAcceptor",

"Complex",

"NoCall",

NULL, NULL, NULL, NULL,

};

assert(type >= 0);

return vartypes[type];

}

static inline const char *var_type_splice_string(enum var_type_splice type)

{

static const char *splicetypes[5] = {

"NotSplice",

"SpliceSite",

"SpliceDonor",

"SpliceAcceptor",

NULL,

};

assert(type >= 0 );

return splicetypes[type];

}

// 1 on yes, 0 on no

static inline int check_is_stop(char *codon)

{

return codon_matrix[seq2code4(codon[0])][seq2code4(codon[1])][seq2code4(codon[2])] == C4_Stop;

}

static inline void compl_seq(char *seq, int l)

{

int i;

for ( i = 0; i < l/2; i++ ) {

char c = revseqarr[seq2code4(seq[i])];

seq[i] = revseqarr[seq2code4(seq[l-i-1])];

seq[l-i-1] = c;

}

if ( l & 1 ) {

seq[l/2] = revseqarr[seq2code4(seq[l/2])];

}

}

extern int same_DNA_seqs(const char *a, const char *b, int l );

extern int check_stop_codon(char *seq, char *p_end);

extern enum var_type check_var_type(char *block, int block_length, int start, char *ref, int ref_length, char *alt, int alt_length );

#endif