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stdaln.c
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stdaln.c
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/* The MIT License
Copyright (c) 2003-2006, 2008, 2009, by Heng Li <[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.
*/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <stdint.h>
#include "stdaln.h"
/* char -> 17 (=16+1) nucleotides */
unsigned char aln_nt16_table[256] = {
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,16 /*'-'*/,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15, 1,14, 4, 11,15,15, 2, 13,15,15,10, 15, 5,15,15,
15,15, 3, 6, 8,15, 7, 9, 0,12,15,15, 15,15,15,15,
15, 1,14, 4, 11,15,15, 2, 13,15,15,10, 15, 5,15,15,
15,15, 3, 6, 8,15, 7, 9, 0,12,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
};
char aln_nt16_rev_table[] = "XAGRCMSVTWKDYHBN-";
/* char -> 5 (=4+1) nucleotides */
unsigned char aln_nt4_table[256] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5 /*'-'*/, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 2, 4, 4, 4, 1, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 2, 4, 4, 4, 1, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
};
char aln_nt4_rev_table[] = "AGCTN-";
/* char -> 22 (=20+1+1) amino acids */
unsigned char aln_aa_table[256] = {
21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
21,21,21,21, 21,21,21,21, 21,21,20,21, 21,22 /*'-'*/,21,21,
21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
21, 0,21, 4, 3, 6,13, 7, 8, 9,21,11, 10,12, 2,21,
14, 5, 1,15, 16,21,19,17, 21,18,21,21, 21,21,21,21,
21, 0,21, 4, 3, 6,13, 7, 8, 9,21,11, 10,12, 2,21,
14, 5, 1,15, 16,21,19,17, 21,18,21,21, 21,21,21,21,
21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21,
21,21,21,21, 21,21,21,21, 21,21,21,21, 21,21,21,21
};
char aln_aa_rev_table[] = "ARNDCQEGHILKMFPSTWYV*X-";
/* 01234567890123456789012 */
/* translation table. They are useless in stdaln.c, but when you realize you need it, you need not write the table again. */
unsigned char aln_trans_table_eu[66] = {
11,11, 2, 2, 1, 1,15,15, 16,16,16,16, 9,12, 9, 9,
6, 6, 3, 3, 7, 7, 7, 7, 0, 0, 0, 0, 19,19,19,19,
5, 5, 8, 8, 1, 1, 1, 1, 14,14,14,14, 10,10,10,10,
20,20,18,18, 20,17, 4, 4, 15,15,15,15, 10,10,13,13, 21, 22
};
char aln_trans_table_eu_char[] = "KKNNRRSSTTTTIMIIEEDDGGGGAAAAVVVVQQHHRRRRPPPPLLLL**YY*WCCSSSSLLFFX";
/* 01234567890123456789012345678901234567890123456789012345678901234 */
int aln_sm_blosum62[] = {
/* A R N D C Q E G H I L K M F P S T W Y V * X */
4,-1,-2,-2, 0,-1,-1, 0,-2,-1,-1,-1,-1,-2,-1, 1, 0,-3,-2, 0,-4, 0,
-1, 5, 0,-2,-3, 1, 0,-2, 0,-3,-2, 2,-1,-3,-2,-1,-1,-3,-2,-3,-4,-1,
-2, 0, 6, 1,-3, 0, 0, 0, 1,-3,-3, 0,-2,-3,-2, 1, 0,-4,-2,-3,-4,-1,
-2,-2, 1, 6,-3, 0, 2,-1,-1,-3,-4,-1,-3,-3,-1, 0,-1,-4,-3,-3,-4,-1,
0,-3,-3,-3, 9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-4,-2,
-1, 1, 0, 0,-3, 5, 2,-2, 0,-3,-2, 1, 0,-3,-1, 0,-1,-2,-1,-2,-4,-1,
-1, 0, 0, 2,-4, 2, 5,-2, 0,-3,-3, 1,-2,-3,-1, 0,-1,-3,-2,-2,-4,-1,
0,-2, 0,-1,-3,-2,-2, 6,-2,-4,-4,-2,-3,-3,-2, 0,-2,-2,-3,-3,-4,-1,
-2, 0, 1,-1,-3, 0, 0,-2, 8,-3,-3,-1,-2,-1,-2,-1,-2,-2, 2,-3,-4,-1,
-1,-3,-3,-3,-1,-3,-3,-4,-3, 4, 2,-3, 1, 0,-3,-2,-1,-3,-1, 3,-4,-1,
-1,-2,-3,-4,-1,-2,-3,-4,-3, 2, 4,-2, 2, 0,-3,-2,-1,-2,-1, 1,-4,-1,
-1, 2, 0,-1,-3, 1, 1,-2,-1,-3,-2, 5,-1,-3,-1, 0,-1,-3,-2,-2,-4,-1,
-1,-1,-2,-3,-1, 0,-2,-3,-2, 1, 2,-1, 5, 0,-2,-1,-1,-1,-1, 1,-4,-1,
-2,-3,-3,-3,-2,-3,-3,-3,-1, 0, 0,-3, 0, 6,-4,-2,-2, 1, 3,-1,-4,-1,
-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4, 7,-1,-1,-4,-3,-2,-4,-2,
1,-1, 1, 0,-1, 0, 0, 0,-1,-2,-2, 0,-1,-2,-1, 4, 1,-3,-2,-2,-4, 0,
0,-1, 0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1, 1, 5,-2,-2, 0,-4, 0,
-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1, 1,-4,-3,-2,11, 2,-3,-4,-2,
-2,-2,-2,-3,-2,-1,-2,-3, 2,-1,-1,-2,-1, 3,-3,-2,-2, 2, 7,-1,-4,-1,
0,-3,-3,-3,-1,-2,-2,-3,-3, 3, 1,-2, 1,-1,-2,-2, 0,-3,-1, 4,-4,-1,
-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4, 1,-4,
0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2, 0, 0,-2,-1,-1,-4,-1
};
int aln_sm_blosum45[] = {
/* A R N D C Q E G H I L K M F P S T W Y V * X */
5,-2,-1,-2,-1,-1,-1, 0,-2,-1,-1,-1,-1,-2,-1, 1, 0,-2,-2, 0,-5, 0,
-2, 7, 0,-1,-3, 1, 0,-2, 0,-3,-2, 3,-1,-2,-2,-1,-1,-2,-1,-2,-5,-1,
-1, 0, 6, 2,-2, 0, 0, 0, 1,-2,-3, 0,-2,-2,-2, 1, 0,-4,-2,-3,-5,-1,
-2,-1, 2, 7,-3, 0, 2,-1, 0,-4,-3, 0,-3,-4,-1, 0,-1,-4,-2,-3,-5,-1,
-1,-3,-2,-3,12,-3,-3,-3,-3,-3,-2,-3,-2,-2,-4,-1,-1,-5,-3,-1,-5,-2,
-1, 1, 0, 0,-3, 6, 2,-2, 1,-2,-2, 1, 0,-4,-1, 0,-1,-2,-1,-3,-5,-1,
-1, 0, 0, 2,-3, 2, 6,-2, 0,-3,-2, 1,-2,-3, 0, 0,-1,-3,-2,-3,-5,-1,
0,-2, 0,-1,-3,-2,-2, 7,-2,-4,-3,-2,-2,-3,-2, 0,-2,-2,-3,-3,-5,-1,
-2, 0, 1, 0,-3, 1, 0,-2,10,-3,-2,-1, 0,-2,-2,-1,-2,-3, 2,-3,-5,-1,
-1,-3,-2,-4,-3,-2,-3,-4,-3, 5, 2,-3, 2, 0,-2,-2,-1,-2, 0, 3,-5,-1,
-1,-2,-3,-3,-2,-2,-2,-3,-2, 2, 5,-3, 2, 1,-3,-3,-1,-2, 0, 1,-5,-1,
-1, 3, 0, 0,-3, 1, 1,-2,-1,-3,-3, 5,-1,-3,-1,-1,-1,-2,-1,-2,-5,-1,
-1,-1,-2,-3,-2, 0,-2,-2, 0, 2, 2,-1, 6, 0,-2,-2,-1,-2, 0, 1,-5,-1,
-2,-2,-2,-4,-2,-4,-3,-3,-2, 0, 1,-3, 0, 8,-3,-2,-1, 1, 3, 0,-5,-1,
-1,-2,-2,-1,-4,-1, 0,-2,-2,-2,-3,-1,-2,-3, 9,-1,-1,-3,-3,-3,-5,-1,
1,-1, 1, 0,-1, 0, 0, 0,-1,-2,-3,-1,-2,-2,-1, 4, 2,-4,-2,-1,-5, 0,
0,-1, 0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-1,-1, 2, 5,-3,-1, 0,-5, 0,
-2,-2,-4,-4,-5,-2,-3,-2,-3,-2,-2,-2,-2, 1,-3,-4,-3,15, 3,-3,-5,-2,
-2,-1,-2,-2,-3,-1,-2,-3, 2, 0, 0,-1, 0, 3,-3,-2,-1, 3, 8,-1,-5,-1,
0,-2,-3,-3,-1,-3,-3,-3,-3, 3, 1,-2, 1, 0,-3,-1, 0,-3,-1, 5,-5,-1,
-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5,-5, 1,-5,
0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1, 0, 0,-2,-1,-1,-5,-1
};
int aln_sm_nt[] = {
/* X A G R C M S V T W K D Y H B N */
-2,-2,-2,-2,-2,-2,-2,-2,-2,-2,-2,-2,-2,-2,-2,-2,
-2, 2,-1, 1,-2, 1,-2, 0,-2, 1,-2, 0,-2, 0,-2, 0,
-2,-1, 2, 1,-2,-2, 1, 0,-2,-2, 1, 0,-2,-2, 0, 0,
-2, 1, 1, 1,-2,-1,-1, 0,-2,-1,-1, 0,-2, 0, 0, 0,
-2,-2,-2,-2, 2, 1, 1, 0,-1,-2,-2,-2, 1, 0, 0, 0,
-2, 1,-2,-1, 1, 1,-1, 0,-2,-1,-2, 0,-1, 0, 0, 0,
-2,-2, 1,-1, 1,-1, 1, 0,-2,-2,-1, 0,-1, 0, 0, 0,
-2, 0, 0, 0, 0, 0, 0, 0,-2, 0, 0, 0, 0, 0, 0, 0,
-2,-2,-2,-2,-1,-2,-2,-2, 2, 1, 1, 0, 1, 0, 0, 0,
-2, 1,-2,-1,-2,-1,-2, 0, 1, 1,-1, 0,-1, 0, 0, 0,
-2,-2, 1,-1,-2,-2,-1, 0, 1,-1, 1, 0,-1, 0, 0, 0,
-2, 0, 0, 0,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-2,-2,-2,-2, 1,-1,-1, 0, 1,-1,-1, 0, 1, 0, 0, 0,
-2, 0,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-2,-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
};
int aln_sm_read[] = {
/* X A G R C M S V T W K D Y H B N */
-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,-17,
-17, 2,-17, 1,-17, 1,-17, 0,-17, 1,-17, 0,-17, 0,-17, 0,
-17,-17, 2, 1,-17,-17, 1, 0,-17,-17, 1, 0,-17,-17, 0, 0,
-17, 1, 1, 1,-17,-17,-17, 0,-17,-17,-17, 0,-17, 0, 0, 0,
-17,-17,-17,-17, 2, 1, 1, 0,-17,-17,-17,-17, 1, 0, 0, 0,
-17, 1,-17,-17, 1, 1,-17, 0,-17,-17,-17, 0,-17, 0, 0, 0,
-17,-17, 1,-17, 1,-17, 1, 0,-17,-17,-17, 0,-17, 0, 0, 0,
-17, 0, 0, 0, 0, 0, 0, 0,-17, 0, 0, 0, 0, 0, 0, 0,
-17,-17,-17,-17,-17,-17,-17,-17, 2, 1, 1, 0, 1, 0, 0, 0,
-17, 1,-17,-17,-17,-17,-17, 0, 1, 1,-17, 0,-17, 0, 0, 0,
-17,-17, 1,-17,-17,-17,-17, 0, 1,-17, 1, 0,-17, 0, 0, 0,
-17, 0, 0, 0,-17, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-17,-17,-17,-17, 1,-17,-17, 0, 1,-17,-17, 0, 1, 0, 0, 0,
-17, 0,-17, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-17,-17, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-17, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
};
int aln_sm_hs[] = {
/* A G C T N */
91, -31,-114,-123, -44,
-31, 100,-125,-114, -42,
-123,-125, 100, -31, -42,
-114,-114, -31, 91, -42,
-44, -42, -42, -42, -43
};
int aln_sm_maq[] = {
11, -19, -19, -19, -13,
-19, 11, -19, -19, -13,
-19, -19, 11, -19, -13,
-19, -19, -19, 11, -13,
-13, -13, -13, -13, -13
};
int aln_sm_blast[] = {
1, -3, -3, -3, -2,
-3, 1, -3, -3, -2,
-3, -3, 1, -3, -2,
-3, -3, -3, 1, -2,
-2, -2, -2, -2, -2
};
/********************/
/* START OF align.c */
/********************/
AlnParam aln_param_blast = { 5, 2, 2, aln_sm_blast, 5, 50 };
AlnParam aln_param_bwa = { 26, 9, 5, aln_sm_maq, 5, 50 };
AlnParam aln_param_nt2nt = { 8, 2, 2, aln_sm_nt, 16, 75 };
AlnParam aln_param_rd2rd = { 1, 19, 19, aln_sm_read, 16, 75 };
AlnParam aln_param_aa2aa = { 10, 2, 2, aln_sm_blosum62, 22, 50 };
AlnAln *aln_init_AlnAln()
{
AlnAln *aa;
aa = (AlnAln*)malloc(sizeof(AlnAln));
aa->path = 0;
aa->out1 = aa->out2 = aa->outm = 0;
aa->path_len = 0;
return aa;
}
void aln_free_AlnAln(AlnAln *aa)
{
free(aa->path); free(aa->cigar32);
free(aa->out1); free(aa->out2); free(aa->outm);
free(aa);
}
/***************************/
/* START OF common_align.c */
/***************************/
#define LOCAL_OVERFLOW_THRESHOLD 32000
#define LOCAL_OVERFLOW_REDUCE 16000
#define NT_LOCAL_SCORE int
#define NT_LOCAL_SHIFT 16
#define NT_LOCAL_MASK 0xffff
#define SET_INF(s) (s).M = (s).I = (s).D = MINOR_INF;
#define set_M(MM, cur, p, sc) \
{ \
if ((p)->M >= (p)->I) { \
if ((p)->M >= (p)->D) { \
(MM) = (p)->M + (sc); (cur)->Mt = FROM_M; \
} else { \
(MM) = (p)->D + (sc); (cur)->Mt = FROM_D; \
} \
} else { \
if ((p)->I > (p)->D) { \
(MM) = (p)->I + (sc); (cur)->Mt = FROM_I; \
} else { \
(MM) = (p)->D + (sc); (cur)->Mt = FROM_D; \
} \
} \
}
#define set_I(II, cur, p) \
{ \
if ((p)->M - gap_open > (p)->I) { \
(cur)->It = FROM_M; \
(II) = (p)->M - gap_open - gap_ext; \
} else { \
(cur)->It = FROM_I; \
(II) = (p)->I - gap_ext; \
} \
}
#define set_end_I(II, cur, p) \
{ \
if (gap_end >= 0) { \
if ((p)->M - gap_open > (p)->I) { \
(cur)->It = FROM_M; \
(II) = (p)->M - gap_open - gap_end; \
} else { \
(cur)->It = FROM_I; \
(II) = (p)->I - gap_end; \
} \
} else set_I(II, cur, p); \
}
#define set_D(DD, cur, p) \
{ \
if ((p)->M - gap_open > (p)->D) { \
(cur)->Dt = FROM_M; \
(DD) = (p)->M - gap_open - gap_ext; \
} else { \
(cur)->Dt = FROM_D; \
(DD) = (p)->D - gap_ext; \
} \
}
#define set_end_D(DD, cur, p) \
{ \
if (gap_end >= 0) { \
if ((p)->M - gap_open > (p)->D) { \
(cur)->Dt = FROM_M; \
(DD) = (p)->M - gap_open - gap_end; \
} else { \
(cur)->Dt = FROM_D; \
(DD) = (p)->D - gap_end; \
} \
} else set_D(DD, cur, p); \
}
typedef struct
{
unsigned char Mt:3, It:2, Dt:2;
} dpcell_t;
typedef struct
{
int M, I, D;
//M is the score if the last nucleotide so far is a match, I if a insertion, D if a deletion
//If the current step is a match, then I and D should be set to INF
//so the score can be used to track the type fo alignment of the this last nucleotide
} dpscore_t;
/* build score profile for accelerating alignment, in theory */
void aln_init_score_array(unsigned char *seq, int len, int row, int *score_matrix, int **s_array)
{
int *tmp, *tmp2, i, k;
for (i = 0; i != row; ++i) {
tmp = score_matrix + i * row;
tmp2 = s_array[i];
for (k = 0; k != len; ++k)
tmp2[k] = tmp[seq[k]];
}
}
/***************************
* banded global alignment *
***************************/
/*return the alignment score*/
int aln_global_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
path_t *path, int *path_len)
{
register int i, j;
dpcell_t **dpcell, *q;
dpscore_t *curr, *last, *s;
path_t *p;
int b1, b2, tmp_end;
int *mat, end, max;
unsigned char type, ctype;
int gap_open, gap_ext, gap_end, b;
int *score_matrix, N_MATRIX_ROW;
/* initialize some align-related parameters. just for compatibility */
gap_open = ap->gap_open; //26
gap_ext = ap->gap_ext; //9
gap_end = ap->gap_end; //5, punishment of gap at end of sequences
b = ap->band_width; //50
score_matrix = ap->matrix;
N_MATRIX_ROW = ap->row; //5
if (len1 == 0 || len2 == 0) {
*path_len = 0;
return 0;
}
/* calculate b1 and b2 */
if (len1 > len2) {
b1 = len1 - len2 + b;
b2 = b;
} else {
b1 = b;
b2 = len2 - len1 + b;
}
if (b1 > len1) b1 = len1;
if (b2 > len2) b2 = len2;
--seq1; --seq2;
/* allocate memory */
end = (b1 + b2 <= len1)? (b1 + b2 + 1) : (len1 + 1); //number of columns
//dpcell record all the movement in dynamic programming
dpcell = (dpcell_t**)malloc(sizeof(dpcell_t*) * (len2 + 1));
for (j = 0; j <= len2; ++j) //number of rows
dpcell[j] = (dpcell_t*)malloc(sizeof(dpcell_t) * end);
for (j = b2 + 1; j <= len2; ++j)
dpcell[j] -= j - b2;
//a trick to change the index to access each elements
//so that the dpcells can be indexed in a more natural way (diagonal)
//only the score of the previous and current rows need to be recorded
curr = (dpscore_t*)malloc(sizeof(dpscore_t) * (len1 + 1)); //current row
last = (dpscore_t*)malloc(sizeof(dpscore_t) * (len1 + 1)); //last row
/* set first row */
SET_INF(*curr); curr->M = 0;
for (i = 1, s = curr + 1; i < b1; ++i, ++s) {
SET_INF(*s);
//move right, a gap in seq2, or deletion
set_end_D(s->D, dpcell[0] + i, s - 1);
}
s = curr; curr = last; last = s;
/* core dynamic programming, part 1 */
tmp_end = (b2 < len2)? b2 : len2 - 1;
for (j = 1; j <= tmp_end; ++j) {
q = dpcell[j]; s = curr; SET_INF(*s);
//move down, a gap in seq1, or insertion
//this is the first column of the table
set_end_I(s->I, q, last);
//the last element in the band of row j
end = (j + b1 <= len1 + 1)? (j + b1 - 1) : len1;
//score of nucleotide j in seq2 with any nucleotide in seq1
mat = score_matrix + seq2[j] * N_MATRIX_ROW;
//all other nucleotides in the band of seq1 (except the very last nucleotide) in the row
++s; ++q;
for (i = 1; i != end; ++i, ++s, ++q) {
set_M(s->M, q, last + i - 1, mat[seq1[i]]); /* this will change s->M ! */
set_I(s->I, q, last + i);
set_D(s->D, q, s - 1);
}
//the very last nucleotide in the band of seq1
set_M(s->M, q, last + i - 1, mat[seq1[i]]);
set_D(s->D, q, s - 1);
if (j + b1 - 1 > len1) { /* bug fixed, 040227 */
//the band reaches the end of seq1
set_end_I(s->I, q, last + i);
} else s->I = MINOR_INF; //the band does not reach the end of seq1
s = curr; curr = last; last = s;
}
/* last row for part 1, use set_end_D() instead of set_D() */
//if j==len2, then tmp_end == len2-1, which means b2 >= len2
//so the second part of the following condition will actually never happen ??
if (j == len2 && b2 != len2 - 1) {
q = dpcell[j]; s = curr; SET_INF(*s);
//the first position of the last row
set_end_I(s->I, q, last);
end = (j + b1 <= len1 + 1)? (j + b1 - 1) : len1;
mat = score_matrix + seq2[j] * N_MATRIX_ROW;
++s; ++q;
for (i = 1; i != end; ++i, ++s, ++q) {
set_M(s->M, q, last + i - 1, mat[seq1[i]]); /* this will change s->M ! */
set_I(s->I, q, last + i);
set_end_D(s->D, q, s - 1);
}
set_M(s->M, q, last + i - 1, mat[seq1[i]]);
set_end_D(s->D, q, s - 1);
if (j + b1 - 1 > len1) { /* bug fixed, 040227 */
set_end_I(s->I, q, last + i);
} else s->I = MINOR_INF;
s = curr; curr = last; last = s;
++j;
}
/* core dynamic programming, part 2 */
for (; j <= len2 - b2 + 1; ++j) {
SET_INF(curr[j - b2]);
mat = score_matrix + seq2[j] * N_MATRIX_ROW;
end = j + b1 - 1;
for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i != end; ++i, ++s, ++q) {
set_M(s->M, q, last + i - 1, mat[seq1[i]]);
set_I(s->I, q, last + i);
set_D(s->D, q, s - 1);
}
set_M(s->M, q, last + i - 1, mat[seq1[i]]);
set_D(s->D, q, s - 1);
s->I = MINOR_INF;//the band will not reach the end of seq1 in part2
s = curr; curr = last; last = s;
}
/* core dynamic programming, part 3 */
for (; j < len2; ++j) {
SET_INF(curr[j - b2]);
mat = score_matrix + seq2[j] * N_MATRIX_ROW;
for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i < len1; ++i, ++s, ++q) {
set_M(s->M, q, last + i - 1, mat[seq1[i]]);
set_I(s->I, q, last + i);
set_D(s->D, q, s - 1);
}
set_M(s->M, q, last + len1 - 1, mat[seq1[i]]);
set_end_I(s->I, q, last + i);//the band will reach the end of seq1 in part2
set_D(s->D, q, s - 1);
s = curr; curr = last; last = s;
}
/* last row */
if (j == len2) {
SET_INF(curr[j - b2]);
mat = score_matrix + seq2[j] * N_MATRIX_ROW;
for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i < len1; ++i, ++s, ++q) {
set_M(s->M, q, last + i - 1, mat[seq1[i]]);
set_I(s->I, q, last + i);
set_end_D(s->D, q, s - 1);
}
set_M(s->M, q, last + len1 - 1, mat[seq1[i]]);
set_end_I(s->I, q, last + i);
set_end_D(s->D, q, s - 1);
s = curr; curr = last; last = s;
}
/* backtrace */
i = len1; j = len2;
q = dpcell[j] + i;
s = last + len1;
max = s->M; type = q->Mt; ctype = FROM_M;
if (s->I > max) { max = s->I; type = q->It; ctype = FROM_I; }
if (s->D > max) { max = s->D; type = q->Dt; ctype = FROM_D; }
p = path;
//ctype is the type of the current nucleotide
//type is the type of the parent nucleotide
p->ctype = ctype; p->i = i; p->j = j; /* bug fixed 040408 */
++p;
do {
switch (ctype) {
case FROM_M: --i; --j; break;
case FROM_I: --j; break;
case FROM_D: --i; break;
}
q = dpcell[j] + i;
ctype = type;
switch (type) {
case FROM_M: type = q->Mt; break;
case FROM_I: type = q->It; break;
case FROM_D: type = q->Dt; break;
}
p->ctype = ctype; p->i = i; p->j = j;
++p;
} while (i || j);
*path_len = p - path - 1;
/* free memory */
for (j = b2 + 1; j <= len2; ++j)
dpcell[j] += j - b2;
for (j = 0; j <= len2; ++j)
free(dpcell[j]);
free(dpcell);
free(curr); free(last);
return max;
}
/*************************************************
* local alignment combined with banded strategy *
*************************************************/
int aln_local_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
path_t *path, int *path_len, int _thres, int *_subo)
{
register NT_LOCAL_SCORE *s;
register int i;
int q, r, qr, tmp_len, qr_shift;
int **s_array, *score_array;
int e, f;
int is_overflow, of_base;
NT_LOCAL_SCORE *eh, curr_h, last_h, curr_last_h;
int j, start_i, start_j, end_i, end_j;
path_t *p;
int score_f, score_r, score_g;
int start, end, max_score;
int thres, *suba, *ss;
int gap_open, gap_ext, b;
int *score_matrix, N_MATRIX_ROW;
/* initialize some align-related parameters. just for compatibility */
gap_open = ap->gap_open;
gap_ext = ap->gap_ext;
b = ap->band_width;
score_matrix = ap->matrix;
N_MATRIX_ROW = ap->row;
thres = _thres > 0? _thres : -_thres;
if (len1 == 0 || len2 == 0) return -1;
/* allocate memory */
suba = (int*)malloc(sizeof(int) * (len2 + 1));
eh = (NT_LOCAL_SCORE*)malloc(sizeof(NT_LOCAL_SCORE) * (len1 + 1));
s_array = (int**)malloc(sizeof(int*) * N_MATRIX_ROW);
for (i = 0; i != N_MATRIX_ROW; ++i)
s_array[i] = (int*)malloc(sizeof(int) * len1);
/* initialization */
aln_init_score_array(seq1, len1, N_MATRIX_ROW, score_matrix, s_array);
q = gap_open;
r = gap_ext;
qr = q + r;
qr_shift = (qr+1) << NT_LOCAL_SHIFT;
tmp_len = len1 + 1;
start_i = start_j = end_i = end_j = 0;
for (i = 0, max_score = 0; i != N_MATRIX_ROW * N_MATRIX_ROW; ++i)
if (max_score < score_matrix[i]) max_score = score_matrix[i];
/* convert the coordinate */
--seq1; --seq2;
for (i = 0; i != N_MATRIX_ROW; ++i) --s_array[i];
/* forward dynamic programming */
for (i = 0, s = eh; i != tmp_len; ++i, ++s) *s = 0;
score_f = 0;
is_overflow = of_base = 0;
suba[0] = 0;
for (j = 1, ss = suba + 1; j <= len2; ++j, ++ss) {
int subo = 0;
last_h = f = 0;
score_array = s_array[seq2[j]];
if (is_overflow) { /* adjust eh[] array if overflow occurs. */
/* If LOCAL_OVERFLOW_REDUCE is too small, optimal alignment might be missed.
* If it is too large, this block will be excuted frequently and therefore
* slow down the whole program.
* Acually, smaller LOCAL_OVERFLOW_REDUCE might also help to reduce the
* number of assignments because it sets some cells to zero when overflow
* happens. */
int tmp, tmp2;
score_f -= LOCAL_OVERFLOW_REDUCE;
of_base += LOCAL_OVERFLOW_REDUCE;
is_overflow = 0;
for (i = 1, s = eh; i <= tmp_len; ++i, ++s) {
tmp = *s >> NT_LOCAL_SHIFT; tmp2 = *s & NT_LOCAL_MASK;
if (tmp2 < LOCAL_OVERFLOW_REDUCE) tmp2 = 0;
else tmp2 -= LOCAL_OVERFLOW_REDUCE;
if (tmp < LOCAL_OVERFLOW_REDUCE) tmp = 0;
else tmp -= LOCAL_OVERFLOW_REDUCE;
*s = (tmp << NT_LOCAL_SHIFT) | tmp2;
}
}
for (i = 1, s = eh; i != tmp_len; ++i, ++s) {
/* prepare for calculate current h */
curr_h = (*s >> NT_LOCAL_SHIFT) + score_array[i];
if (curr_h < 0) curr_h = 0;
if (last_h > 0) { /* initialize f */
f = (f > last_h - q)? f - r : last_h - qr;
if (curr_h < f) curr_h = f;
}
if (*(s+1) >= qr_shift) { /* initialize e */
curr_last_h = *(s+1) >> NT_LOCAL_SHIFT;
e = ((*s & NT_LOCAL_MASK) > curr_last_h - q)? (*s & NT_LOCAL_MASK) - r : curr_last_h - qr;
if (curr_h < e) curr_h = e;
*s = (last_h << NT_LOCAL_SHIFT) | e;
} else *s = last_h << NT_LOCAL_SHIFT; /* e = 0 */
last_h = curr_h;
if (subo < curr_h) subo = curr_h;
if (score_f < curr_h) {
score_f = curr_h; end_i = i; end_j = j;
if (score_f > LOCAL_OVERFLOW_THRESHOLD) is_overflow = 1;
}
}
*s = last_h << NT_LOCAL_SHIFT;
*ss = subo + of_base;
}
score_f += of_base;
if (score_f < thres) { /* no matching residue at all, 090218 */
*path_len = 0;
goto end_func;
}
if (path == 0) goto end_func; /* skip path-filling */
/* reverse dynamic programming */
for (i = end_i, s = eh + end_i; i >= 0; --i, --s) *s = 0;
if (end_i == 0 || end_j == 0) goto end_func; /* no local match */
score_r = score_matrix[seq1[end_i] * N_MATRIX_ROW + seq2[end_j]];
is_overflow = of_base = 0;
start_i = end_i; start_j = end_j;
eh[end_i] = ((NT_LOCAL_SCORE)(qr + score_r)) << NT_LOCAL_SHIFT; /* in order to initialize f and e, 040408 */
start = end_i - 1;
end = end_i - 3;
if (end <= 0) end = 0;
/* second pass DP can be done in a band, speed will thus be enhanced */
for (j = end_j - 1; j != 0; --j) {
last_h = f = 0;
score_array = s_array[seq2[j]];
if (is_overflow) { /* adjust eh[] array if overflow occurs. */
int tmp, tmp2;
score_r -= LOCAL_OVERFLOW_REDUCE;
of_base += LOCAL_OVERFLOW_REDUCE;
is_overflow = 0;
for (i = start, s = eh + start + 1; i >= end; --i, --s) {
tmp = *s >> NT_LOCAL_SHIFT; tmp2 = *s & NT_LOCAL_MASK;
if (tmp2 < LOCAL_OVERFLOW_REDUCE) tmp2 = 0;
else tmp2 -= LOCAL_OVERFLOW_REDUCE;
if (tmp < LOCAL_OVERFLOW_REDUCE) tmp = 0;
else tmp -= LOCAL_OVERFLOW_REDUCE;
*s = (tmp << NT_LOCAL_SHIFT) | tmp2;
}
}
for (i = start, s = eh + start + 1; i != end; --i, --s) {
/* prepare for calculate current h */
curr_h = (*s >> NT_LOCAL_SHIFT) + score_array[i];
if (curr_h < 0) curr_h = 0;
if (last_h > 0) { /* initialize f */
f = (f > last_h - q)? f - r : last_h - qr;
if (curr_h < f) curr_h = f;
}
curr_last_h = *(s-1) >> NT_LOCAL_SHIFT;
e = ((*s & NT_LOCAL_MASK) > curr_last_h - q)? (*s & NT_LOCAL_MASK) - r : curr_last_h - qr;
if (e < 0) e = 0;
if (curr_h < e) curr_h = e;
*s = (last_h << NT_LOCAL_SHIFT) | e;
last_h = curr_h;
if (score_r < curr_h) {
score_r = curr_h; start_i = i; start_j = j;
if (score_r + of_base - qr == score_f) {
j = 1; break;
}
if (score_r > LOCAL_OVERFLOW_THRESHOLD) is_overflow = 1;
}
}
*s = last_h << NT_LOCAL_SHIFT;
/* recalculate start and end, the boundaries of the band */
if ((eh[start] >> NT_LOCAL_SHIFT) <= qr) --start;
if (start <= 0) start = 0;
end = start_i - (start_j - j) - (score_r + of_base + (start_j - j) * max_score) / r - 1;
if (end <= 0) end = 0;
}
if (_subo) {
int tmp2 = 0, tmp = (int)(start_j - .33 * (end_j - start_j) + .499);
for (j = 1; j <= tmp; ++j)
if (tmp2 < suba[j]) tmp2 = suba[j];
tmp = (int)(end_j + .33 * (end_j - start_j) + .499);
for (j = tmp; j <= len2; ++j)
if (tmp2 < suba[j]) tmp2 = suba[j];
*_subo = tmp2;
}
if (path_len == 0) {
path[0].i = start_i; path[0].j = start_j;
path[1].i = end_i; path[1].j = end_j;
goto end_func;
}
score_r += of_base;
score_r -= qr;
#ifdef DEBUG
/* this seems not a bug */
if (score_f != score_r)
fprintf(stderr, "[aln_local_core] unknown flaw occurs: score_f(%d) != score_r(%d)\n", score_f, score_r);
#endif
if (_thres > 0) { /* call global alignment to fill the path */
score_g = 0;
j = (end_i - start_i > end_j - start_j)? end_i - start_i : end_j - start_j;
++j; /* j is the maximum band_width */
for (i = ap->band_width;; i <<= 1) {
AlnParam ap_real = *ap;
ap_real.gap_end = -1;
ap_real.band_width = i;
score_g = aln_global_core(seq1 + start_i, end_i - start_i + 1, seq2 + start_j,
end_j - start_j + 1, &ap_real, path, path_len);
if (score_g == score_r || score_f == score_g) break;
if (i > j) break;
}
if (score_r > score_g && score_f > score_g) {
fprintf(stderr, "[aln_local_core] Potential bug: (%d,%d) > %d\n", score_f, score_r, score_g);
score_f = score_r = -1;
} else score_f = score_g;
/* convert coordinate */
for (p = path + *path_len - 1; p >= path; --p) {
p->i += start_i - 1;
p->j += start_j - 1;
}
} else { /* just store the start and end */
*path_len = 2;
path[1].i = start_i; path[1].j = start_j;
path->i = end_i; path->j = end_j;
}
end_func:
/* free */
free(eh); free(suba);
for (i = 0; i != N_MATRIX_ROW; ++i) {
++s_array[i];
free(s_array[i]);
}
free(s_array);
return score_f;
}
AlnAln *aln_stdaln_aux(const char *seq1, const char *seq2, const AlnParam *ap,
int type, int thres, int len1, int len2)
{
unsigned char *seq11, *seq22;
int score;
int i, j, l;
path_t *p;
char *out1, *out2, *outm;
AlnAln *aa;
if (len1 < 0) len1 = strlen(seq1);
if (len2 < 0) len2 = strlen(seq2);
aa = aln_init_AlnAln();
seq11 = (unsigned char*)malloc(sizeof(unsigned char) * len1);
seq22 = (unsigned char*)malloc(sizeof(unsigned char) * len2);
aa->path = (path_t*)malloc(sizeof(path_t) * (len1 + len2 + 1));
if (ap->row < 10) { /* 4-nucleotide alignment */
for (i = 0; i < len1; ++i)
seq11[i] = aln_nt4_table[(int)seq1[i]];
for (j = 0; j < len2; ++j)
seq22[j] = aln_nt4_table[(int)seq2[j]];
} else if (ap->row < 20) { /* 16-nucleotide alignment */
for (i = 0; i < len1; ++i)
seq11[i] = aln_nt16_table[(int)seq1[i]];
for (j = 0; j < len2; ++j)
seq22[j] = aln_nt16_table[(int)seq2[j]];
} else { /* amino acids */
for (i = 0; i < len1; ++i)
seq11[i] = aln_aa_table[(int)seq1[i]];
for (j = 0; j < len2; ++j)
seq22[j] = aln_aa_table[(int)seq2[j]];
}
if (type == ALN_TYPE_GLOBAL) score = aln_global_core(seq11, len1, seq22, len2, ap, aa->path, &aa->path_len);
else if (type == ALN_TYPE_LOCAL) score = aln_local_core(seq11, len1, seq22, len2, ap, aa->path, &aa->path_len, thres, &aa->subo);
else if (type == ALN_TYPE_EXTEND) score = aln_extend_core(seq11, len1, seq22, len2, ap, aa->path, &aa->path_len, 1, 0);
else {
free(seq11); free(seq22); free(aa->path);
aln_free_AlnAln(aa);
return 0;
}
aa->score = score;
if (thres > 0) {
out1 = aa->out1 = (char*)malloc(sizeof(char) * (aa->path_len + 1));
out2 = aa->out2 = (char*)malloc(sizeof(char) * (aa->path_len + 1));
outm = aa->outm = (char*)malloc(sizeof(char) * (aa->path_len + 1));
--seq1; --seq2;
--seq11; --seq22;
p = aa->path + aa->path_len - 1;
for (l = 0; p >= aa->path; --p, ++l) {
switch (p->ctype) {
case FROM_M: out1[l] = seq1[p->i]; out2[l] = seq2[p->j];
outm[l] = (seq11[p->i] == seq22[p->j] && seq11[p->i] != ap->row)? '|' : ' ';
break;
case FROM_I: out1[l] = '-'; out2[l] = seq2[p->j]; outm[l] = ' '; break;
case FROM_D: out1[l] = seq1[p->i]; out2[l] = '-'; outm[l] = ' '; break;
}
}
out1[l] = out2[l] = outm[l] = '\0';
++seq11; ++seq22;
}
free(seq11);
free(seq22);
p = aa->path + aa->path_len - 1;
aa->start1 = p->i? p->i : 1;
aa->end1 = aa->path->i;
aa->start2 = p->j? p->j : 1;
aa->end2 = aa->path->j;
aa->cigar32 = aln_path2cigar32(aa->path, aa->path_len, &aa->n_cigar);
return aa;
}
AlnAln *aln_stdaln(const char *seq1, const char *seq2, const AlnParam *ap, int type, int thres)
{
return aln_stdaln_aux(seq1, seq2, ap, type, thres, -1, -1);
}
/* for backward compatibility */
uint16_t *aln_path2cigar(const path_t *path, int path_len, int *n_cigar)
{
uint32_t *cigar32;
uint16_t *cigar;
int i;
cigar32 = aln_path2cigar32(path, path_len, n_cigar);
cigar = (uint16_t*)cigar32;
for (i = 0; i < *n_cigar; ++i)
cigar[i] = (cigar32[i]&0xf)<<14 | (cigar32[i]>>4&0x3fff);
return cigar;
}
/* newly added functions (2009-07-21) */
int aln_extend_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
path_t *path, int *path_len, int G0, uint8_t *_mem)
{
int q, r, qr, tmp_len;
int32_t **s_array, *score_array;
int is_overflow, of_base;
uint32_t *eh;
int i, j, end_i, end_j;
int score, start, end;
int *score_matrix, N_MATRIX_ROW;
uint8_t *mem, *_p;
/* initialize some align-related parameters. just for compatibility */
q = ap->gap_open;
r = ap->gap_ext;
qr = q + r;
score_matrix = ap->matrix;
N_MATRIX_ROW = ap->row;
if (len1 == 0 || len2 == 0) return -1;
/* allocate memory */
mem = _mem? _mem : (uint8_t*)calloc((len1 + 2) * (N_MATRIX_ROW + 1), 4);
_p = mem;
eh = (uint32_t*)_p, _p += 4 * (len1 + 2);
s_array = (int32_t**)calloc(N_MATRIX_ROW, sizeof(void*));
for (i = 0; i != N_MATRIX_ROW; ++i)
s_array[i] = (int32_t*)_p, _p += 4 * len1;
/* initialization */
aln_init_score_array(seq1, len1, N_MATRIX_ROW, score_matrix, s_array);
tmp_len = len1 + 1;
start = 1; end = 2;
end_i = end_j = 0;
score = 0;
is_overflow = of_base = 0;
/* convert the coordinate */
--seq1; --seq2;
for (i = 0; i != N_MATRIX_ROW; ++i) --s_array[i];
/* dynamic programming */
memset(eh, 0, 4 * (len1 + 2));
eh[1] = (uint32_t)G0<<16;
for (j = 1; j <= len2; ++j) {
int _start, _end;
int h1 = 0, f = 0;
score_array = s_array[seq2[j]];
/* set start and end */
_start = j - ap->band_width;
if (_start < 1) _start = 1;
if (_start > start) start = _start;
_end = j + ap->band_width;
if (_end > len1 + 1) _end = len1 + 1;
if (_end < end) end = _end;
if (start == end) break;
/* adjust eh[] array if overflow occurs. */
if (is_overflow) {
int tmp, tmp2;
score -= LOCAL_OVERFLOW_REDUCE;
of_base += LOCAL_OVERFLOW_REDUCE;
is_overflow = 0;
for (i = start; i <= end; ++i) {
uint32_t *s = &eh[i];
tmp = *s >> 16; tmp2 = *s & 0xffff;
if (tmp2 < LOCAL_OVERFLOW_REDUCE) tmp2 = 0;
else tmp2 -= LOCAL_OVERFLOW_REDUCE;
if (tmp < LOCAL_OVERFLOW_REDUCE) tmp = 0;
else tmp -= LOCAL_OVERFLOW_REDUCE;
*s = (tmp << 16) | tmp2;
}
}
_start = _end = 0;
/* the inner loop */
for (i = start; i < end; ++i) {
/* At the beginning of each cycle:
eh[i] -> h[j-1,i-1]<<16 | e[j,i]
f -> f[j,i]
h1 -> h[j,i-1]
*/
uint32_t *s = &eh[i];
int h = (int)(*s >> 16);
int e = *s & 0xffff; /* this is e[j,i] */
*s = (uint32_t)h1 << 16; /* eh[i] now stores h[j,i-1]<<16 */
h += h? score_array[i] : 0; /* this is left_core() specific */
/* calculate h[j,i]; don't need to test 0, as {e,f}>=0 */
h = h > e? h : e;
h = h > f? h : f; /* h now is h[j,i] */
h1 = h;
if (h > 0) {
if (_start == 0) _start = i;
_end = i;
if (score < h) {
score = h; end_i = i; end_j = j;
if (score > LOCAL_OVERFLOW_THRESHOLD) is_overflow = 1;
}
}
/* calculate e[j+1,i] and f[j,i+1] */
h -= qr;
h = h > 0? h : 0;
e -= r;
e = e > h? e : h;
f -= r;
f = f > h? f : h;
*s |= e;
}
eh[end] = h1 << 16;
/* recalculate start and end, the boundaries of the band */
if (_end <= 0) break; /* no cell in this row has a positive score */
start = _start;
end = _end + 3;