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blast.cc
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/**
* @file blast.cc
*
* @brief reimplementation of the blast_SemiGappedAlign algorithm
* (original implementation found in <ncbi-blast>/c++/src/algo/blast/core/blast_gapalign.c)
*/
#include <string.h>
#include "util.h"
#define MIN ( -32768 + 30 )
/**
* @fn blast_affine
*/
int
blast_affine(
void *work,
char const *a,
uint64_t alen,
char const *b,
uint64_t blen,
int8_t *score_matrix, int8_t _gi, int8_t _ge, int16_t _xt,
uint32_t bw) /* unused */
{
if(alen == 0 || blen == 0) { return(0); }
debug("%s, %s", a, b);
int32_t gi = _gi, ge = _ge, xt = _xt, best_score = 0;
uint64_t first_b_index = 0, last_b_index = blen + 1; /* [first_b_index, last_b_index) */
uint64_t amax = 0, bmax = 0;
struct _dp { int16_t s, e, f; };
struct _dp *ptr = (struct _dp *)work + sizeof(maxpos_t), *prev;
/* initialize the top row */
ptr[0].s = 0; ptr[0].e = gi; ptr[0].f = gi;
for(uint64_t i = 0; i < blen; i++) {
if(ptr[i].s + ge < -xt) { last_b_index = i + 1; break; }
ptr[i + 1].s = ptr[i].f + ge;
ptr[i + 1].e = MIN;
ptr[i + 1].f = ptr[i].f + ge;
debug("init, b_index(%llu), score(%d)", i + 1, ptr[i + 1].s);
}
ptr[last_b_index].s = best_score;
ptr[last_b_index].e = last_b_index - first_b_index;
ptr[last_b_index].f = first_b_index;
#define _sc(_ach, _i) ( score_matrix[_ach | encode_b(b[_i])] )
prev = ptr;
for(uint64_t a_index = 0; a_index < alen; a_index++) {
prev = ptr; ptr += last_b_index + 1 - first_b_index;
int8_t ach = encode_a(a[a_index]);
debug("a_index(%llu), ch(%d), b_range(%llu, %llu)", a_index, ach, first_b_index, last_b_index);
int32_t e = MAX2(MIN, MAX2(prev[first_b_index].e, prev[first_b_index].s + gi) + ge);
int32_t f = MIN;
int32_t s = e;
debug("initial, b_index(%llu), score(%d, %d, %d)", first_b_index, s, e, f);
while(s < best_score - xt) {
e = MAX2(prev[first_b_index + 1].e, prev[first_b_index + 1].s + gi) + ge;
f = MAX2(f, s + gi) + ge;
s = MAX3(prev[first_b_index].s + _sc(ach, first_b_index), e, f);
first_b_index++; ptr--;
debug("forward head, b_index(%llu), ch(%x), score(%d, %d, %d)", first_b_index, encode_b(b[first_b_index]) | ach, s, e, f);
}
debug("ptr(%p, %p), b_range(%llu, %llu)", prev, ptr, first_b_index, last_b_index);
ptr[first_b_index].s = s;
ptr[first_b_index].e = e;
ptr[first_b_index].f = f;
uint64_t next_last_b_index = last_b_index;
for(uint64_t b_index = first_b_index + 1; b_index < last_b_index; b_index++) {
e = MAX2(prev[b_index].e, prev[b_index].s + gi) + ge;
f = MAX2(f, s + gi) + ge;
s = MAX3(prev[b_index - 1].s + _sc(ach, b_index - 1), e, f);
if(s > best_score) { best_score = s; amax = a_index + 1; bmax = b_index; }
if(s >= best_score - xt) { next_last_b_index = b_index + 1; }
ptr[b_index].s = s;
ptr[b_index].e = e;
ptr[b_index].f = f;
debug("fill, b_index(%llu, %p, %p), ch(%x), score(%d, %d, %d)", b_index, &ptr[b_index].s, &prev[b_index].s, encode_b(b[b_index - 1]) | ach, s, e, f);
}
last_b_index = next_last_b_index;
if(last_b_index <= blen) {
int32_t d = prev[last_b_index - 1].s + _sc(ach, last_b_index - 1);
debug("tail, b_index(%llu, %p, %p), ch(%x), d(%d, %d)", last_b_index, &ptr[last_b_index].s, &prev[last_b_index].s, encode_b(b[last_b_index - 1]) | ach, prev[last_b_index - 1].s, d);
if(d > best_score) { best_score = d; amax = a_index + 1; bmax = last_b_index; }
while(last_b_index <= blen) {
e = MIN;
f = MAX2(f, s + gi) + ge;
s = MAX2(d, f);
if(s < best_score - xt) { debug("xdrop failed, s(%d, %d)", s, best_score - xt); break; }
d = MIN;
ptr[last_b_index].s = s;
ptr[last_b_index].e = e;
ptr[last_b_index].f = f;
last_b_index++;
debug("forward tail, a_index(%llu, %p), score(%d, %d, %d)", last_b_index, &ptr[last_b_index - 1].s, s, e, f);
}
}
ptr[last_b_index].s = best_score;
ptr[last_b_index].e = last_b_index - first_b_index;
ptr[last_b_index].f = first_b_index;
}
/* save the maxpos */
maxpos_t *r = (maxpos_t *)work;
r->alen = alen;
r->blen = blen;
r->apos = amax;
r->bpos = bmax;
return(best_score);
}
#ifdef MAIN
#include <assert.h>
#include <stdlib.h>
int main_ext(int argc, char *argv[])
{
uint64_t alen = strlen(argv[2]);
uint64_t blen = strlen(argv[3]);
char *a = argv[2];
char *b = argv[3];
int8_t score_matrix[16] __attribute__(( aligned(16) ));
build_score_matrix(score_matrix, atoi(argv[4]), atoi(argv[5]));
void *work = aligned_malloc(128 * 1024 * 1024, 16);
if(0) {
printf("./a.out linear AAA AAA 2 -3 -5 -1 30\n");
}
int score = blast_affine(
work,
a, alen, b, blen,
score_matrix,
atoi(argv[6]),
atoi(argv[7]),
atoi(argv[8]));
printf("%d\n", score);
free(work);
return(0);
}
int main(int argc, char *argv[])
{
char const *a = "aattcccccc";
char const *b = "aacccccc";
// char const *a = "abefpppbbqqqqghijkltttt";
// char const *b = "abcdefpppqqqqijklggtttt";
if(argc > 1) { return(main_ext(argc, argv)); }
int8_t score_matrix[16] __attribute__(( aligned(16) ));
build_score_matrix(score_matrix, 1, -1);
void *work = aligned_malloc(128 * 1024 * 1024, 16);
#define a(s, p, q) { \
assert(blast_affine(work, p, strlen(p), q, strlen(q), score_matrix, -1, -1, 10) == (s)); \
}
a( 0, "", "");
a( 0, "A", "");
a( 1, "A", "A");
a( 3, "AAA", "AAA");
a( 0, "AAA", "TTT");
a( 3, "AAAGGG", "AAATTTTTT");
a( 3, "TTTGGGGGAAAA", "TTTCCCCCCCCAAAA");
a( 4, "AAACAAAGGG", "AAAAAATTTTTTT");
a( 3, "AAACCAAAGGG", "AAAAAATTTTTTT");
int sa = blast_affine(work, a, strlen(a), b, strlen(b), score_matrix, -1, -1, 30);
printf("%d\n", sa);
free(work);
return(0);
}
#endif
/**
* end of blast.cc
*/