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#include <stdio.h>
#include <stdlib.h>
#include "align.h"
/* Turn vector into single (most likely) nucleotide */
char consen_6(FastInt B[6]) {
FastInt a = B[0], b = 0;
if (B[1] > a)
a = B[1], b = 1;
if (B[2] > a)
a = B[2], b = 2;
if (B[3] > a)
a = B[3], b = 3;
if (B[4] > a)
a = B[4], b = 4;
if (B[5] > a)
a = B[5], b = 5;
return a == 0 ? '-' : "ACGT*-"[b];
}
void expand(char *A, char *B, int M, int N,
char *A2, char *B2, int *AL, int *BL, FastInt *S, int keep_pads)
{
register int i, j, op;
char *a = A2, *b = B2;
A--; B--;
i = j = op = 0;
/* fpad= abs(S[0]);
for(i=0; i<M; i++){
if (S[i] !=0 )
lpad = i;
}
i=0;*/
while (i < M || j < N)
{
if (op == 0 && *S == 0)
{
op = *S++;
*a++ = A[++i];
*b++ = B[++j];
} else {
if (op == 0)
op = *S++;
if (op > 0)
{
*a++ = '.';
*b++ = B[++j];
op--;
} else {
*a++ = A[++i];
*b++ = '.';
op++;
}
}
}
/* Strip back expanded sequences to first non pad character */
if (!keep_pads) {
while (*--a == '.');
while (*--b == '.');
} else {
--a;
--b;
}
/* & NULL terminate */
*++a = 0;
*++b = 0;
*AL = (int)(a - A2);
*BL = (int)(b - B2);
}
void expand_6(char *A, FastInt (*B)[6], int M, int N,
char *A2, FastInt (*B2)[6], int *AL, int *BL, FastInt *S,
int keep_pads)
{
register int i, j, k, op;
char *a = A2;
FastInt (*b)[6] = B2;
extern char base_val[128];
A--; B--;
i = j = op = 0;
while (i < M || j < N)
{
if (op == 0 && *S == 0)
{
op = *S++;
*a++ = A[++i];
for (k=0; k<6; k++) {
(*b)[k] = B[j][k];
}
b++;j++;
} else {
if (op == 0)
op = *S++;
if (op > 0)
{
*a++ = ' ';
for (k=0; k<6; k++) {
(*b)[k] = B[j][k];
}
b++;j++;
op--;
} else {
*a++ = A[++i];
for (k=0; k<6; k++) {
(*b)[k] = base_val['*'];
}
b++;j++;
op++;
}
}
}
/* Strip back expanded sequences to first non pad character */
if (!keep_pads) {
while (*--a == '*');
while ((*b)[0] == base_val['*']) b--;
} else {
--a;
--b;
}
*AL = (int)(a - A2);
*BL = (int)(b - B2);
}
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