saidx_t
divbwt(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n) {
saidx_t *B;
saidx_t *bucket_A, *bucket_B;
saidx_t m, pidx, i;
/* Check arguments. */
if((T == NULL) || (U == NULL) || (n < 0)) { return -1; }
else if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }
if((B = A) == NULL) { B = (saidx_t *)malloc((size_t)(n + 1) * sizeof(saidx_t)); }
bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t));
bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t));
/* Burrows-Wheeler Transform. */
if((B != NULL) && (bucket_A != NULL) && (bucket_B != NULL)) {
m = sort_typeBstar(T, B, bucket_A, bucket_B, n);
pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m);
/* Copy to output string. */
U[0] = T[n - 1];
for(i = 0; i < pidx; ++i) { U[i + 1] = (sauchar_t)B[i]; }
for(i += 1; i < n; ++i) { U[i] = (sauchar_t)B[i]; }
pidx += 1;
} else {
pidx = -2;
}
free(bucket_B);
free(bucket_A);
if(A == NULL) { free(B); }
return pidx;
}
saidx_t
divbwtf(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n,
unsigned *LFpowers, unsigned nLFpowers, unsigned freqs[256]) {
saidx_t *B;
saidx_t *bucket_A, *bucket_B;
saidx_t m, pidx, i;
/* Check arguments. */
if((T == NULL) || (U == NULL) || (n < 0)) { return -1; }
else if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }
if((B = A) == NULL) { B = (saidx_t *)malloc((size_t)(n + 1) * sizeof(saidx_t)); }
bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t));
bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t));
/* Burrows-Wheeler Transform. */
if((B != NULL) && (bucket_A != NULL) && (bucket_B != NULL)) {
m = sort_typeBstar(T, B, bucket_A, bucket_B, n);
if(nLFpowers > 1) {
pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m, LFpowers, nLFpowers);
LFpowers[0] = pidx;
} else {
pidx = construct_BWT_orig(T, B, bucket_A, bucket_B, n, m);
*LFpowers = pidx;
}
/* Copy to output string. */
for(i = 0; i < n; ++i) {
if(i != pidx) {
U[i] = (sauchar_t)B[i];
++freqs[U[i]];
}
}
} else {
pidx = -2;
}
free(bucket_B);
free(bucket_A);
if(A == NULL) { free(B); }
return pidx;
}
int32_t
divbwt(const uint8_t *T, uint8_t *U, int32_t *A, int32_t n) {
int32_t *B;
int32_t m, pidx, i;
/* Check arguments. */
if ((T == NULL) || (U == NULL) || (n < 0)) {
return -1;
} else if (n <= 1) {
if (n == 1) {
U[0] = T[0];
}
return n;
}
if ((B = A) == NULL) {
B = new int32_t [ (n + 1)];
}
int32_t bucket_A [BUCKET_A_SIZE];
int32_t bucket_B [BUCKET_B_SIZE];
/* Burrows-Wheeler Transform. */
m = sort_typeBstar(T, B, bucket_A, bucket_B, n);
pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m);
/* Copy to output string. */
U[0] = T[n - 1];
for (i = 0; i < pidx; ++i) {
U[i + 1] = (uint8_t) B[i];
}
for (i += 1; i < n; ++i) {
U[i] = (uint8_t) B[i];
}
pidx += 1;
if (A == NULL)
delete[] B;
return pidx;
}