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diff --git a/tools/apultra/src/libdivsufsort/lib/divsufsort.c b/tools/apultra/src/libdivsufsort/lib/divsufsort.c
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+++ b/tools/apultra/src/libdivsufsort/lib/divsufsort.c
@@ -0,0 +1,431 @@
+/*
+ * divsufsort.c for libdivsufsort
+ * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
+ *
+ * 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 "divsufsort_private.h"
+#ifdef _OPENMP
+# include <omp.h>
+#endif
+
+
+/*- Private Functions -*/
+
+/* Sorts suffixes of type B*. */
+static
+saidx_t
+sort_typeBstar(const sauchar_t *T, saidx_t *SA,
+               saidx_t *bucket_A, saidx_t *bucket_B,
+               saidx_t n) {
+  saidx_t *PAb, *ISAb, *buf;
+#ifdef _OPENMP
+  saidx_t *curbuf;
+  saidx_t l;
+#endif
+  saidx_t i, j, k, t, m, bufsize;
+  saint_t c0, c1;
+#ifdef _OPENMP
+  saint_t d0, d1;
+  int tmp;
+#endif
+
+  /* Initialize bucket arrays. */
+  for(i = 0; i < BUCKET_A_SIZE; ++i) { bucket_A[i] = 0; }
+  for(i = 0; i < BUCKET_B_SIZE; ++i) { bucket_B[i] = 0; }
+
+  /* Count the number of occurrences of the first one or two characters of each
+     type A, B and B* suffix. Moreover, store the beginning position of all
+     type B* suffixes into the array SA. */
+  for(i = n - 1, m = n, c0 = T[n - 1]; 0 <= i;) {
+    /* type A suffix. */
+    do { ++BUCKET_A(c1 = c0); } while((0 <= --i) && ((c0 = T[i]) >= c1));
+    if(0 <= i) {
+      /* type B* suffix. */
+      ++BUCKET_BSTAR(c0, c1);
+      SA[--m] = i;
+      /* type B suffix. */
+      for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) {
+        ++BUCKET_B(c0, c1);
+      }
+    }
+  }
+  m = n - m;
+/*
+note:
+  A type B* suffix is lexicographically smaller than a type B suffix that
+  begins with the same first two characters.
+*/
+
+  /* Calculate the index of start/end point of each bucket. */
+  for(c0 = 0, i = 0, j = 0; c0 < ALPHABET_SIZE; ++c0) {
+    t = i + BUCKET_A(c0);
+    BUCKET_A(c0) = i + j; /* start point */
+    i = t + BUCKET_B(c0, c0);
+    for(c1 = c0 + 1; c1 < ALPHABET_SIZE; ++c1) {
+      j += BUCKET_BSTAR(c0, c1);
+      BUCKET_BSTAR(c0, c1) = j; /* end point */
+      i += BUCKET_B(c0, c1);
+    }
+  }
+
+  if(0 < m) {
+    /* Sort the type B* suffixes by their first two characters. */
+    PAb = SA + n - m; ISAb = SA + m;
+    for(i = m - 2; 0 <= i; --i) {
+      t = PAb[i], c0 = T[t], c1 = T[t + 1];
+      SA[--BUCKET_BSTAR(c0, c1)] = i;
+    }
+    t = PAb[m - 1], c0 = T[t], c1 = T[t + 1];
+    SA[--BUCKET_BSTAR(c0, c1)] = m - 1;
+
+    /* Sort the type B* substrings using sssort. */
+#ifdef _OPENMP
+    tmp = omp_get_max_threads();
+    buf = SA + m, bufsize = (n - (2 * m)) / tmp;
+    c0 = ALPHABET_SIZE - 2, c1 = ALPHABET_SIZE - 1, j = m;
+#pragma omp parallel default(shared) private(curbuf, k, l, d0, d1, tmp)
+    {
+      tmp = omp_get_thread_num();
+      curbuf = buf + tmp * bufsize;
+      k = 0;
+      for(;;) {
+        #pragma omp critical(sssort_lock)
+        {
+          if(0 < (l = j)) {
+            d0 = c0, d1 = c1;
+            do {
+              k = BUCKET_BSTAR(d0, d1);
+              if(--d1 <= d0) {
+                d1 = ALPHABET_SIZE - 1;
+                if(--d0 < 0) { break; }
+              }
+            } while(((l - k) <= 1) && (0 < (l = k)));
+            c0 = d0, c1 = d1, j = k;
+          }
+        }
+        if(l == 0) { break; }
+        sssort(T, PAb, SA + k, SA + l,
+               curbuf, bufsize, 2, n, *(SA + k) == (m - 1));
+      }
+    }
+#else
+    buf = SA + m, bufsize = n - (2 * m);
+    for(c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) {
+      for(c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) {
+        i = BUCKET_BSTAR(c0, c1);
+        if(1 < (j - i)) {
+          sssort(T, PAb, SA + i, SA + j,
+                 buf, bufsize, 2, n, *(SA + i) == (m - 1));
+        }
+      }
+    }
+#endif
+
+    /* Compute ranks of type B* substrings. */
+    for(i = m - 1; 0 <= i; --i) {
+      if(0 <= SA[i]) {
+        j = i;
+        do { ISAb[SA[i]] = i; } while((0 <= --i) && (0 <= SA[i]));
+        SA[i + 1] = i - j;
+        if(i <= 0) { break; }
+      }
+      j = i;
+      do { ISAb[SA[i] = ~SA[i]] = j; } while(SA[--i] < 0);
+      ISAb[SA[i]] = j;
+    }
+
+    /* Construct the inverse suffix array of type B* suffixes using trsort. */
+    trsort(ISAb, SA, m, 1);
+
+    /* Set the sorted order of tyoe B* suffixes. */
+    for(i = n - 1, j = m, c0 = T[n - 1]; 0 <= i;) {
+      for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) >= c1); --i, c1 = c0) { }
+      if(0 <= i) {
+        t = i;
+        for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { }
+        SA[ISAb[--j]] = ((t == 0) || (1 < (t - i))) ? t : ~t;
+      }
+    }
+
+    /* Calculate the index of start/end point of each bucket. */
+    BUCKET_B(ALPHABET_SIZE - 1, ALPHABET_SIZE - 1) = n; /* end point */
+    for(c0 = ALPHABET_SIZE - 2, k = m - 1; 0 <= c0; --c0) {
+      i = BUCKET_A(c0 + 1) - 1;
+      for(c1 = ALPHABET_SIZE - 1; c0 < c1; --c1) {
+        t = i - BUCKET_B(c0, c1);
+        BUCKET_B(c0, c1) = i; /* end point */
+
+        /* Move all type B* suffixes to the correct position. */
+        for(i = t, j = BUCKET_BSTAR(c0, c1);
+            j <= k;
+            --i, --k) { SA[i] = SA[k]; }
+      }
+      BUCKET_BSTAR(c0, c0 + 1) = i - BUCKET_B(c0, c0) + 1; /* start point */
+      BUCKET_B(c0, c0) = i; /* end point */
+    }
+  }
+
+  return m;
+}
+
+/* Constructs the suffix array by using the sorted order of type B* suffixes. */
+static
+void
+construct_SA(const sauchar_t *T, saidx_t *SA,
+             saidx_t *bucket_A, saidx_t *bucket_B,
+             saidx_t n, saidx_t m) {
+  saidx_t *i, *j, *k;
+  saidx_t s;
+  saint_t c0, c1, c2;
+
+  if(0 < m) {
+    /* Construct the sorted order of type B suffixes by using
+       the sorted order of type B* suffixes. */
+    for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
+      /* Scan the suffix array from right to left. */
+      for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
+          j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
+          i <= j;
+          --j) {
+        if(0 < (s = *j)) {
+          assert(T[s] == c1);
+          assert(((s + 1) < n) && (T[s] <= T[s + 1]));
+          assert(T[s - 1] <= T[s]);
+          *j = ~s;
+          c0 = T[--s];
+          if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
+          if(c0 != c2) {
+            if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
+            k = SA + BUCKET_B(c2 = c0, c1);
+          }
+          assert(k < j);
+          *k-- = s;
+        } else {
+          assert(((s == 0) && (T[s] == c1)) || (s < 0));
+          *j = ~s;
+        }
+      }
+    }
+  }
+
+  /* Construct the suffix array by using
+     the sorted order of type B suffixes. */
+  k = SA + BUCKET_A(c2 = T[n - 1]);
+  *k++ = (T[n - 2] < c2) ? ~(n - 1) : (n - 1);
+  /* Scan the suffix array from left to right. */
+  for(i = SA, j = SA + n; i < j; ++i) {
+    if(0 < (s = *i)) {
+      assert(T[s - 1] >= T[s]);
+      c0 = T[--s];
+      if((s == 0) || (T[s - 1] < c0)) { s = ~s; }
+      if(c0 != c2) {
+        BUCKET_A(c2) = k - SA;
+        k = SA + BUCKET_A(c2 = c0);
+      }
+      assert(i < k);
+      *k++ = s;
+    } else {
+      assert(s < 0);
+      *i = ~s;
+    }
+  }
+}
+
+#if 0
+/* Constructs the burrows-wheeler transformed string directly
+   by using the sorted order of type B* suffixes. */
+static
+saidx_t
+construct_BWT(const sauchar_t *T, saidx_t *SA,
+              saidx_t *bucket_A, saidx_t *bucket_B,
+              saidx_t n, saidx_t m) {
+  saidx_t *i, *j, *k, *orig;
+  saidx_t s;
+  saint_t c0, c1, c2;
+
+  if(0 < m) {
+    /* Construct the sorted order of type B suffixes by using
+       the sorted order of type B* suffixes. */
+    for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
+      /* Scan the suffix array from right to left. */
+      for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
+          j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
+          i <= j;
+          --j) {
+        if(0 < (s = *j)) {
+          assert(T[s] == c1);
+          assert(((s + 1) < n) && (T[s] <= T[s + 1]));
+          assert(T[s - 1] <= T[s]);
+          c0 = T[--s];
+          *j = ~((saidx_t)c0);
+          if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
+          if(c0 != c2) {
+            if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
+            k = SA + BUCKET_B(c2 = c0, c1);
+          }
+          assert(k < j);
+          *k-- = s;
+        } else if(s != 0) {
+          *j = ~s;
+#ifndef NDEBUG
+        } else {
+          assert(T[s] == c1);
+#endif
+        }
+      }
+    }
+  }
+
+  /* Construct the BWTed string by using
+     the sorted order of type B suffixes. */
+  k = SA + BUCKET_A(c2 = T[n - 1]);
+  *k++ = (T[n - 2] < c2) ? ~((saidx_t)T[n - 2]) : (n - 1);
+  /* Scan the suffix array from left to right. */
+  for(i = SA, j = SA + n, orig = SA; i < j; ++i) {
+    if(0 < (s = *i)) {
+      assert(T[s - 1] >= T[s]);
+      c0 = T[--s];
+      *i = c0;
+      if((0 < s) && (T[s - 1] < c0)) { s = ~((saidx_t)T[s - 1]); }
+      if(c0 != c2) {
+        BUCKET_A(c2) = k - SA;
+        k = SA + BUCKET_A(c2 = c0);
+      }
+      assert(i < k);
+      *k++ = s;
+    } else if(s != 0) {
+      *i = ~s;
+    } else {
+      orig = i;
+    }
+  }
+
+  return orig - SA;
+}
+#endif
+
+/*---------------------------------------------------------------------------*/
+
+/**
+ * Initialize suffix array context
+ *
+ * @return 0 for success, or non-zero in case of an error
+ */
+int divsufsort_init(divsufsort_ctx_t *ctx) {
+   ctx->bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t));
+   ctx->bucket_B = NULL;
+
+   if (ctx->bucket_A) {
+      ctx->bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t));
+
+      if (ctx->bucket_B)
+         return 0;
+   }
+
+   divsufsort_destroy(ctx);
+   return -1;
+}
+
+/**
+ * Destroy suffix array context
+ *
+ * @param ctx suffix array context to destroy
+ */
+void divsufsort_destroy(divsufsort_ctx_t *ctx) {
+   if (ctx->bucket_B) {
+      free(ctx->bucket_B);
+      ctx->bucket_B = NULL;
+   }
+
+   if (ctx->bucket_A) {
+      free(ctx->bucket_A);
+      ctx->bucket_A = NULL;
+   }
+}
+
+/*- Function -*/
+
+saint_t
+divsufsort_build_array(divsufsort_ctx_t *ctx, const sauchar_t *T, saidx_t *SA, saidx_t n) {
+  saidx_t m;
+  saint_t err = 0;
+
+  /* Check arguments. */
+  if((T == NULL) || (SA == NULL) || (n < 0)) { return -1; }
+  else if(n == 0) { return 0; }
+  else if(n == 1) { SA[0] = 0; return 0; }
+  else if(n == 2) { m = (T[0] < T[1]); SA[m ^ 1] = 0, SA[m] = 1; return 0; }
+
+  /* Suffixsort. */
+  if((ctx->bucket_A != NULL) && (ctx->bucket_B != NULL)) {
+    m = sort_typeBstar(T, SA, ctx->bucket_A, ctx->bucket_B, n);
+    construct_SA(T, SA, ctx->bucket_A, ctx->bucket_B, n, m);
+  } else {
+    err = -2;
+  }
+
+  return err;
+}
+
+#if 0
+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;
+}
+
+const char *
+divsufsort_version(void) {
+  return PROJECT_VERSION_FULL;
+}
+#endif