--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/bwa-0.5.7-mh/is.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,218 @@
+/*
+ * sais.c for sais-lite
+ * Copyright (c) 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 <stdlib.h>
+
+typedef unsigned char ubyte_t;
+#define chr(i) (cs == sizeof(int) ? ((const int *)T)[i]:((const unsigned char *)T)[i])
+
+/* find the start or end of each bucket */
+static void getCounts(const unsigned char *T, int *C, int n, int k, int cs)
+{
+	int i;
+	for (i = 0; i < k; ++i) C[i] = 0;
+	for (i = 0; i < n; ++i) ++C[chr(i)];
+}
+static void getBuckets(const int *C, int *B, int k, int end)
+{
+	int i, sum = 0;
+	if (end) {
+		for (i = 0; i < k; ++i) {
+			sum += C[i];
+			B[i] = sum;
+		}
+	} else {
+		for (i = 0; i < k; ++i) {
+			sum += C[i];
+			B[i] = sum - C[i];
+		}
+	}
+}
+
+/* compute SA */
+static void induceSA(const unsigned char *T, int *SA, int *C, int *B, int n, int k, int cs)
+{
+	int *b, i, j;
+	int  c0, c1;
+	/* compute SAl */
+	if (C == B) getCounts(T, C, n, k, cs);
+	getBuckets(C, B, k, 0);	/* find starts of buckets */
+	j = n - 1;
+	b = SA + B[c1 = chr(j)];
+	*b++ = ((0 < j) && (chr(j - 1) < c1)) ? ~j : j;
+	for (i = 0; i < n; ++i) {
+		j = SA[i], SA[i] = ~j;
+		if (0 < j) {
+			--j;
+			if ((c0 = chr(j)) != c1) {
+				B[c1] = b - SA;
+				b = SA + B[c1 = c0];
+			}
+			*b++ = ((0 < j) && (chr(j - 1) < c1)) ? ~j : j;
+		}
+	}
+	/* compute SAs */
+	if (C == B) getCounts(T, C, n, k, cs);
+	getBuckets(C, B, k, 1);	/* find ends of buckets */
+	for (i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) {
+		if (0 < (j = SA[i])) {
+			--j;
+			if ((c0 = chr(j)) != c1) {
+				B[c1] = b - SA;
+				b = SA + B[c1 = c0];
+			}
+			*--b = ((j == 0) || (chr(j - 1) > c1)) ? ~j : j;
+		} else SA[i] = ~j;
+	}
+}
+
+/*
+ * find the suffix array SA of T[0..n-1] in {0..k-1}^n use a working
+ * space (excluding T and SA) of at most 2n+O(1) for a constant alphabet
+ */
+static int sais_main(const unsigned char *T, int *SA, int fs, int n, int k, int cs)
+{
+	int *C, *B, *RA;
+	int  i, j, c, m, p, q, plen, qlen, name;
+	int  c0, c1;
+	int  diff;
+
+	/* stage 1: reduce the problem by at least 1/2 sort all the
+	 * S-substrings */
+	if (k <= fs) {
+		C = SA + n;
+		B = (k <= (fs - k)) ? C + k : C;
+	} else if ((C = B = (int *) malloc(k * sizeof(int))) == NULL) return -2;
+	getCounts(T, C, n, k, cs);
+	getBuckets(C, B, k, 1);	/* find ends of buckets */
+	for (i = 0; i < n; ++i) SA[i] = 0;
+	for (i = n - 2, c = 0, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
+		if ((c0 = chr(i)) < (c1 + c)) c = 1;
+		else if (c != 0) SA[--B[c1]] = i + 1, c = 0;
+	}
+	induceSA(T, SA, C, B, n, k, cs);
+	if (fs < k) free(C);
+	/* compact all the sorted substrings into the first m items of SA
+	 * 2*m must be not larger than n (proveable) */
+	for (i = 0, m = 0; i < n; ++i) {
+		p = SA[i];
+		if ((0 < p) && (chr(p - 1) > (c0 = chr(p)))) {
+			for (j = p + 1; (j < n) && (c0 == (c1 = chr(j))); ++j);
+			if ((j < n) && (c0 < c1)) SA[m++] = p;
+		}
+	}
+	for (i = m; i < n; ++i) SA[i] = 0;	/* init the name array buffer */
+	/* store the length of all substrings */
+	for (i = n - 2, j = n, c = 0, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
+		if ((c0 = chr(i)) < (c1 + c)) c = 1;
+		else if (c != 0) {
+			SA[m + ((i + 1) >> 1)] = j - i - 1;
+			j = i + 1;
+			c = 0;
+		}
+	}
+	/* find the lexicographic names of all substrings */
+	for (i = 0, name = 0, q = n, qlen = 0; i < m; ++i) {
+		p = SA[i], plen = SA[m + (p >> 1)], diff = 1;
+		if (plen == qlen) {
+			for (j = 0; (j < plen) && (chr(p + j) == chr(q + j)); j++);
+			if (j == plen) diff = 0;
+		}
+		if (diff != 0) ++name, q = p, qlen = plen;
+		SA[m + (p >> 1)] = name;
+	}
+
+	/* stage 2: solve the reduced problem recurse if names are not yet
+	 * unique */
+	if (name < m) {
+		RA = SA + n + fs - m;
+		for (i = n - 1, j = m - 1; m <= i; --i) {
+			if (SA[i] != 0) RA[j--] = SA[i] - 1;
+		}
+		if (sais_main((unsigned char *) RA, SA, fs + n - m * 2, m, name, sizeof(int)) != 0) return -2;
+		for (i = n - 2, j = m - 1, c = 0, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
+			if ((c0 = chr(i)) < (c1 + c)) c = 1;
+			else if (c != 0) RA[j--] = i + 1, c = 0; /* get p1 */
+		}
+		for (i = 0; i < m; ++i) SA[i] = RA[SA[i]]; /* get index */
+	}
+	/* stage 3: induce the result for the original problem */
+	if (k <= fs) {
+		C = SA + n;
+		B = (k <= (fs - k)) ? C + k : C;
+	} else if ((C = B = (int *) malloc(k * sizeof(int))) == NULL) return -2;
+	/* put all left-most S characters into their buckets */
+	getCounts(T, C, n, k, cs);
+	getBuckets(C, B, k, 1);	/* find ends of buckets */
+	for (i = m; i < n; ++i) SA[i] = 0; /* init SA[m..n-1] */
+	for (i = m - 1; 0 <= i; --i) {
+		j = SA[i], SA[i] = 0;
+		SA[--B[chr(j)]] = j;
+	}
+	induceSA(T, SA, C, B, n, k, cs);
+	if (fs < k) free(C);
+	return 0;
+}
+
+/**
+ * Constructs the suffix array of a given string.
+ * @param T[0..n-1] The input string.
+ * @param SA[0..n] The output array of suffixes.
+ * @param n The length of the given string.
+ * @return 0 if no error occurred
+ */
+int is_sa(const ubyte_t *T, int *SA, int n)
+{
+	if ((T == NULL) || (SA == NULL) || (n < 0)) return -1;
+	SA[0] = n;
+	if (n <= 1) {
+		if (n == 1) SA[1] = 0;
+		return 0;
+	}
+	return sais_main(T, SA+1, 0, n, 256, 1);
+}
+
+/**
+ * Constructs the burrows-wheeler transformed string of a given string.
+ * @param T[0..n-1] The input string.
+ * @param n The length of the given string.
+ * @return The primary index if no error occurred, -1 or -2 otherwise.
+ */
+int is_bwt(ubyte_t *T, int n)
+{
+	int *SA, i, primary = 0;
+	SA = (int*)calloc(n+1, sizeof(int));
+	is_sa(T, SA, n);
+
+	for (i = 0; i <= n; ++i) {
+		if (SA[i] == 0) primary = i;
+		else SA[i] = T[SA[i] - 1];
+	}
+	for (i = 0; i < primary; ++i) T[i] = SA[i];
+	for (; i < n; ++i) T[i] = SA[i + 1];
+	free(SA);
+	return primary;
+}