--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/samtools-0.1.16/misc/md5.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,296 @@
+/*
+ * This code implements the MD5 message-digest algorithm.
+ * The algorithm is due to Ron Rivest.	This code was
+ * written by Colin Plumb in 1993, no copyright is claimed.
+ * This code is in the public domain; do with it what you wish.
+ *
+ * Equivalent code is available from RSA Data Security, Inc.
+ * This code has been tested against that, and is equivalent,
+ * except that you don't need to include two pages of legalese
+ * with every copy.
+ *
+ * To compute the message digest of a chunk of bytes, declare an
+ * MD5Context structure, pass it to MD5Init, call MD5Update as
+ * needed on buffers full of bytes, and then call MD5Final, which
+ * will fill a supplied 16-byte array with the digest.
+ */
+
+/* Brutally hacked by John Walker back from ANSI C to K&R (no
+   prototypes) to maintain the tradition that Netfone will compile
+   with Sun's original "cc". */
+
+#include <string.h>
+#include "md5.h"
+
+#ifndef HIGHFIRST
+#define byteReverse(buf, len)	/* Nothing */
+#else
+/*
+ * Note: this code is harmless on little-endian machines.
+ */
+void byteReverse(buf, longs)
+    unsigned char *buf; unsigned longs;
+{
+    uint32_t t;
+    do {
+	t = (uint32_t) ((unsigned) buf[3] << 8 | buf[2]) << 16 |
+	    ((unsigned) buf[1] << 8 | buf[0]);
+	*(uint32_t *) buf = t;
+	buf += 4;
+    } while (--longs);
+}
+#endif
+
+void MD5Transform(uint32_t buf[4], uint32_t in[16]);
+
+
+/*
+ * Start MD5 accumulation.  Set bit count to 0 and buffer to mysterious
+ * initialization constants.
+ */
+void MD5Init(ctx)
+    struct MD5Context *ctx;
+{
+    ctx->buf[0] = 0x67452301;
+    ctx->buf[1] = 0xefcdab89;
+    ctx->buf[2] = 0x98badcfe;
+    ctx->buf[3] = 0x10325476;
+
+    ctx->bits[0] = 0;
+    ctx->bits[1] = 0;
+}
+
+/*
+ * Update context to reflect the concatenation of another buffer full
+ * of bytes.
+ */
+void MD5Update(ctx, buf, len)
+    struct MD5Context *ctx; unsigned char *buf; unsigned len;
+{
+    uint32_t t;
+
+    /* Update bitcount */
+
+    t = ctx->bits[0];
+    if ((ctx->bits[0] = t + ((uint32_t) len << 3)) < t)
+	ctx->bits[1]++; 	/* Carry from low to high */
+    ctx->bits[1] += len >> 29;
+
+    t = (t >> 3) & 0x3f;	/* Bytes already in shsInfo->data */
+
+    /* Handle any leading odd-sized chunks */
+
+    if (t) {
+	unsigned char *p = (unsigned char *) ctx->in + t;
+
+	t = 64 - t;
+	if (len < t) {
+	    memcpy(p, buf, len);
+	    return;
+	}
+	memcpy(p, buf, t);
+	byteReverse(ctx->in, 16);
+	MD5Transform(ctx->buf, (uint32_t *) ctx->in);
+	buf += t;
+	len -= t;
+    }
+    /* Process data in 64-byte chunks */
+
+    while (len >= 64) {
+	memcpy(ctx->in, buf, 64);
+	byteReverse(ctx->in, 16);
+	MD5Transform(ctx->buf, (uint32_t *) ctx->in);
+	buf += 64;
+	len -= 64;
+    }
+
+    /* Handle any remaining bytes of data. */
+
+    memcpy(ctx->in, buf, len);
+}
+
+/*
+ * Final wrapup - pad to 64-byte boundary with the bit pattern 
+ * 1 0* (64-bit count of bits processed, MSB-first)
+ */
+void MD5Final(digest, ctx)
+    unsigned char digest[16]; struct MD5Context *ctx;
+{
+    unsigned count;
+    unsigned char *p;
+
+    /* Compute number of bytes mod 64 */
+    count = (ctx->bits[0] >> 3) & 0x3F;
+
+    /* Set the first char of padding to 0x80.  This is safe since there is
+       always at least one byte free */
+    p = ctx->in + count;
+    *p++ = 0x80;
+
+    /* Bytes of padding needed to make 64 bytes */
+    count = 64 - 1 - count;
+
+    /* Pad out to 56 mod 64 */
+    if (count < 8) {
+	/* Two lots of padding:  Pad the first block to 64 bytes */
+	memset(p, 0, count);
+	byteReverse(ctx->in, 16);
+	MD5Transform(ctx->buf, (uint32_t *) ctx->in);
+
+	/* Now fill the next block with 56 bytes */
+	memset(ctx->in, 0, 56);
+    } else {
+	/* Pad block to 56 bytes */
+	memset(p, 0, count - 8);
+    }
+    byteReverse(ctx->in, 14);
+
+    /* Append length in bits and transform */
+    ((uint32_t *) ctx->in)[14] = ctx->bits[0];
+    ((uint32_t *) ctx->in)[15] = ctx->bits[1];
+
+    MD5Transform(ctx->buf, (uint32_t *) ctx->in);
+    byteReverse((unsigned char *) ctx->buf, 4);
+    memcpy(digest, ctx->buf, 16);
+    memset(ctx, 0, sizeof(ctx));        /* In case it's sensitive */
+}
+
+
+/* The four core functions - F1 is optimized somewhat */
+
+/* #define F1(x, y, z) (x & y | ~x & z) */
+#define F1(x, y, z) (z ^ (x & (y ^ z)))
+#define F2(x, y, z) F1(z, x, y)
+#define F3(x, y, z) (x ^ y ^ z)
+#define F4(x, y, z) (y ^ (x | ~z))
+
+/* This is the central step in the MD5 algorithm. */
+#define MD5STEP(f, w, x, y, z, data, s) \
+	( w += f(x, y, z) + data,  w = w<<s | w>>(32-s),  w += x )
+
+/*
+ * The core of the MD5 algorithm, this alters an existing MD5 hash to
+ * reflect the addition of 16 longwords of new data.  MD5Update blocks
+ * the data and converts bytes into longwords for this routine.
+ */
+void MD5Transform(buf, in)
+    uint32_t buf[4]; uint32_t in[16];
+{
+    register uint32_t a, b, c, d;
+
+    a = buf[0];
+    b = buf[1];
+    c = buf[2];
+    d = buf[3];
+
+    MD5STEP(F1, a, b, c, d, in[0] + 0xd76aa478, 7);
+    MD5STEP(F1, d, a, b, c, in[1] + 0xe8c7b756, 12);
+    MD5STEP(F1, c, d, a, b, in[2] + 0x242070db, 17);
+    MD5STEP(F1, b, c, d, a, in[3] + 0xc1bdceee, 22);
+    MD5STEP(F1, a, b, c, d, in[4] + 0xf57c0faf, 7);
+    MD5STEP(F1, d, a, b, c, in[5] + 0x4787c62a, 12);
+    MD5STEP(F1, c, d, a, b, in[6] + 0xa8304613, 17);
+    MD5STEP(F1, b, c, d, a, in[7] + 0xfd469501, 22);
+    MD5STEP(F1, a, b, c, d, in[8] + 0x698098d8, 7);
+    MD5STEP(F1, d, a, b, c, in[9] + 0x8b44f7af, 12);
+    MD5STEP(F1, c, d, a, b, in[10] + 0xffff5bb1, 17);
+    MD5STEP(F1, b, c, d, a, in[11] + 0x895cd7be, 22);
+    MD5STEP(F1, a, b, c, d, in[12] + 0x6b901122, 7);
+    MD5STEP(F1, d, a, b, c, in[13] + 0xfd987193, 12);
+    MD5STEP(F1, c, d, a, b, in[14] + 0xa679438e, 17);
+    MD5STEP(F1, b, c, d, a, in[15] + 0x49b40821, 22);
+
+    MD5STEP(F2, a, b, c, d, in[1] + 0xf61e2562, 5);
+    MD5STEP(F2, d, a, b, c, in[6] + 0xc040b340, 9);
+    MD5STEP(F2, c, d, a, b, in[11] + 0x265e5a51, 14);
+    MD5STEP(F2, b, c, d, a, in[0] + 0xe9b6c7aa, 20);
+    MD5STEP(F2, a, b, c, d, in[5] + 0xd62f105d, 5);
+    MD5STEP(F2, d, a, b, c, in[10] + 0x02441453, 9);
+    MD5STEP(F2, c, d, a, b, in[15] + 0xd8a1e681, 14);
+    MD5STEP(F2, b, c, d, a, in[4] + 0xe7d3fbc8, 20);
+    MD5STEP(F2, a, b, c, d, in[9] + 0x21e1cde6, 5);
+    MD5STEP(F2, d, a, b, c, in[14] + 0xc33707d6, 9);
+    MD5STEP(F2, c, d, a, b, in[3] + 0xf4d50d87, 14);
+    MD5STEP(F2, b, c, d, a, in[8] + 0x455a14ed, 20);
+    MD5STEP(F2, a, b, c, d, in[13] + 0xa9e3e905, 5);
+    MD5STEP(F2, d, a, b, c, in[2] + 0xfcefa3f8, 9);
+    MD5STEP(F2, c, d, a, b, in[7] + 0x676f02d9, 14);
+    MD5STEP(F2, b, c, d, a, in[12] + 0x8d2a4c8a, 20);
+
+    MD5STEP(F3, a, b, c, d, in[5] + 0xfffa3942, 4);
+    MD5STEP(F3, d, a, b, c, in[8] + 0x8771f681, 11);
+    MD5STEP(F3, c, d, a, b, in[11] + 0x6d9d6122, 16);
+    MD5STEP(F3, b, c, d, a, in[14] + 0xfde5380c, 23);
+    MD5STEP(F3, a, b, c, d, in[1] + 0xa4beea44, 4);
+    MD5STEP(F3, d, a, b, c, in[4] + 0x4bdecfa9, 11);
+    MD5STEP(F3, c, d, a, b, in[7] + 0xf6bb4b60, 16);
+    MD5STEP(F3, b, c, d, a, in[10] + 0xbebfbc70, 23);
+    MD5STEP(F3, a, b, c, d, in[13] + 0x289b7ec6, 4);
+    MD5STEP(F3, d, a, b, c, in[0] + 0xeaa127fa, 11);
+    MD5STEP(F3, c, d, a, b, in[3] + 0xd4ef3085, 16);
+    MD5STEP(F3, b, c, d, a, in[6] + 0x04881d05, 23);
+    MD5STEP(F3, a, b, c, d, in[9] + 0xd9d4d039, 4);
+    MD5STEP(F3, d, a, b, c, in[12] + 0xe6db99e5, 11);
+    MD5STEP(F3, c, d, a, b, in[15] + 0x1fa27cf8, 16);
+    MD5STEP(F3, b, c, d, a, in[2] + 0xc4ac5665, 23);
+
+    MD5STEP(F4, a, b, c, d, in[0] + 0xf4292244, 6);
+    MD5STEP(F4, d, a, b, c, in[7] + 0x432aff97, 10);
+    MD5STEP(F4, c, d, a, b, in[14] + 0xab9423a7, 15);
+    MD5STEP(F4, b, c, d, a, in[5] + 0xfc93a039, 21);
+    MD5STEP(F4, a, b, c, d, in[12] + 0x655b59c3, 6);
+    MD5STEP(F4, d, a, b, c, in[3] + 0x8f0ccc92, 10);
+    MD5STEP(F4, c, d, a, b, in[10] + 0xffeff47d, 15);
+    MD5STEP(F4, b, c, d, a, in[1] + 0x85845dd1, 21);
+    MD5STEP(F4, a, b, c, d, in[8] + 0x6fa87e4f, 6);
+    MD5STEP(F4, d, a, b, c, in[15] + 0xfe2ce6e0, 10);
+    MD5STEP(F4, c, d, a, b, in[6] + 0xa3014314, 15);
+    MD5STEP(F4, b, c, d, a, in[13] + 0x4e0811a1, 21);
+    MD5STEP(F4, a, b, c, d, in[4] + 0xf7537e82, 6);
+    MD5STEP(F4, d, a, b, c, in[11] + 0xbd3af235, 10);
+    MD5STEP(F4, c, d, a, b, in[2] + 0x2ad7d2bb, 15);
+    MD5STEP(F4, b, c, d, a, in[9] + 0xeb86d391, 21);
+
+    buf[0] += a;
+    buf[1] += b;
+    buf[2] += c;
+    buf[3] += d;
+}
+
+/* lh3: the following code is added by me */
+
+#ifdef MD5SUM_MAIN
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#define HEX_STR "0123456789abcdef"
+
+static void md5_one(const char *fn)
+{
+	unsigned char buf[4096], digest[16];
+	MD5_CTX md5;
+	int l;
+	FILE *fp;
+
+	fp = strcmp(fn, "-")? fopen(fn, "r") : stdin;
+	if (fp == 0) {
+		fprintf(stderr, "md5sum: %s: No such file or directory\n", fn);
+		exit(1);
+	}
+	MD5Init(&md5);
+	while ((l = fread(buf, 1, 4096, fp)) > 0)
+		MD5Update(&md5, buf, l);
+	MD5Final(digest, &md5);
+	if (fp != stdin) fclose(fp);
+	for (l = 0; l < 16; ++l)
+		printf("%c%c", HEX_STR[digest[l]>>4&0xf], HEX_STR[digest[l]&0xf]);
+	printf("  %s\n", fn);
+}
+int main(int argc, char *argv[])
+{
+	int i;
+	if (argc == 1) md5_one("-");
+	else for (i = 1; i < argc; ++i) md5_one(argv[i]);
+	return 0;
+}
+#endif