X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fmisc%2Fmd5.c.pysam.c;fp=samtools%2Fmisc%2Fmd5.c.pysam.c;h=771084447e8ea62f39b513978f5a72112cd46f55;hp=0000000000000000000000000000000000000000;hb=d02fe5283ed7a93a2f76a5d6dc6e37b40c11b9b1;hpb=d828f9c9aa78e3d1687265b52de841f3f3852089 diff --git a/samtools/misc/md5.c.pysam.c b/samtools/misc/md5.c.pysam.c new file mode 100644 index 0000000..7710844 --- /dev/null +++ b/samtools/misc/md5.c.pysam.c @@ -0,0 +1,298 @@ +#include "pysam.h" + +/* + * 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 +#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<>(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 +#include +#include +#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(pysamerr, "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