From c41114488f4daad5679b1617029b4fef4acad3d8 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 7 Aug 2009 20:56:38 +0000 Subject: [PATCH] * samtools-0.1.5-26 (r442) * replace RSA Inc md5.* with ones under permissive lincense * fixed a bug in detecting unsorted bam in pileup --- bam_pileup.c | 10 +- bamtk.c | 2 +- misc/md5.c | 493 +++++++++++++++++++++++++-------------------------- misc/md5.h | 99 +++++------ misc/md5fa.c | 12 +- 5 files changed, 299 insertions(+), 317 deletions(-) diff --git a/bam_pileup.c b/bam_pileup.c index d2d2aa6..983c08e 100644 --- a/bam_pileup.c +++ b/bam_pileup.c @@ -166,9 +166,13 @@ int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf) if (b->core.flag & buf->flag_mask) return 0; bam_copy1(&buf->tail->b, b); buf->tail->beg = b->core.pos; buf->tail->end = bam_calend(&b->core, bam1_cigar(b)); - if (!(b->core.tid >= buf->max_tid || (b->core.tid == buf->max_tid && buf->tail->beg >= buf->max_pos))) { - fprintf(stderr, "[bam_pileup_core] the input is not sorted. Abort!\n"); - abort(); + if (b->core.tid < buf->max_tid) { + fprintf(stderr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n"); + return -1; + } + if ((b->core.tid == buf->max_tid) && (buf->tail->beg < buf->max_pos)) { + fprintf(stderr, "[bam_pileup_core] the input is not sorted (reads out of order)\n"); + return -1; } buf->max_tid = b->core.tid; buf->max_pos = buf->tail->beg; if (buf->tail->end > buf->pos || buf->tail->b.core.tid > buf->tid) { diff --git a/bamtk.c b/bamtk.c index 08d0fdc..56fa73a 100644 --- a/bamtk.c +++ b/bamtk.c @@ -9,7 +9,7 @@ #endif #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.1.5-25 (r436)" +#define PACKAGE_VERSION "0.1.5-26 (r442)" #endif int bam_taf2baf(int argc, char *argv[]); diff --git a/misc/md5.c b/misc/md5.c index ccead0e..55ae181 100644 --- a/misc/md5.c +++ b/misc/md5.c @@ -1,271 +1,260 @@ /* - ********************************************************************** - ** md5.c ** - ** RSA Data Security, Inc. MD5 Message Digest Algorithm ** - ** Created: 2/17/90 RLR ** - ** Revised: 1/91 SRD,AJ,BSK,JT Reference C Version ** - ********************************************************************** + * 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 /* - ********************************************************************** - ** Copyright (C) 1990, RSA Data Security, Inc. All rights reserved. ** - ** ** - ** License to copy and use this software is granted provided that ** - ** it is identified as the "RSA Data Security, Inc. MD5 Message ** - ** Digest Algorithm" in all material mentioning or referencing this ** - ** software or this function. ** - ** ** - ** License is also granted to make and use derivative works ** - ** provided that such works are identified as "derived from the RSA ** - ** Data Security, Inc. MD5 Message Digest Algorithm" in all ** - ** material mentioning or referencing the derived work. ** - ** ** - ** RSA Data Security, Inc. makes no representations concerning ** - ** either the merchantability of this software or the suitability ** - ** of this software for any particular purpose. It is provided "as ** - ** is" without express or implied warranty of any kind. ** - ** ** - ** These notices must be retained in any copies of any part of this ** - ** documentation and/or software. ** - ********************************************************************** + * 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]); -#include "md5.h" -/* forward declaration */ -static void Transform (); - -static unsigned char PADDING[64] = { - 0x80, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, - 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, - 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, - 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, - 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, - 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, - 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, - 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00 -}; - -/* F, G and H are basic MD5 functions: selection, majority, parity */ -#define F(x, y, z) (((x) & (y)) | ((~x) & (z))) -#define G(x, y, z) (((x) & (z)) | ((y) & (~z))) -#define H(x, y, z) ((x) ^ (y) ^ (z)) -#define I(x, y, z) ((y) ^ ((x) | (~z))) - -/* ROTATE_LEFT rotates x left n bits */ -#define ROTATE_LEFT(x, n) (((x) << (n)) | ((x) >> (32-(n)))) - -/* FF, GG, HH, and II transformations for rounds 1, 2, 3, and 4 */ -/* Rotation is separate from addition to prevent recomputation */ -#define FF(a, b, c, d, x, s, ac) \ - {(a) += F ((b), (c), (d)) + (x) + (UINT4)(ac); \ - (a) = ROTATE_LEFT ((a), (s)); \ - (a) += (b); \ - } -#define GG(a, b, c, d, x, s, ac) \ - {(a) += G ((b), (c), (d)) + (x) + (UINT4)(ac); \ - (a) = ROTATE_LEFT ((a), (s)); \ - (a) += (b); \ - } -#define HH(a, b, c, d, x, s, ac) \ - {(a) += H ((b), (c), (d)) + (x) + (UINT4)(ac); \ - (a) = ROTATE_LEFT ((a), (s)); \ - (a) += (b); \ - } -#define II(a, b, c, d, x, s, ac) \ - {(a) += I ((b), (c), (d)) + (x) + (UINT4)(ac); \ - (a) = ROTATE_LEFT ((a), (s)); \ - (a) += (b); \ - } - -void MD5Init (mdContext) -MD5_CTX *mdContext; +/* + * Start MD5 accumulation. Set bit count to 0 and buffer to mysterious + * initialization constants. + */ +void MD5Init(ctx) + struct MD5Context *ctx; { - mdContext->i[0] = mdContext->i[1] = (UINT4)0; - - /* Load magic initialization constants. - */ - mdContext->buf[0] = (UINT4)0x67452301; - mdContext->buf[1] = (UINT4)0xefcdab89; - mdContext->buf[2] = (UINT4)0x98badcfe; - mdContext->buf[3] = (UINT4)0x10325476; + ctx->buf[0] = 0x67452301; + ctx->buf[1] = 0xefcdab89; + ctx->buf[2] = 0x98badcfe; + ctx->buf[3] = 0x10325476; + + ctx->bits[0] = 0; + ctx->bits[1] = 0; } -void MD5Update (mdContext, inBuf, inLen) -MD5_CTX *mdContext; -unsigned char *inBuf; -unsigned int inLen; +/* + * 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; { - UINT4 in[16]; - int mdi; - unsigned int i, ii; - - /* compute number of bytes mod 64 */ - mdi = (int)((mdContext->i[0] >> 3) & 0x3F); - - /* update number of bits */ - if ((mdContext->i[0] + ((UINT4)inLen << 3)) < mdContext->i[0]) - mdContext->i[1]++; - mdContext->i[0] += ((UINT4)inLen << 3); - mdContext->i[1] += ((UINT4)inLen >> 29); - - while (inLen--) { - /* add new character to buffer, increment mdi */ - mdContext->in[mdi++] = *inBuf++; - - /* transform if necessary */ - if (mdi == 0x40) { - for (i = 0, ii = 0; i < 16; i++, ii += 4) - in[i] = (((UINT4)mdContext->in[ii+3]) << 24) | - (((UINT4)mdContext->in[ii+2]) << 16) | - (((UINT4)mdContext->in[ii+1]) << 8) | - ((UINT4)mdContext->in[ii]); - Transform (mdContext->buf, in); - mdi = 0; + 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); } -void MD5Final (mdContext) -MD5_CTX *mdContext; +/* + * 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; { - UINT4 in[16]; - int mdi; - unsigned int i, ii; - unsigned int padLen; - - /* save number of bits */ - in[14] = mdContext->i[0]; - in[15] = mdContext->i[1]; - - /* compute number of bytes mod 64 */ - mdi = (int)((mdContext->i[0] >> 3) & 0x3F); - - /* pad out to 56 mod 64 */ - padLen = (mdi < 56) ? (56 - mdi) : (120 - mdi); - MD5Update (mdContext, PADDING, padLen); - - /* append length in bits and transform */ - for (i = 0, ii = 0; i < 14; i++, ii += 4) - in[i] = (((UINT4)mdContext->in[ii+3]) << 24) | - (((UINT4)mdContext->in[ii+2]) << 16) | - (((UINT4)mdContext->in[ii+1]) << 8) | - ((UINT4)mdContext->in[ii]); - Transform (mdContext->buf, in); - - /* store buffer in digest */ - for (i = 0, ii = 0; i < 4; i++, ii += 4) { - mdContext->digest[ii] = (unsigned char)(mdContext->buf[i] & 0xFF); - mdContext->digest[ii+1] = - (unsigned char)((mdContext->buf[i] >> 8) & 0xFF); - mdContext->digest[ii+2] = - (unsigned char)((mdContext->buf[i] >> 16) & 0xFF); - mdContext->digest[ii+3] = - (unsigned char)((mdContext->buf[i] >> 24) & 0xFF); - } + 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 */ } -/* Basic MD5 step. Transform buf based on in. + +/* 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. */ -static void Transform (buf, in) -UINT4 *buf; -UINT4 *in; +void MD5Transform(buf, in) + uint32_t buf[4]; uint32_t in[16]; { - UINT4 a = buf[0], b = buf[1], c = buf[2], d = buf[3]; - - /* Round 1 */ -#define S11 7 -#define S12 12 -#define S13 17 -#define S14 22 - FF ( a, b, c, d, in[ 0], S11, 3614090360u); /* 1 */ - FF ( d, a, b, c, in[ 1], S12, 3905402710u); /* 2 */ - FF ( c, d, a, b, in[ 2], S13, 606105819u); /* 3 */ - FF ( b, c, d, a, in[ 3], S14, 3250441966u); /* 4 */ - FF ( a, b, c, d, in[ 4], S11, 4118548399u); /* 5 */ - FF ( d, a, b, c, in[ 5], S12, 1200080426u); /* 6 */ - FF ( c, d, a, b, in[ 6], S13, 2821735955u); /* 7 */ - FF ( b, c, d, a, in[ 7], S14, 4249261313u); /* 8 */ - FF ( a, b, c, d, in[ 8], S11, 1770035416u); /* 9 */ - FF ( d, a, b, c, in[ 9], S12, 2336552879u); /* 10 */ - FF ( c, d, a, b, in[10], S13, 4294925233u); /* 11 */ - FF ( b, c, d, a, in[11], S14, 2304563134u); /* 12 */ - FF ( a, b, c, d, in[12], S11, 1804603682u); /* 13 */ - FF ( d, a, b, c, in[13], S12, 4254626195u); /* 14 */ - FF ( c, d, a, b, in[14], S13, 2792965006u); /* 15 */ - FF ( b, c, d, a, in[15], S14, 1236535329u); /* 16 */ - - /* Round 2 */ -#define S21 5 -#define S22 9 -#define S23 14 -#define S24 20 - GG ( a, b, c, d, in[ 1], S21, 4129170786u); /* 17 */ - GG ( d, a, b, c, in[ 6], S22, 3225465664u); /* 18 */ - GG ( c, d, a, b, in[11], S23, 643717713u); /* 19 */ - GG ( b, c, d, a, in[ 0], S24, 3921069994u); /* 20 */ - GG ( a, b, c, d, in[ 5], S21, 3593408605u); /* 21 */ - GG ( d, a, b, c, in[10], S22, 38016083u); /* 22 */ - GG ( c, d, a, b, in[15], S23, 3634488961u); /* 23 */ - GG ( b, c, d, a, in[ 4], S24, 3889429448u); /* 24 */ - GG ( a, b, c, d, in[ 9], S21, 568446438u); /* 25 */ - GG ( d, a, b, c, in[14], S22, 3275163606u); /* 26 */ - GG ( c, d, a, b, in[ 3], S23, 4107603335u); /* 27 */ - GG ( b, c, d, a, in[ 8], S24, 1163531501u); /* 28 */ - GG ( a, b, c, d, in[13], S21, 2850285829u); /* 29 */ - GG ( d, a, b, c, in[ 2], S22, 4243563512u); /* 30 */ - GG ( c, d, a, b, in[ 7], S23, 1735328473u); /* 31 */ - GG ( b, c, d, a, in[12], S24, 2368359562u); /* 32 */ - - /* Round 3 */ -#define S31 4 -#define S32 11 -#define S33 16 -#define S34 23 - HH ( a, b, c, d, in[ 5], S31, 4294588738u); /* 33 */ - HH ( d, a, b, c, in[ 8], S32, 2272392833u); /* 34 */ - HH ( c, d, a, b, in[11], S33, 1839030562u); /* 35 */ - HH ( b, c, d, a, in[14], S34, 4259657740u); /* 36 */ - HH ( a, b, c, d, in[ 1], S31, 2763975236u); /* 37 */ - HH ( d, a, b, c, in[ 4], S32, 1272893353u); /* 38 */ - HH ( c, d, a, b, in[ 7], S33, 4139469664u); /* 39 */ - HH ( b, c, d, a, in[10], S34, 3200236656u); /* 40 */ - HH ( a, b, c, d, in[13], S31, 681279174u); /* 41 */ - HH ( d, a, b, c, in[ 0], S32, 3936430074u); /* 42 */ - HH ( c, d, a, b, in[ 3], S33, 3572445317u); /* 43 */ - HH ( b, c, d, a, in[ 6], S34, 76029189u); /* 44 */ - HH ( a, b, c, d, in[ 9], S31, 3654602809u); /* 45 */ - HH ( d, a, b, c, in[12], S32, 3873151461u); /* 46 */ - HH ( c, d, a, b, in[15], S33, 530742520u); /* 47 */ - HH ( b, c, d, a, in[ 2], S34, 3299628645u); /* 48 */ - - /* Round 4 */ -#define S41 6 -#define S42 10 -#define S43 15 -#define S44 21 - II ( a, b, c, d, in[ 0], S41, 4096336452u); /* 49 */ - II ( d, a, b, c, in[ 7], S42, 1126891415u); /* 50 */ - II ( c, d, a, b, in[14], S43, 2878612391u); /* 51 */ - II ( b, c, d, a, in[ 5], S44, 4237533241u); /* 52 */ - II ( a, b, c, d, in[12], S41, 1700485571u); /* 53 */ - II ( d, a, b, c, in[ 3], S42, 2399980690u); /* 54 */ - II ( c, d, a, b, in[10], S43, 4293915773u); /* 55 */ - II ( b, c, d, a, in[ 1], S44, 2240044497u); /* 56 */ - II ( a, b, c, d, in[ 8], S41, 1873313359u); /* 57 */ - II ( d, a, b, c, in[15], S42, 4264355552u); /* 58 */ - II ( c, d, a, b, in[ 6], S43, 2734768916u); /* 59 */ - II ( b, c, d, a, in[13], S44, 1309151649u); /* 60 */ - II ( a, b, c, d, in[ 4], S41, 4149444226u); /* 61 */ - II ( d, a, b, c, in[11], S42, 3174756917u); /* 62 */ - II ( c, d, a, b, in[ 2], S43, 718787259u); /* 63 */ - II ( b, c, d, a, in[ 9], S44, 3951481745u); /* 64 */ - - buf[0] += a; - buf[1] += b; - buf[2] += c; - buf[3] += d; + 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 */ @@ -278,7 +267,7 @@ UINT4 *in; static void md5_one(const char *fn) { - unsigned char buf[4096]; + unsigned char buf[4096], digest[16]; MD5_CTX md5; int l; FILE *fp; @@ -291,10 +280,10 @@ static void md5_one(const char *fn) MD5Init(&md5); while ((l = fread(buf, 1, 4096, fp)) > 0) MD5Update(&md5, buf, l); - MD5Final(&md5); + MD5Final(digest, &md5); if (fp != stdin) fclose(fp); for (l = 0; l < 16; ++l) - printf("%c%c", HEX_STR[md5.digest[l]>>4&0xf], HEX_STR[md5.digest[l]&0xf]); + printf("%c%c", HEX_STR[digest[l]>>4&0xf], HEX_STR[digest[l]&0xf]); printf(" %s\n", fn); } int main(int argc, char *argv[]) diff --git a/misc/md5.h b/misc/md5.h index 678ac27..44121e4 100644 --- a/misc/md5.h +++ b/misc/md5.h @@ -1,68 +1,57 @@ /* - ********************************************************************** - ** md5.h -- Header file for implementation of MD5 ** - ** RSA Data Security, Inc. MD5 Message Digest Algorithm ** - ** Created: 2/17/90 RLR ** - ** Revised: 12/27/90 SRD,AJ,BSK,JT Reference C version ** - ** Revised (for MD5): RLR 4/27/91 ** - ** -- G modified to have y&~z instead of y&z ** - ** -- FF, GG, HH modified to add in last register done ** - ** -- Access pattern: round 2 works mod 5, round 3 works mod 3 ** - ** -- distinct additive constant for each step ** - ** -- round 4 added, working mod 7 ** - ********************************************************************** - */ + This file is adapted from a program in this page: -/* - ********************************************************************** - ** Copyright (C) 1990, RSA Data Security, Inc. All rights reserved. ** - ** ** - ** License to copy and use this software is granted provided that ** - ** it is identified as the "RSA Data Security, Inc. MD5 Message ** - ** Digest Algorithm" in all material mentioning or referencing this ** - ** software or this function. ** - ** ** - ** License is also granted to make and use derivative works ** - ** provided that such works are identified as "derived from the RSA ** - ** Data Security, Inc. MD5 Message Digest Algorithm" in all ** - ** material mentioning or referencing the derived work. ** - ** ** - ** RSA Data Security, Inc. makes no representations concerning ** - ** either the merchantability of this software or the suitability ** - ** of this software for any particular purpose. It is provided "as ** - ** is" without express or implied warranty of any kind. ** - ** ** - ** These notices must be retained in any copies of any part of this ** - ** documentation and/or software. ** - ********************************************************************** + http://www.fourmilab.ch/md5/ + + The original source code does not work on 64-bit machines due to the + wrong typedef "uint32". I also added prototypes. + + -lh3 */ #ifndef MD5_H #define MD5_H -#include +/* The following tests optimise behaviour on little-endian + machines, where there is no need to reverse the byte order + of 32 bit words in the MD5 computation. By default, + HIGHFIRST is defined, which indicates we're running on a + big-endian (most significant byte first) machine, on which + the byteReverse function in md5.c must be invoked. However, + byteReverse is coded in such a way that it is an identity + function when run on a little-endian machine, so calling it + on such a platform causes no harm apart from wasting time. + If the platform is known to be little-endian, we speed + things up by undefining HIGHFIRST, which defines + byteReverse as a null macro. Doing things in this manner + insures we work on new platforms regardless of their byte + order. */ + +#define HIGHFIRST + +#if __LITTLE_ENDIAN__ != 0 +#undef HIGHFIRST +#endif -/* typedef a 32 bit type */ -typedef uint32_t UINT4; +#include -/* Data structure for MD5 (Message Digest) computation */ -typedef struct { - UINT4 i[2]; /* number of _bits_ handled mod 2^64 */ - UINT4 buf[4]; /* scratch buffer */ - unsigned char in[64]; /* input buffer */ - unsigned char digest[16]; /* actual digest after MD5Final call */ -} MD5_CTX; +struct MD5Context { + uint32_t buf[4]; + uint32_t bits[2]; + unsigned char in[64]; +}; -#ifdef __cplusplus -extern "C" { -#endif +void MD5Init(struct MD5Context *ctx); +void MD5Update(struct MD5Context *ctx, unsigned char *buf, unsigned len); +void MD5Final(unsigned char digest[16], struct MD5Context *ctx); - void MD5Init(MD5_CTX *mdContext); - void MD5Update(MD5_CTX *mdContext, unsigned char *inBuf, unsigned intinLen); - void MD5Final(MD5_CTX *mdContext); +/* + * This is needed to make RSAREF happy on some MS-DOS compilers. + */ +typedef struct MD5Context MD5_CTX; -#ifdef __cplusplus -} -#endif +/* Define CHECK_HARDWARE_PROPERTIES to have main,c verify + byte order and uint32_t settings. */ +#define CHECK_HARDWARE_PROPERTIES -#endif +#endif /* !MD5_H */ diff --git a/misc/md5fa.c b/misc/md5fa.c index c41db2d..7a165bf 100644 --- a/misc/md5fa.c +++ b/misc/md5fa.c @@ -13,7 +13,7 @@ static void md5_one(const char *fn) int l, i, k; gzFile fp; kseq_t *seq; - unsigned char unordered[16]; + unsigned char unordered[16], digest[16]; for (l = 0; l < 16; ++l) unordered[l] = 0; fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r"); @@ -31,18 +31,18 @@ static void md5_one(const char *fn) } MD5Init(&md5_one); MD5Update(&md5_one, (unsigned char*)seq->seq.s, k); - MD5Final(&md5_one); + MD5Final(digest, &md5_one); for (l = 0; l < 16; ++l) { - printf("%c%c", HEX_STR[md5_one.digest[l]>>4&0xf], HEX_STR[md5_one.digest[l]&0xf]); - unordered[l] ^= md5_one.digest[l]; + printf("%c%c", HEX_STR[digest[l]>>4&0xf], HEX_STR[digest[l]&0xf]); + unordered[l] ^= digest[l]; } printf(" %s %s\n", fn, seq->name.s); MD5Update(&md5_all, (unsigned char*)seq->seq.s, k); } - MD5Final(&md5_all); + MD5Final(digest, &md5_all); kseq_destroy(seq); for (l = 0; l < 16; ++l) - printf("%c%c", HEX_STR[md5_all.digest[l]>>4&0xf], HEX_STR[md5_all.digest[l]&0xf]); + printf("%c%c", HEX_STR[digest[l]>>4&0xf], HEX_STR[digest[l]&0xf]); printf(" %s >ordered\n", fn); for (l = 0; l < 16; ++l) printf("%c%c", HEX_STR[unordered[l]>>4&0xf], HEX_STR[unordered[l]&0xf]); -- 2.39.5