5148ded61163c9564fdffdf5d72e43208cc166b2
galt
  Sat Apr 22 03:00:54 2017 -0700
Changed unnecessary and unavailable fread_unlocked to simply use fread instead.

diff --git src/lib/sha1.c src/lib/sha1.c
index 0f40972..263cfc5 100644
--- src/lib/sha1.c
+++ src/lib/sha1.c
@@ -1,242 +1,242 @@
 /* SHA-1 in C
 By Steve Reid <sreid@sea-to-sky.net>
 100% Public Domain
 http://svn.ghostscript.com/jbig2dec/trunk/sha1.c
 */
 #define SHA1HANDSOFF    /* Copies data before messing with it. */
 
 #include <stdio.h>
 #include <string.h>
 #include <stdint.h>
 #include <stddef.h>
 
 #include "common.h"
 #include "hex.h"
 #include "errAbort.h"
 #include "sha1.h"
 
 void SHA1_Transform(uint32_t state[5], const uint8_t buffer[64]);
 
 #define rol(value, bits) (((value) << (bits)) | ((value) >> (32 - (bits))))
 
 /* blk0() and blk() perform the initial expand. */
 /* I got the idea of expanding during the round function from SSLeay */
 /* FIXME: can we do this in an endian-proof way? */
 #ifdef WORDS_BIGENDIAN
 #define blk0(i) block->l[i]
 #else
 #define blk0(i) (block->l[i] = (rol(block->l[i],24)&0xFF00FF00) \
     |(rol(block->l[i],8)&0x00FF00FF))
 #endif
 #define blk(i) (block->l[i&15] = rol(block->l[(i+13)&15]^block->l[(i+8)&15] \
     ^block->l[(i+2)&15]^block->l[i&15],1))
 
 /* (R0+R1), R2, R3, R4 are the different operations used in SHA1 */
 #define R0(v,w,x,y,z,i) z+=((w&(x^y))^y)+blk0(i)+0x5A827999+rol(v,5);w=rol(w,30);
 #define R1(v,w,x,y,z,i) z+=((w&(x^y))^y)+blk(i)+0x5A827999+rol(v,5);w=rol(w,30);
 #define R2(v,w,x,y,z,i) z+=(w^x^y)+blk(i)+0x6ED9EBA1+rol(v,5);w=rol(w,30);
 #define R3(v,w,x,y,z,i) z+=(((w|x)&y)|(w&x))+blk(i)+0x8F1BBCDC+rol(v,5);w=rol(w,30);
 #define R4(v,w,x,y,z,i) z+=(w^x^y)+blk(i)+0xCA62C1D6+rol(v,5);w=rol(w,30);
 
 
 /* Hash a single 512-bit block. This is the core of the algorithm. */
 void SHA1_Transform(uint32_t state[5], const uint8_t buffer[64])
 {
     uint32_t a, b, c, d, e;
     typedef union {
         uint8_t c[64];
         uint32_t l[16];
     } CHAR64LONG16;
     CHAR64LONG16* block;
 
 #ifdef SHA1HANDSOFF
     static uint8_t workspace[64];
     block = (CHAR64LONG16*)workspace;
     memcpy(block, buffer, 64);
 #else
     block = (CHAR64LONG16*)buffer;
 #endif
 
     /* Copy context->state[] to working vars */
     a = state[0];
     b = state[1];
     c = state[2];
     d = state[3];
     e = state[4];
 
     /* 4 rounds of 20 operations each. Loop unrolled. */
     R0(a,b,c,d,e, 0); R0(e,a,b,c,d, 1); R0(d,e,a,b,c, 2); R0(c,d,e,a,b, 3);
     R0(b,c,d,e,a, 4); R0(a,b,c,d,e, 5); R0(e,a,b,c,d, 6); R0(d,e,a,b,c, 7);
     R0(c,d,e,a,b, 8); R0(b,c,d,e,a, 9); R0(a,b,c,d,e,10); R0(e,a,b,c,d,11);
     R0(d,e,a,b,c,12); R0(c,d,e,a,b,13); R0(b,c,d,e,a,14); R0(a,b,c,d,e,15);
     R1(e,a,b,c,d,16); R1(d,e,a,b,c,17); R1(c,d,e,a,b,18); R1(b,c,d,e,a,19);
     R2(a,b,c,d,e,20); R2(e,a,b,c,d,21); R2(d,e,a,b,c,22); R2(c,d,e,a,b,23);
     R2(b,c,d,e,a,24); R2(a,b,c,d,e,25); R2(e,a,b,c,d,26); R2(d,e,a,b,c,27);
     R2(c,d,e,a,b,28); R2(b,c,d,e,a,29); R2(a,b,c,d,e,30); R2(e,a,b,c,d,31);
     R2(d,e,a,b,c,32); R2(c,d,e,a,b,33); R2(b,c,d,e,a,34); R2(a,b,c,d,e,35);
     R2(e,a,b,c,d,36); R2(d,e,a,b,c,37); R2(c,d,e,a,b,38); R2(b,c,d,e,a,39);
     R3(a,b,c,d,e,40); R3(e,a,b,c,d,41); R3(d,e,a,b,c,42); R3(c,d,e,a,b,43);
     R3(b,c,d,e,a,44); R3(a,b,c,d,e,45); R3(e,a,b,c,d,46); R3(d,e,a,b,c,47);
     R3(c,d,e,a,b,48); R3(b,c,d,e,a,49); R3(a,b,c,d,e,50); R3(e,a,b,c,d,51);
     R3(d,e,a,b,c,52); R3(c,d,e,a,b,53); R3(b,c,d,e,a,54); R3(a,b,c,d,e,55);
     R3(e,a,b,c,d,56); R3(d,e,a,b,c,57); R3(c,d,e,a,b,58); R3(b,c,d,e,a,59);
     R4(a,b,c,d,e,60); R4(e,a,b,c,d,61); R4(d,e,a,b,c,62); R4(c,d,e,a,b,63);
     R4(b,c,d,e,a,64); R4(a,b,c,d,e,65); R4(e,a,b,c,d,66); R4(d,e,a,b,c,67);
     R4(c,d,e,a,b,68); R4(b,c,d,e,a,69); R4(a,b,c,d,e,70); R4(e,a,b,c,d,71);
     R4(d,e,a,b,c,72); R4(c,d,e,a,b,73); R4(b,c,d,e,a,74); R4(a,b,c,d,e,75);
     R4(e,a,b,c,d,76); R4(d,e,a,b,c,77); R4(c,d,e,a,b,78); R4(b,c,d,e,a,79);
 
     /* Add the working vars back into context.state[] */
     state[0] += a;
     state[1] += b;
     state[2] += c;
     state[3] += d;
     state[4] += e;
 
     /* Wipe variables */
     a = b = c = d = e = 0;
 }
 
 
 /* SHA1Init - Initialize new context */
 void SHA1_Init(SHA1_CTX* context)
 {
     /* SHA1 initialization constants */
     context->state[0] = 0x67452301;
     context->state[1] = 0xEFCDAB89;
     context->state[2] = 0x98BADCFE;
     context->state[3] = 0x10325476;
     context->state[4] = 0xC3D2E1F0;
     context->count[0] = context->count[1] = 0;
 }
 
 
 /* Run your data through this. */
 void SHA1_Update(SHA1_CTX* context, const uint8_t* data, const size_t len)
 {
     size_t i, j;
 
     j = (context->count[0] >> 3) & 63;
     if ((context->count[0] += len << 3) < (len << 3)) context->count[1]++;
     context->count[1] += (len >> 29);
     if ((j + len) > 63) {
         memcpy(&context->buffer[j], data, (i = 64-j));
         SHA1_Transform(context->state, context->buffer);
         for ( ; i + 63 < len; i += 64) {
             SHA1_Transform(context->state, data + i);
         }
         j = 0;
     }
     else i = 0;
     memcpy(&context->buffer[j], &data[i], len - i);
 
 }
 
 
 /* Add padding and return the message digest. */
 void SHA1_Final(SHA1_CTX* context, uint8_t digest[SHA1_DIGEST_SIZE])
 {
     uint32_t i;
     uint8_t  finalcount[8];
 
     for (i = 0; i < 8; i++) {
         finalcount[i] = (unsigned char)((context->count[(i >= 4 ? 0 : 1)]
          >> ((3-(i & 3)) * 8) ) & 255);  /* Endian independent */
     }
     SHA1_Update(context, (uint8_t *)"\200", 1);
     while ((context->count[0] & 504) != 448) {
         SHA1_Update(context, (uint8_t *)"\0", 1);
     }
     SHA1_Update(context, finalcount, 8);  /* Should cause a SHA1_Transform() */
     for (i = 0; i < SHA1_DIGEST_SIZE; i++) {
         digest[i] = (uint8_t)
          ((context->state[i>>2] >> ((3-(i & 3)) * 8) ) & 255);
     }
 
     /* Wipe variables */
     i = 0;
     memset(context->buffer, 0, 64);
     memset(context->state, 0, 20);
     memset(context->count, 0, 8);
     memset(finalcount, 0, 8);	/* SWR */
 
 #ifdef SHA1HANDSOFF  /* make SHA1Transform overwrite its own static vars */
     SHA1_Transform(context->state, context->buffer);
 #endif
 }
 
 /* ==================== Routines added by UCSC genome browser ========================= */
 
 
 char *sha1ToHex(unsigned char hash[20])
 /* Convert binary representation of sha1 to hex string. Do a freeMem on result when done. */
 {
 int hexSize = 20*2;
 char hex[hexSize+1];
 char *h;
 int i;
 for (i = 0, h=hex; i < 20; ++i, h += 2)
     byteToHex( hash[i], h);  
 hex[hexSize] = 0;
 return cloneString(hex);
 }
 
 
 void sha1ForFile(char *fileName, unsigned char hash[20])
 /* Make sha1 hash from file */
 {
 FILE *fp = fopen (fileName, "r");
 if (!fp) errAbort("missing file %s", fileName);
 #define BS 4096 /* match coreutils */
 SHA1_CTX ctx;
 SHA1_Init(&ctx);
 size_t nr;
 char buf[BS];
-while ((nr=fread_unlocked(buf, 1, sizeof(buf), fp)))
+while ((nr=fread(buf, 1, sizeof(buf), fp)))
     { 
     SHA1_Update(&ctx, (const uint8_t*)buf, nr);
     };
 SHA1_Final(&ctx, hash);
 }
 
 char *sha1HexForFile(char *fileName)
 /* Return Sha1 as Hex string */
 {
 unsigned char hash[20];
 sha1ForFile(fileName, hash);
 return sha1ToHex(hash);
 }
 
 void sha1ForBuf(char *buffer, size_t bufSize, unsigned char hash[20])
 /* Return sha1 hash of buffer. */
 {
 #define BS 4096 /* match coreutils */
 SHA1_CTX ctx;
 SHA1_Init(&ctx);
 size_t remaining = bufSize;
 while (remaining > 0)
     {
     int bufSize = BS;
     if (bufSize > remaining)
 	bufSize = remaining;
     SHA1_Update(&ctx, (const uint8_t*)buffer, bufSize);
     buffer += bufSize;
     remaining -= bufSize;
     }
 SHA1_Final(&ctx, hash);
 }
 
 char *sha1HexForBuf(char *buf, size_t bufSize)
 /* Return Sha1 as Hex string */
 {
 unsigned char hash[20];
 sha1ForBuf(buf, bufSize, hash);
 return sha1ToHex(hash);
 }
 
 char *sha1HexForString(char *string)
 /* Return sha sum of zero-terminated string. */
 {
 return sha1HexForBuf(string, strlen(string));
 }