src/shortReads/bwtMake/bwtMake.c 1.4

Index: src/shortReads/bwtMake/bwtMake.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/shortReads/bwtMake/bwtMake.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 1000000 -r1.3 -r1.4
--- src/shortReads/bwtMake/bwtMake.c	7 Nov 2008 23:54:52 -0000	1.3
+++ src/shortReads/bwtMake/bwtMake.c	24 Nov 2009 15:49:14 -0000	1.4
@@ -1,111 +1,112 @@
 /* bwtMake - Create a bwt transformed version of a file. */
 
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "obscure.h"
 
 static char const rcsid[] = "$Id$";
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bwtMake - Create a bwt transformed version of dna sequence\n"
   "usage:\n"
   "   bwtMake in.txt out.bwt\n"
   "The out.bwt will be mostly text, but will have a zero in it.\n"
   "   -suffix=file Output suffix tree to file.\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"suffix", OPTION_STRING},
    {NULL, 0},
 };
 
 char *inBuf;
 
 int cmpInBufAtOffset(const void *va, const void *vb)
 {
 int a = *((const int *)va), b = *((const int *)vb);
 return strcmp(inBuf+a, inBuf+b);
 }
 
 void writeUpTo(FILE *f,  char *s,  int maxSize)
 /* Write string to file, up to either end of string of maxSize chars */
 {
 int i;
 for (i=0; i<maxSize; ++i)
     {
     char c = *s++;
     if (c == 0)
        break;
     if (c == '\n')
        fprintf(f, "\\n");
     else
 	fputc(c, f);
     }
 if (i == maxSize)
     fprintf(f, "...");
 fputc('$', f);
 }
 
 void bwtMake(char *in, char *out)
 /* This makes the bwt in a straightforward but inefficient way. */
 {
 size_t inSize;
 readInGulp(in, &inBuf, &inSize);
-if (inSize >= 1LL<<32LL)
-   errAbort("%s is too big, (%zd bytes), can only handle up to %lld",  in, inSize, (1LL<<32LL));
+long long longSize = inSize;
+if (longSize >= (1LL << 32LL))
+    errAbort("In is too big, can only handle up to 4 Gig");
 bits32 *offsets;
 bits32 i, size=inSize+1;
 AllocArray(offsets, size);
 for (i=0; i<size; ++i)
     offsets[i] = i;
 qsort(offsets, size, sizeof(offsets[0]), cmpInBufAtOffset);
 FILE *f = mustOpen(out, "w");
 for (i=0; i<size; ++i)
     {
     int offset = offsets[i];
     if (offset == 0)
 	fputc(0, f);
     else
         fputc(inBuf[offset-1], f);
     }
 carefulClose(&f);
 
 char *suffixFile = optionVal("suffix", NULL);
 if (suffixFile)
    {
    FILE *f = mustOpen(suffixFile, "w");
    for (i=0; i<size; ++i)
        {
        int offset = offsets[i];
        char c;
        if (offset == 0)
           c = '$';
        else
           c = inBuf[offset-1];
        if (c == '\n')
            fprintf(f, "%u \\n", i);
        else
 	   fprintf(f, "%u %c ", i, c);
 	   writeUpTo(f, inBuf +offset,  60);
 	   fprintf(f, "\n");
        }
    carefulClose(&f);
    }
 }
 
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 bwtMake(argv[1], argv[2]);
 return 0;
 }