c9ddb99c248fff004d4635c0208e18f8ae928d60
tdreszer
  Mon Apr 16 13:14:40 2012 -0700
Changed name of global var to avoid conflict with Galt's lib changes.
diff --git src/utils/findMotif/findMotif.c src/utils/findMotif/findMotif.c
index 444494f..730a66e 100644
--- src/utils/findMotif/findMotif.c
+++ src/utils/findMotif/findMotif.c
@@ -4,31 +4,31 @@
 #include "hash.h"
 #include "options.h"
 #include "dnautil.h"
 #include "dnaseq.h"
 #include "dnaLoad.h"
 #include "portable.h"
 #include "memalloc.h"
 #include "obscure.h"
 
 
 char *chr = (char *)NULL;	/*	process the one chromosome listed */
 char *motif = (char *)NULL;	/*	specified motif string */
 unsigned motifLen = 0;		/*	length of motif	*/
 unsigned long long motifVal;	/*	motif converted to a number	*/
 unsigned long long complementVal;	/*	- strand complement	*/
-boolean bedOutput = TRUE;	/*	output bed file (default) */
+boolean bedOutputOpt = TRUE;	/*	output bed file (default) */
 boolean wigOutput = FALSE;	/*  output wiggle format instead of bed file */
 char *strand = (char *)NULL;
 boolean doPlusStrand = TRUE;	/*	output bed file instead of wiggle */
 boolean doMinusStrand = TRUE;	/*	output bed file instead of wiggle */
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "findMotif - find specified motif in sequence\n"
   "usage:\n"
   "   findMotif [options] -motif=<acgt...> sequence\n"
   "where:\n"
   "   sequence is a .fa , .nib or .2bit file or a file which is a list of sequence files.\n"
   "options:\n"
@@ -201,37 +201,37 @@
 
 maxAlloc = 2100000000 *
 	 (((sizeof(size_t)/4)*(sizeof(size_t)/4)*(sizeof(size_t)/4)));
 sprintLongWithCommas(asciiAlloc, (long long) maxAlloc);
 verbose(4, "#\tmaxAlloc: %s\n", asciiAlloc);
 setMaxAlloc(maxAlloc);
 /* produces: size_t is 4 == 2100000000 ~= 2^31 = 2Gb
  *      size_t is 8 = 16800000000 ~= 2^34 = 16 Gb
  */
 
 dnaUtilOpen();
 
 motif = optionVal("motif", NULL);
 chr = optionVal("chr", NULL);
 strand = optionVal("strand", NULL);
-bedOutput = optionExists("bedOutput");
+bedOutputOpt = optionExists("bedOutput");
 wigOutput = optionExists("wigOutput");
 
 if (wigOutput)
-    bedOutput = FALSE;
+    bedOutputOpt = FALSE;
 else
-    bedOutput = TRUE;
+    bedOutputOpt = TRUE;
 
 if (chr)
     verbose(2, "#\tprocessing chr: %s\n", chr);
 if (strand)
     verbose(2, "#\tprocessing strand: '%s'\n", strand);
 if (motif)
     verbose(2, "#\tsearching for motif: %s\n", motif);
 else {
     warn("ERROR: -motif string empty, please specify a motif\n");
     usage();
 }
 verbose(2, "#\ttype output: %s\n", wigOutput ? "wiggle data" : "bed format");
 verbose(2, "#\tspecified sequence: %s\n", argv[1]);
 verbose(2, "#\tsizeof(motifVal): %d\n", (int)sizeof(motifVal));
 if (strand)