1ed3d40ffbe5dbf9059f99e71b757f26d136fe8f
braney
  Fri Jul 1 14:44:05 2022 -0700
make usage message a bit more clear.

diff --git src/hg/ratStuff/mafCounts/mafCounts.c src/hg/ratStuff/mafCounts/mafCounts.c
index cda522a..ff991b6 100644
--- src/hg/ratStuff/mafCounts/mafCounts.c
+++ src/hg/ratStuff/mafCounts/mafCounts.c
@@ -21,31 +21,31 @@
 struct strandHead *strandHeads;
 struct bbiFile *scaleBbi ;
 struct bigWigValsOnChrom *scaleVals;
 double dataMin, dataRange;
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "mafCounts - count the number of A,T,C,G in a maf and output four wiggles with values that sum to one\n"
   "usage:\n"
   "   mafCounts mafIn wigPrefix\n"
   "WARNING:  requires a maf with only a single target sequence\n"
   "options:\n"
-  "   -scale=file.bw     scale logo by bigWig value\n"
+  "   -scale=file.bw     scale each wiggle by the bigWig value at that base.  This might be something like a phyloP score.\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"scale", OPTION_STRING},
    {NULL, 0},
 };
 
 unsigned char letterBox[256];  // to make ASCII values to indices
 unsigned ourBufSize =  256 *1024;   // this is the max size of a maf block
 
 #define NUMBER_OF_NUCS   4
 
 void mafCounts(char *mafIn, char *wigPrefix)
 /* mafCounts - count A,C,T,G */