198c9b8daecc44fbda6a6494c566c723920f030a
lrnassar
  Wed Mar 11 18:25:21 2026 -0700
Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.

diff --git src/utils/methylateGenome/methylateGenome.c src/utils/methylateGenome/methylateGenome.c
index ed180874b94..2fdae7518f2 100644
--- src/utils/methylateGenome/methylateGenome.c
+++ src/utils/methylateGenome/methylateGenome.c
@@ -1,16 +1,16 @@
-/* methylateGenome - Creates a methylated version of an input genome, in which any occurance of CG becomes TG. */
+/* methylateGenome - Creates a methylated version of an input genome, in which any occurrence of CG becomes TG. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "dnautil.h"
 #include "dnaLoad.h"
 #include "dnaseq.h"
 #include "fa.h"
 
 void usage()
 /* Explain usage and exit. */
 {
@@ -146,31 +146,31 @@
                 seq->dna[i] = 'T';
             else
                 seq->dna[i] = 't';
             }
         }*/
     
     // Write out the modified line
     faWriteNext(f, seq->name, seq->dna, seq->size);
     }
     
 if (fclose(f) != 0)
     errnoAbort("fclose failed");
 }
 
 void methylateGenome(char *fileName, char *outputPrefix)
-/* methylateGenome - Creates a methylated version of an input genome, in which any occurance of CG becomes TG. */
+/* methylateGenome - Creates a methylated version of an input genome, in which any occurrence of CG becomes TG. */
 {
 int nameSize = 64;
 
 char forwardNoMethylName[nameSize];
 safef(forwardNoMethylName, nameSize, "%s_forwardNoMethyl.fa", outputPrefix);
 performConversion(fileName, forwardNoMethylName, &forwardStrandNoMethylation);
 
 char reverseNoMethylName[nameSize];
 safef(reverseNoMethylName, nameSize, "%s_reverseNoMethyl.fa", outputPrefix);
 performConversion(fileName, reverseNoMethylName, &reverseStrandNoMethylation);
 
 char forwardMethylName[nameSize];
 safef(forwardMethylName, nameSize, "%s_forwardMethyl.fa", outputPrefix);
 performConversion(fileName, forwardMethylName, &forwardStrandWithMethylation);