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/jimgrep/jimgrep.c src/utils/jimgrep/jimgrep.c
index e830a9f2ab5..0daf0a0df7e 100644
--- src/utils/jimgrep/jimgrep.c
+++ src/utils/jimgrep/jimgrep.c
@@ -1,149 +1,149 @@
 /* Jim grep - crude approximation of grep. */
 #include "common.h"
 #include <io.h>
 
 
 _inline toUp(char c)
 {
 if (isalpha(c))
     c |= 0x20;
 return c;
 }
 
 char *findInString(const char *string, const char *pattern)
 /* Return first occurrence of pattern in string.
  * (Ignores case) */
 {
 char c1 = toUp(*pattern++);
 int patSize = strlen(pattern);
 char c;
 
 while ((c = *string++) != 0)
     {
     if (c1 == toUp(c))
         {
         int i;
         for (i=0; i<patSize; ++i)
             {
             if (toUp(string[i]) != toUp(pattern[i]))
                 break;
             }
         if (i == patSize)
             return (char*)(string-1);
         }
     }
 return NULL;
 }
 
 char *findBefore(char *bufStart, char *pos, char c)
 /* Scan backwards from pos to bufStart looking for first
- * occurence of character.  Return position right after
+ * occurrence of character.  Return position right after
  * that.  */
 {
 for (;;)
     {
     if (--pos == bufStart)
         return bufStart;
     if (*pos == c)
         return pos+1;
     }
 }
 
 char *findAfter(char *pos, char *bufEnd, char c)
 /* Scan forwards from pos to bufEnd looking for 
- * last occurence of character. Return position 
+ * last occurrence of character. Return position 
  * just before that. */
 {
 for (;;)
     {
     if (++pos == bufEnd)
         return bufEnd;
     if (*pos == c)
         return pos;
     }
 }
 
 void fgrepOne(char *pattern, char *fileName, boolean ignoreCase, boolean singleFile)
 /* Gnarly, speed tweaked, unbuffered i/o grep. Why? Because it's
  * 4x faster, which matters on those huge GenBank files! */
 {
 char buf[8*1024+1];
 int bufRead;
 int remainder = 0;
 int fd;
 char *s;
 int patSize = strlen(pattern);
 char *(*searcher)(const char *string, const char *pat); 
 
 searcher = (ignoreCase ? findInString : strstr);
 
 fd = open(fileName, _O_RDONLY|_O_BINARY);
 if (fd < 0)
     errAbort("Couldn't open %s\n", fileName);
 
 for (;;)
     {
     bufRead = read(fd, buf + remainder, sizeof(buf)-1-remainder) + remainder;
     if (bufRead == 0)
         break;
     buf[bufRead] = 0;
     s = buf;
     while ((s = searcher(s, pattern)) != NULL)
         {
         char *lineStart = findBefore(buf, s, '\n');
         char *lineAfter = findAfter(s, buf+bufRead, '\n');
         if (lineAfter[-1] == '\r')
             --lineAfter;
         if (!singleFile)
             printf("%s: ", fileName);
         mustWrite(stdout, lineStart, lineAfter-lineStart);
         putchar('\n');
         s += patSize;
         }
     s = findBefore(buf, buf+bufRead, '\n');
     if (s == buf)
         remainder = 0;
     else
         {
         remainder = buf + bufRead - s;
         memmove(buf, s, remainder);
         }
     if (bufRead < sizeof(buf)-1)
         break;
     }
 close(fd);
 }
 
 int main(int argc, char *argv[])
 {
 char *fileName, *pattern;
 int i;
 boolean ignoreCase = FALSE;
 int startFileIx = 2;
 boolean singleFile = FALSE;
 
 if (argc < 3 || (argv[1][0] == '-' && argc < 4))
     {
     errAbort("grep - print lines of file that include pattern\n"
              "usage:\n"
              "    grep pattern file(s)\n"
              "or\n"
              "    grep -i pattern file(s)\n"
              "The -i makes the program ignore case.\n");
     }
 
 pattern = argv[1];
 if (sameString(pattern, "-i"))
     {
     startFileIx = 3;
     pattern = argv[2];
     ignoreCase = TRUE;
     }
 singleFile = (startFileIx+1 == argc);
 for (i=startFileIx; i<argc; ++i)
     {
     fileName = argv[i];
     fgrepOne(pattern, fileName, ignoreCase, singleFile);
     }
 return 0;
 }
\ No newline at end of file