f952b14fca3833e9d8fef0ae8a086ad15485b552
galt
  Wed Jan 1 02:11:38 2025 -0800
fix various errors for utils compiled on Rocky 9 hgwdev-new.

diff --git src/hg/trfBig/trfBig.c src/hg/trfBig/trfBig.c
index 1799932..80fa7ad 100644
--- src/hg/trfBig/trfBig.c
+++ src/hg/trfBig/trfBig.c
@@ -88,31 +88,31 @@
     if (e > end) e = end;
     if (s < e)
         {
 	fprintf(out, "%s\t%d\t%d\ttrf", chromName, s+chromOffset, e+chromOffset);
 	for (i=2; i<14; ++i)
 	    fprintf(out, "\t%s", row[i]);
 	fprintf(out, "\n");
 	}
     }
 lineFileClose(&lf);
 }
 
 void removeWild(char *pat)
 /* Remove all files matching wildcard. */
 {
-char dir[256], fn[128], ext[64];
+char dir[PATH_LEN], fn[FILENAME_LEN], ext[FILEEXT_LEN];
 char wild[256];
 struct fileInfo *list, *el;
 
 splitPath(pat, dir, fn, ext);
 sprintf(wild, "%s%s", fn, ext);
 if (dir[0] == 0) strcpy(dir, ".");
 
 list = listDirX(tempDir, wild, TRUE);
 for (el = list; el != NULL; el = el->next)
     {
     remove(el->name);
     verbose(1, "Removed %s\n", el->name);
     }
 slFreeList(&list);
 }
@@ -165,32 +165,32 @@
     {
     oneSize = size - i;
     if (oneSize > lineSize) oneSize = lineSize;
     mustWrite(out, s+i, oneSize);
     fputc('\n', out);
     }
 }
 
 void trfBig(char *input, char *output)
 /* trfBig - Mask tandem repeats on a big sequence file.. */
 {
 int maxSize = 5000000;
 int overlapSize = 10000;
 int start, end, s, e;
 int halfOverlapSize = overlapSize/2;
-char tempFile[512], trfRootName[512], trfTemp[512], bedFileName[512];
-char dir[256], seqName[128], ext[64];
+char tempFile[512], trfRootName[512], trfTemp[1024], bedFileName[1024];
+char dir[PATH_LEN], seqName[FILENAME_LEN], ext[FILEEXT_LEN];
 FILE *bedFile = NULL;
 struct dnaSeq  *maskedSeq = NULL;
 
 if (doBed)
     {
     if (optionExists("bedAt"))
         strcpy(bedFileName, optionVal("bedAt", NULL));
     else
 	{
 	splitPath(output, dir, seqName, ext);
 	sprintf(bedFileName, "%s%s.bed", dir, seqName);
 	}
     bedFile = mustOpen(bedFileName, "w");
     }
 splitPath(input, dir, seqName, ext);