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/liftUp/liftUp.c src/hg/liftUp/liftUp.c
index 930420e..53fe622 100644
--- src/hg/liftUp/liftUp.c
+++ src/hg/liftUp/liftUp.c
@@ -1129,31 +1129,31 @@
 
 void liftAgp(char *destFile, struct hash *liftHash, int sourceCount, char *sources[])
     /* Lift up coordinates in .agp file. */
 {
     FILE *dest = mustOpen(destFile, "w");
     char *source;
     int i;
     struct lineFile *lf;
     int lineSize, wordCount;
     char *line, *words[32];
     char *s;
     struct liftSpec *spec;
     int start = 0;
     int end = 0;
     int ix = 0;
-    char newDir[256], newName[128], newExt[64];
+    char newDir[PATH_LEN], newName[FILENAME_LEN], newExt[FILEEXT_LEN];
     struct bigInsert *bi;
     struct chromInserts *chromInserts;
     struct hash *insertHash = newHash(8);
     struct hash *contigsHash = newHash(10);
     boolean firstContig = TRUE;
     char lastContig[256];
     char *contig;
     int lastEnd = 0;
 
     if (sourceCount < 2)
         usage();
 
     if (how == carryMissing)
         warn("'carry' doesn't work for .agp files, ignoring");
 
@@ -1240,31 +1240,31 @@
 
 void liftGap(char *destFile, struct hash *liftHash, int sourceCount, char *sources[])
     /* Lift up coordinates in .gap file (just the gaps from .agp).  Negative strad allowed */
 {
     FILE *dest = mustOpen(destFile, "w");
     char *source;
     int i;
     struct lineFile *lf;
     int lineSize, wordCount;
     char *line, *words[32];
     char *s;
     struct liftSpec *spec;
     int start = 0;
     int end = 0;
     int ix = 0;
-    char newDir[256], newName[128], newExt[64];
+    char newDir[PATH_LEN], newName[FILENAME_LEN], newExt[FILEEXT_LEN];
     char lastContig[256];
     char *contig;
     int lastEnd = 0;
     int fragStart, fragEnd;
 
     if (how == carryMissing)
         warn("'carry' doesn't work for .gap files, ignoring");
 
     splitPath(destFile, newDir, newName, newExt);
 
     strcpy(lastContig, "");
     for (i=0; i<sourceCount; ++i)
         {
         source = sources[i];
         verbose(1, "Lifting %s\n", source);
@@ -1625,58 +1625,58 @@
 /* Lift up coordinates of a .bscore */
 {
 if (querySide)
     liftTabbed(destFile, liftHash, sourceCount, sources, 1, 2, 3, FALSE, 0, 0, 0, 0, 1);
 else
     liftTabbed(destFile, liftHash, sourceCount, sources, 4, 5, 6, FALSE, 0, 0, 0, 0, 1);
 }
 
 void liftBlast(char *destFile, struct hash *liftHash, int sourceCount, char *sources[])
 /* Lift up coordinates of a .gdup. */
 {
 liftTabbed(destFile, liftHash, sourceCount, sources, 1, 8, 9, FALSE, 0, 0, 0, 1, -1);
 }
 
 
-char *contigInDir(char *name, char dirBuf[256])
+char *contigInDir(char *name, char dirBuf[PATH_LEN])
 /* Figure out which contig we're in by the file name. It should be the directory
  * before us. */
 {
-char root[128], ext[64];
+char root[FILENAME_LEN], ext[FILEEXT_LEN];
 char *s, *contig;
 int len;
 
 verbose(2,"#\tname: %s\n", name);
 splitPath(name, dirBuf, root, ext);
 len = strlen(dirBuf);
 if (len == 0)
     errAbort("Need contig directory in file name to lift .gl files\n");
 if (dirBuf[len-1] == '/')
     dirBuf[len-1] = 0;
 verbose(2,"#\tdirBuf: %s\n", dirBuf);
 if ((s = strrchr(dirBuf, '/')) != NULL)
     contig = s+1;
 else
     contig = dirBuf;
 verbose(2,"#\ts: %s\n", s);
 return contig;
 }
 
 void liftGl(char *destFile, struct hash *liftHash, int sourceCount, char *sources[])
 /* Lift up coordinates in .gl file. */
 {
-char dirBuf[256], chromName[256];
+char dirBuf[PATH_LEN], chromName[256];
 int i;
 char *source;
 char *contig;
 FILE *dest = mustOpen(destFile, "w");
 struct lineFile *lf = NULL;
 int lineSize, wordCount;
 char *line, *words[32];
 struct liftSpec *spec;
 int offset;
 
 if (how == carryMissing)
     warn("'carry' doesn't work for .gl files, ignoring");
 for (i=0; i<sourceCount; ++i)
     {
     source = sources[i];