4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/oneShot/flagMhcClones/flagMhcClones.c src/hg/oneShot/flagMhcClones/flagMhcClones.c
index c8e9dc1..ecc07e1 100644
--- src/hg/oneShot/flagMhcClones/flagMhcClones.c
+++ src/hg/oneShot/flagMhcClones/flagMhcClones.c
@@ -1,76 +1,76 @@
 /* flagMhcClones - Look for clones Stephan wants in MHC.. */
 
 /* Copyright (C) 2011 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "cheapcgi.h"
 #include "dnaseq.h"
 #include "fa.h"
 #include "portable.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "flagMhcClones - Look for clones Stephan wants in MHC.\n"
   "usage:\n"
   "   flagMhcClones mhcClones.txt gs.N\n");
 }
 
 
 void flagMhcClones(char *mhcFile, char *gsDir)
 /* flagMhcClones - Look for clones Stephan wants in MHC.. */
 {
 struct lineFile *lf = lineFileOpen(mhcFile, TRUE);
 char *line, *words[16];
 int lineSize, wordCount, i;
 char clonePath[512];
 char *clone, *cloneVer;
 static char *phases[3] = {"fin", "draft", "predraft",};
 boolean found;
 
 while (lineFileNext(lf, &line, &lineSize))
     {
     if (line[0] == '#')
         continue;
     wordCount = chopLine(line, words);
     if (wordCount == 0)
         continue;
     lineFileExpectWords(lf, 7, wordCount);
     clone = words[0];
     cloneVer = words[1];
     found = FALSE;
     for (i = 0; i < 3; ++i)
         {
 	char *phase = phases[i];
 	sprintf(clonePath, "%s/%s/fa/%s.fa", gsDir, phase, clone);
 	if (fileExists(clonePath))
 	    {
 	    struct dnaSeq *seq = faReadDna(clonePath);
 	    char *e = strchr(seq->name, '_');
 
 	    if (e != NULL) *e = 0;
 	    if (!sameString(seq->name, cloneVer))
 		printf("%s\t(wrong version %s)\n", cloneVer, seq->name);
 	    else if (i != 0)
 	        printf("%s\t(not finished)\n", cloneVer);
 	    found = TRUE;
 	    }
 	}
     if (!found)
         printf("%s\t(not found)\n", cloneVer);
     }
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 cgiSpoof(&argc, argv);
 if (argc != 3)
     usage();
 flagMhcClones(argv[1], argv[2]);
 return 0;
 }