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/ratStuff/mafOrder/mafOrder.c src/hg/ratStuff/mafOrder/mafOrder.c
index bfb0ae5..f94972b 100644
--- src/hg/ratStuff/mafOrder/mafOrder.c
+++ src/hg/ratStuff/mafOrder/mafOrder.c
@@ -1,83 +1,83 @@
 /* mafOrder - Filter out maf files. */
 
 /* 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 "errAbort.h"
 #include "linefile.h"
 #include "hash.h"
 #include "chain.h"
 #include "options.h"
 #include "maf.h"
 #include "bed.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "mafOrder - order components within a maf file\n"
   "usage:\n"
   "   mafOrder mafIn order.lst mafOut\n"
   "where order.lst has one species per line\n"
   "options:\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 struct mafComp *compHolders[100];
 
 void mafOrder(char *mafIn, char *listFile,  char *mafOut)
 /* mafOrder - order the components in a maf file */
 {
 FILE *f = mustOpen(mafOut, "w");
 struct lineFile *lf = lineFileOpen(listFile, TRUE);
 struct mafFile *mf = mafOpen(mafIn);
 struct mafAli *maf;
 char *row[1];
 struct slName *elemList = NULL, *elem;
 
 mafWriteStart(f, mf->scoring);
 
 while (lineFileRow(lf, row))
     slNameStore(&elemList, row[0]);
 
 lineFileClose(&lf);
 slReverse(&elemList);
 
 while((maf = mafNext(mf)) != NULL)
     {
     int numComps = 0;
     int ii;
     struct mafComp *comp;
 
     for(elem = elemList; elem ; elem = elem->next)
 	{
 	if ((comp = mafMayFindComponentDb(maf, elem->name)) != NULL)
 	    {
 	    compHolders[numComps++] = comp;
 	    }
 	}
      
     maf->components = NULL;
     for(ii=0; ii < numComps; ii++)
 	slAddTail(&maf->components, compHolders[ii]);
 
     mafWrite(f, maf);
     mafAliFree(&maf);
     }
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 4)
     usage();
 
 mafOrder(argv[1], argv[2], argv[3]);
 return 0;
 }