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/txGene/txGeneAddOldUnmapped/txGeneAddOldUnmapped.c src/hg/txGene/txGeneAddOldUnmapped/txGeneAddOldUnmapped.c
index 7502f74..622390b 100644
--- src/hg/txGene/txGeneAddOldUnmapped/txGeneAddOldUnmapped.c
+++ src/hg/txGene/txGeneAddOldUnmapped/txGeneAddOldUnmapped.c
@@ -1,69 +1,69 @@
 /* txGeneAddOldUnmapped - Add information about genes that didn't map from old assembly to oldToNew table.. */
 
 /* 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 "options.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "txGeneAddOldUnmapped - Add information about genes that didn't map from old assembly to oldToNew table.\n"
   "usage:\n"
   "   txGeneAddOldUnmapped oldToNewMapped.tab old.unmapped oldToNew.tab\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 void txGeneAddOldUnmapped(char *mappedFile, char *unmappedFile, char *outputFile)
 /* txGeneAddOldUnmapped - Add information about genes that didn't map from old assembly to oldToNew table.. */
 {
 struct lineFile *mappedLf = lineFileOpen(mappedFile, TRUE);
 struct lineFile *unmappedLf = lineFileOpen(unmappedFile, TRUE);
 FILE *f = mustOpen(outputFile, "w");
 
 /* Read through the mapped ones and save to output unchanged, but keep hash of all the accessions
  * we've seen to double check mapped/unmapped go together. */
 struct hash *accHash = hashNew(0);
     {
     char *row[4];
     while (lineFileRowTab(mappedLf, row))
 	{
 	char *acc = row[1];
 	hashAdd(accHash, acc, NULL);
 	fprintf(f, "%s\t%s\t%s\t%s\n", row[0], row[1], row[2], row[3]);
 	}
     }
 
 /* Read through bed file for unmapped and save data. */
     {
     char *row[12];
     while (lineFileRowTab(unmappedLf, row))
         {
 	char *acc = row[3];
 	if (hashLookup(accHash, acc))
 	    errAbort("%s is in both %s and %s\n", acc, mappedFile, unmappedFile);
 	fprintf(f, "\t%s\t\t%s\n", acc, "unmapped");
 	}
     }
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 4)
     usage();
 txGeneAddOldUnmapped(argv[1], argv[2], argv[3]);
 return 0;
 }