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/txCds/txCdsRefBestEvOnly/txCdsRefBestEvOnly.c src/hg/txCds/txCdsRefBestEvOnly/txCdsRefBestEvOnly.c
index da50e79..ef4b7fd 100644
--- src/hg/txCds/txCdsRefBestEvOnly/txCdsRefBestEvOnly.c
+++ src/hg/txCds/txCdsRefBestEvOnly/txCdsRefBestEvOnly.c
@@ -1,70 +1,70 @@
 /* txCdsRefBestEvOnly - Go through a cdsEvidence file, and extract only the bits that refer to the native orf for a RefSeqReviewed transcript.. */
 
 /* 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"
 #include "cdsEvidence.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "txCdsRefBestEvOnly - Go through a cdsEvidence file, and extract only the bits that refer to the native orf for a RefSeqReviewed transcript.\n"
   "usage:\n"
   "   txCdsRefBestEvOnly in.tce out.tce\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 void txCdsRefBestEvOnly(char *inFile, char *outFile)
 /* txCdsRefBestEvOnly - Go through a cdsEvidence file, and extract only the bits that refer to the native orf for a RefSeqReviewed transcript.. */
 {
 struct cdsEvidence *cds, *cdsList = cdsEvidenceLoadAll(inFile);
 struct hash *nativeEvHash = hashNew(18);
 FILE *f = mustOpen(outFile, "w");
 
 /* Make one pass through list adding the native refseq reviewed records to hash. */
 for (cds = cdsList; cds != NULL; cds = cds->next)
     {
     if (sameString(cds->source, "RefSeqReviewed"))
         {
 	char *acc = strrchr(cds->name, '.');
 	assert(acc != NULL);
 	acc += 1;
 	if (sameString(acc, cds->accession))
 	    hashAdd(nativeEvHash, cds->name, cds);
 	}
     }
 
 /* Make another pass through outputting all lines that correspond to
  * reviewd refseq's ORF. */
 for (cds = cdsList; cds != NULL; cds = cds->next)
     {
     struct cdsEvidence *native = hashFindVal(nativeEvHash, cds->name);
     if (native != NULL)
         {
 	if (cds->start == native->start && cds->end == native->end)
 	    cdsEvidenceTabOut(cds, f);
 	}
     }
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 txCdsRefBestEvOnly(argv[1], argv[2]);
 return 0;
 }