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/txCdsWeed/txCdsWeed.c src/hg/txCds/txCdsWeed/txCdsWeed.c
index 9b2c47f..e3c7749 100644
--- src/hg/txCds/txCdsWeed/txCdsWeed.c
+++ src/hg/txCds/txCdsWeed/txCdsWeed.c
@@ -1,80 +1,80 @@
 /* txCdsWeed - Remove bad CDSs including NMD candidates. */
 
 /* 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 "obscure.h"
 #include "txInfo.h"
 #include "cdsEvidence.h"
 #include "cdsOrtho.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "txCdsWeed - Remove bad CDSs including NMD candidates\n"
   "usage:\n"
   "   txCdsWeed in.tce in.info out.tce out.info\n"
   "options:\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 
 void txCdsWeed(char *inTce, char *inInfo, char *outTce, char *outInfo)
 /* txCdsWeed - Remove bad CDSs including NMD candidates. */
 {
 /* Read in txInfo into a hash keyed by transcript name */
 struct hash *infoHash = hashNew(17);
 struct txInfo *info, *infoList = txInfoLoadAll(inInfo);
 for (info = infoList; info != NULL; info = info->next)
     hashAdd(infoHash, info->name, info);
 verbose(2, "Read info on %d transcripts from %s\n", infoHash->elCount, 
 	inInfo);
 
 /* Read in input CDS */
 struct cdsEvidence *cds, *cdsList = cdsEvidenceLoadAll(inTce);
 
 /* Write ones that pass filter to output file. */
 FILE *f = mustOpen(outTce, "w");
 int weedCount = 0;
 for (cds = cdsList; cds != NULL; cds = cds->next)
     {
     struct txInfo *info = hashMustFindVal(infoHash, cds->name);
     if (info->isRefSeq || 
     	(!info->nonsenseMediatedDecay && !info->cdsSingleInIntron && !info->cdsSingleInUtr3))
 	{
 	cdsEvidenceTabOut(cds, f);
 	}
     else
 	{
 	++weedCount;
 	info->orfSize = 0;
 	}
     }
 carefulClose(&f);
 verbose(1, "Weeded %d of %d cds\n", weedCount, slCount(cdsList));
 
 /* Write updated info file. */
 f = mustOpen(outInfo, "w");
 for (info = infoList; info != NULL; info = info->next)
     txInfoTabOut(info, f);
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 5)
     usage();
 txCdsWeed(argv[1], argv[2], argv[3], argv[4]);
 return 0;
 }