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/utils/faUniqify/faUniqify.c src/utils/faUniqify/faUniqify.c
index ebc17b2..c6c8b41 100644
--- src/utils/faUniqify/faUniqify.c
+++ src/utils/faUniqify/faUniqify.c
@@ -1,86 +1,86 @@
 /* faUniqify - Remove redundant sequences from fasta.  Warn if different sequences have same name.. */
 
 /* Copyright (C) 2014 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 "fa.h"
 
 /* Globals that hold command line options. */
 boolean addId = FALSE;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "faUniqify - Remove redundant sequences from fasta.  Warn if different sequences have same name.\n"
   "usage:\n"
   "   faUniqify in.fa out.fa\n"
   "options:\n"
   "   -verbose=0 - suppress warning messages\n"
   "   -addId - add an ID suffix to make things unique\n"
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {"addId", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 int hashCountMatches(struct hash *hash, char *key)
 /* Count number of things matching key in hash */
 {
 int count = 0;
 struct hashEl *hel;
 for (hel = hashLookup(hash, key); hel != NULL; hel = hashLookupNext(hel))
      ++count;
 return count;
 }
 void faUniqify(char *inFile, char *outFile)
 /* faUniqify - Remove redundant sequences from fasta.  Warn if different sequences have same name.. */
 {
 struct hash *uniqHash = hashNew(0);
 struct lineFile *lf = lineFileOpen(inFile, FALSE);
 FILE *f = mustOpen(outFile, "w");
 DNA *dna;
 int size;
 char *name;
 while (faMixedSpeedReadNext(lf, &dna, &size, &name))
     {
     char *newDna = cloneMem(dna, size+1);
     char *oldDna = hashFindVal(uniqHash, name);
     if (oldDna != NULL)
          {
 	 if (!sameString(oldDna, newDna))
 	     warn("Name %s reused for different sequences", name);
 	 }
     if (addId || oldDna == NULL)
          {
 	 hashAdd(uniqHash, name, newDna);
 	 char *fullName = name;
 	 char buf[PATH_LEN];
 	 if (addId)
 	     {
 	     int count = hashCountMatches(uniqHash, name);
 	     safef(buf, sizeof(buf), "%sv%d", name, count);
 	     fullName = buf;
 	     }
 	 faWriteNext(f, fullName, newDna, size);
 	 }
     }
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 addId = optionExists("addId");
 faUniqify(argv[1], argv[2]);
 return 0;
 }