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/twoBitDup/twoBitDup.c src/utils/twoBitDup/twoBitDup.c
index 30624f1..9ce2a14 100644
--- src/utils/twoBitDup/twoBitDup.c
+++ src/utils/twoBitDup/twoBitDup.c
@@ -1,104 +1,104 @@
 /* twoBitDup - check to see if a twobit file has any identical sequences in it. */
 
 /* Copyright (C) 2013 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 "twoBit.h"
 #include "dnaseq.h"
 #include "math.h"
 #include "udc.h"
 #include <openssl/md5.h>
 
 // static char const rcsid[] = "$Id: newProg.c,v 1.30 2010/03/24 21:18:33 hiram Exp $";
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "twoBitDup - check to see if a twobit file has any identical sequences in it\n"
   "usage:\n"
   "   twoBitDup file.2bit\n"
   "options:\n"
   "  -keyList=file - file to write a key list, two columns: md5sum and sequenceName\n"
   "  -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs\n"
   "\nexample: twoBitDup -keyList=stdout db.2bit \\\n"
   "          | grep -v 'are identical' | sort > db.idKeys.txt"
   );
 }
 
 static char *keyList = NULL;
 
 static struct optionSpec options[] = {
    {"keyList", OPTION_STRING},
    {"udcDir", OPTION_STRING},
    {NULL, 0},
 };
 
 void twoBitDup(char *filename)
 /* twoBitDup - check to see if a twobit file has any identical sequences in it. */
 {
 struct twoBitFile *tbf;
 
 tbf = twoBitOpen(filename);
 struct twoBitIndex *index;
 int seqCount = slCount(tbf->indexList);
 int hashSize = log2(seqCount) + 2;	 // +2 for luck
 struct hash *seqHash = newHash(hashSize);
 FILE *keyListFile = NULL;
 
 verbose(2, "hash size is %d\n", hashSize);
 if (keyList)
     {
     verbose(2, "writing key list to %s\n", keyList);
     keyListFile = mustOpen(keyList, "w");
     }
 
 for (index = tbf->indexList; index != NULL; index = index->next)
     {
     verbose(2,"grabbing seq %s\n", index->name);
     int size;
     struct dnaSeq *seq = twoBitReadSeqFragExt(tbf, index->name,
 	0, 0, FALSE, &size);
     struct hashEl *hel;
     if ((hel = hashLookup(seqHash, seq->dna)) != NULL)
 	printf("%s and %s are identical\n", index->name, (char *)hel->val);
     else
 	hel = hashAdd(seqHash, seq->dna, index->name);
     if (keyListFile)
 	{
 /* This used to be extremely slow:
 #include "md5.h"
        char *md5Sum = md5HexForString(seq->dna);
        fprintf(keyListFile, "%s\t%s\n", md5Sum, index->name);
        freeMem(md5Sum);
  * changed to use MD5() in openssl 2020-12-04:
  */
 	unsigned char md5Result[MD5_DIGEST_LENGTH];
 	MD5((unsigned char *)seq->dna, strlen(seq->dna), md5Result);
 	int i;
 	struct dyString *ds = newDyString(MD5_DIGEST_LENGTH);
 	for(i = 0; i < MD5_DIGEST_LENGTH; i++)
 	    {
 	    dyStringPrintf(ds, "%02x", md5Result[i]);
 	    }
 	fprintf(keyListFile, "%s\t%s\n", ds->string, index->name);
 	freeDyString(&ds);
 	}
     freeDnaSeq(&seq);
     }
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 2)
     usage();
 keyList = optionVal("keyList", NULL);
 udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
 twoBitDup(argv[1]);
 return 0;
 }