b3152085521eb7be92e2fcab26fbae5b7e09a57c
hiram
  Thu Jan 7 14:45:47 2016 -0800
usefult to have the unique keys in hand to compare two genome assemblies refs #16589

diff --git src/utils/twoBitDup/twoBitDup.c src/utils/twoBitDup/twoBitDup.c
index 5309671..200b0cf 100644
--- src/utils/twoBitDup/twoBitDup.c
+++ src/utils/twoBitDup/twoBitDup.c
@@ -9,62 +9,75 @@
 #include "twoBit.h"
 #include "dnaseq.h"
 #include "math.h"
 #include "udc.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: key and sequenceName\n"
   "   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs\n"
   );
 }
 
+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
-	hashAdd(seqHash, seq->dna, index->name);
+	hel = hashAdd(seqHash, seq->dna, index->name);
+    if (keyListFile)
+       fprintf(keyListFile, "%x\t%s\n", hel->hashVal, index->name);
     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;
 }