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/oneShot/rcvs/rcvs.c src/hg/oneShot/rcvs/rcvs.c
index 1dfe1c2..d997a9c 100644
--- src/hg/oneShot/rcvs/rcvs.c
+++ src/hg/oneShot/rcvs/rcvs.c
@@ -1,100 +1,100 @@
 /* rcvs - Compare riken noncoding vs. nonspliced. */
 
 /* 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 "jksql.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "rcvs - Compare riken noncoding vs. nonspliced\n"
   "usage:\n"
   "   rcvs TUinfo_for_fig2.txt tu_fantom2cluster.txt\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 void rcvs(char *codingTable, char *clusterTable)
 /* rcvs - Compare riken noncoding vs. nonspliced. */
 {
 struct hash *idHash = newHash(16); // Key id1, val id2
 struct hash *nonCodingHash = newHash(16);  // Key clusterId, value 
 struct hash *splicedHash = newHash(16);  // Key id2, present if spliced
 struct sqlConnection *conn = sqlConnect("mgsc");
 struct sqlResult *sr;
 char **row;
 char *words[16];
 int wordCount;
 struct lineFile *lf;
 int codingSpliced = 0;
 int noncodingSpliced = 0;
 int codingNonspliced = 0;
 int noncodingNonspliced = 0;
 
 /* Read id's into hash */
 sr = sqlGetResult(conn, NOSQLINJ "select id1,id2 from rikenIds");
 while ((row = sqlNextRow(sr)) != NULL)
     hashAdd(idHash, row[0], cloneString(row[1]));
 sqlFreeResult(&sr);
 
 /* Read spliced into hash */
 sr = sqlGetResult(conn,
 	NOSQLINJ "select name from rikenOrientInfo where intronOrientation != 0");
 while ((row = sqlNextRow(sr)) != NULL)
     hashAdd(splicedHash, row[0], NULL);
 sqlFreeResult(&sr);
 
 /* Read noncoding clusters into hash */
 lf = lineFileOpen(codingTable, TRUE);
 while (lineFileNextRow(lf, words, 2))
     {
     if (sameString(words[1], "NoPProt"))
         hashAdd(nonCodingHash, words[0], NULL);
     }
 lineFileClose(&lf);
 
 /* Stream through cluster table counting and correlating. */
 lf = lineFileOpen(clusterTable, TRUE);
 while (lineFileNextRow(lf, words, 2))
     {
     char *cluster = words[0];
     char *id1 = words[1];
     char *id2 = hashMustFindVal(idHash, id1);
     if (hashLookup(nonCodingHash, cluster))
         {
 	if (hashLookup(splicedHash, id2))
 	    ++noncodingSpliced;
 	else
 	    ++noncodingNonspliced;
 	}
     else
         {
 	if (hashLookup(splicedHash, id2))
 	    ++codingSpliced;
 	else
 	    ++codingNonspliced;
 	}
     }
 printf("noncodingNonspliced %d\n", noncodingNonspliced);
 printf("noncodingSpliced %d\n", noncodingSpliced);
 printf("codingNonspliced %d\n", codingNonspliced);
 printf("codingSpliced %d\n", codingSpliced);
 printf("total %d\n", noncodingNonspliced + noncodingSpliced + codingNonspliced + codingSpliced);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionHash(&argc, argv);
 if (argc != 3)
     usage();
 rcvs(argv[1], argv[2]);
 return 0;
 }