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/makeDb/hgGetNrOmimGene/hgGetNrOmimGene.c src/hg/makeDb/hgGetNrOmimGene/hgGetNrOmimGene.c
index 530decf..e3c4f62 100644
--- src/hg/makeDb/hgGetNrOmimGene/hgGetNrOmimGene.c
+++ src/hg/makeDb/hgGetNrOmimGene/hgGetNrOmimGene.c
@@ -1,84 +1,84 @@
 /* hgGetNrOmimGene - Generate omimGene entries related to NR_xxxx RefSeq. */
 
 /* 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 "hdb.h"
 #include "options.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgGetNrOmimGene - Generate omimGene entries related to NR_xxxx RefSeq\n"
   "usage:\n"
   "   hgGetNrOmimGene database outFileName\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 void hgGetNrOmimGene(char *database, char *outFileName)
 /* hgGetNrOmimGene - Generate omimGene entries related to NR_xxxx RefSeq. */
 {
 struct sqlConnection *conn2, *conn3;
  
 char query2[256], query3[256];
 struct sqlResult *sr2, *sr3;
 char **row2, **row3;
 FILE *outf;
 
 char *chrom, *txStart, *txEnd;
 char *omimId;
 
 outf = fopen(outFileName, "w");
 conn2= hAllocConn(database);
 conn3= hAllocConn(database);
 	
 /* first get all RefSeq entries that begin with "NR_" and have related OMIM entries */
 sqlSafef(query2, sizeof query2, "select g.chrom, g.txStart, g.txEnd, omimId from refGene g, refLink l, omimGene o "
     "where l.mrnaAcc=g.name and g.name like 'NR_%c' and omimId <>0 limit 1000", '%');
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     chrom 	= row2[0];
     txStart 	= row2[1];
     txEnd	= row2[2];
     omimId	= row2[3];
 
     /* then check if this omimId is already in the omimGene table */
     sqlSafef(query3, query3, "select name from %s.omimGene where name='%s'",
     	    database, omimId);
     sr3 = sqlMustGetResult(conn3, query3);
     row3 = sqlNextRow(sr3);
 
     /* if not, create a new omimGene entry */
     if (row3 == NULL)
 	{
 	fprintf(outf,"%s\t%s\t%s\t%s\n", chrom, txStart, txEnd, omimId);
 	}
     sqlFreeResult(&sr3);
     row2 = sqlNextRow(sr2);
     }
 sqlFreeResult(&sr2);
 
 hFreeConn(&conn2);
 hFreeConn(&conn3);
 fclose(outf);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 hgGetNrOmimGene(argv[1], argv[2]);
 return 0;
 }