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/outside/hgKegg/hgKegg.c src/hg/makeDb/outside/hgKegg/hgKegg.c
index a3c7317..52b787f 100644
--- src/hg/makeDb/outside/hgKegg/hgKegg.c
+++ src/hg/makeDb/outside/hgKegg/hgKegg.c
@@ -1,105 +1,105 @@
 /* hgKegg - creates keggPathway.tab and keggMapDesc.tab files for KG links to KEGG Pathway Map */
 
 /* 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 "hCommon.h"
 #include "hdb.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgKegg - creates keggPathway.tab and keggMapDesc.tab files for KG links to KEGG Pathway Map"
   "usage:\n"
   "   hgKegg xxxx\n"
   "      xxxx is the genome database name\n"
   "example: hgKegg hg16\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn, *conn2, *conn3;
 char query[256], query2[256], query3[256];
 struct sqlResult *sr, *sr2, *sr3;
 char **row, **row2, **row3;
 
 char *chp;
 FILE *o1, *o2;
 
 char *locusID;	/* LocusLink ID */
 char *gbAC;		/* GenBank accession.version */
 char *locusID2;	/* LocusLink ID */
 char *refAC;	/* Refseq accession.version */
 char *dbName; 
 char cond_str[200];
 char *kgID;
 char *mapID;
 char *desc;
 
 if (argc != 2) usage();
 dbName = argv[1];
 
 conn = hAllocConn(dbName);
 conn2= hAllocConn(dbName);
 conn3= hAllocConn(dbName);
 
 o1 = fopen("j.dat",  "w");
 o2 = fopen("jj.dat", "w");
     
 sqlSafef(query2, sizeof query2, "select * from %sTemp.locus2Ref0;", dbName);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     locusID2 	= row2[0];
     refAC 	= row2[1];
     
     sqlSafef(query, sizeof query, "select * from %sTemp.locus2Acc0 where locusID=%s and seqType='m';", 
 		   dbName, locusID2);
     sr = sqlMustGetResult(conn, query);
     row = sqlNextRow(sr);
     while (row != NULL)
     	{
 	locusID 	= row[0];
 	gbAC 		= row[1];
 	
 	chp = strstr(gbAC, ".");
 	if (chp != NULL) *chp = '\0';
 	chp = strstr(refAC, ".");
 	if (chp != NULL) *chp = '\0';
     
 	sqlSafefFrag(cond_str, sizeof cond_str, "name='%s'", gbAC);
         kgID = sqlGetField(dbName, "knownGene", "name", cond_str);
 	if (kgID != NULL)
 	    {
             sqlSafef(query3, sizeof query3, "select * from %sTemp.keggList where locusID = '%s'", dbName, locusID);
             sr3 = sqlGetResult(conn3, query3);
             while ((row3 = sqlNextRow(sr3)) != NULL)
                 {
                 mapID   = row3[1];
 		desc    = row3[2];
 		fprintf(o1, "%s\t%s\t%s\n", kgID, locusID, mapID);
 		fprintf(o2, "%s\t%s\n", mapID, desc);
 		row3 = sqlNextRow(sr3);
                 }
             sqlFreeResult(&sr3);
 	    }
 	row = sqlNextRow(sr);
 	}
     row2 = sqlNextRow(sr2);
     }
 sqlFreeResult(&sr2);
 
 fclose(o1);
 fclose(o2);
 hFreeConn(&conn);
 hFreeConn(&conn2);
 
 mustSystem("cat j.dat|sort|uniq >keggPathway.tab");
 mustSystem("cat jj.dat|sort|uniq >keggMapDesc.tab");
 mustSystem("rm j.dat");
 mustSystem("rm jj.dat");
 return(0);
 }