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/hgGeneList/hgGeneList.c src/hg/hgGeneList/hgGeneList.c
index d74f99b..36e714b 100644
--- src/hg/hgGeneList/hgGeneList.c
+++ src/hg/hgGeneList/hgGeneList.c
@@ -1,98 +1,98 @@
 /* hgGeneList - Generate Known Genes List. */
 
 /* 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 "cheapcgi.h"
 #include "htmshell.h"
 #include "obscure.h"
 #include "web.h"
 #include "cart.h"
 #include "hdb.h"
 #include "dbDb.h"
 #include "hgFind.h"
 #include "hCommon.h"
 #include "hui.h"
 
 struct cart *cart = NULL;
 struct hash *oldVars = NULL;
 
 void doMiddle(struct cart *theCart)
 /* Set up pretty web display. */
 {
 struct sqlConnection *conn, *conn2;
 struct sqlConnection *connCentral = hConnectCentral();
 char query[256], query2[256];
 struct sqlResult *sr, *sr2;
 char **row, **row2;
 char buf[128];
 char *database;
 char *genome, *genomeDesc;  
 char *kgID, *chrom, *txStart, *txEnd;
 int iCnt = 1;
 
 cart = theCart;
 cartWebStart(theCart, database, "UCSC Known Genes List \n");
 
 getDbAndGenome(cart, &database, &genome, oldVars);
 if (!hTableExistsDb(database, "knownGene"))
     {
     printf("<br>Database %s currently does not have UCSC Known Genes.", database);
     cartWebEnd();
     return;
     }
 
 sqlSafef(query, sizeof query, "select description from dbDb where name = '%s'", database);
 genomeDesc = strdup(sqlQuickQuery(connCentral, query, buf, sizeof(buf)));
 hDisconnectCentral(&connCentral);
 
 printf("<H2>%s Genome (%s Assembly)</H2>\n", genome, genomeDesc);
 
 conn = hAllocConn(database);
 conn2= hAllocConn(database);
 
 sqlSafef(query2, sizeof query2, "select kgID from %s.kgXref order by geneSymbol;",
 	database);
 
 /* use the following for quck testing */
 /*sqlSafef(query2, sizeof query2, "select kgID, geneSymbol, description, spID, refseq from %s.kgXref order by geneSymbol limit 10;", database);
 */
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     kgID = row2[0];
     
     sqlSafef(query, sizeof query, "select chrom, txSTart, txEnd  from %s.knownGene where name='%s'", database, kgID);
     sr = sqlMustGetResult(conn, query);
     row = sqlNextRow(sr);
     chrom 	= row[0];
     txStart 	= row[1];
     txEnd   	= row[2];
 
     printf("<A href=\"/cgi-bin/hgGene?db=%s&hgg_gene=%s", 
     	   database, kgID);
     printf("&hgg_chrom=%s&hgg_start=%s&hgg_end=%s\">", chrom, txStart, txEnd);
     printf("%d</A><BR>\n", iCnt);
     iCnt++;
     if ((iCnt % 1000) == 0) fflush(stdout);
     
     sqlFreeResult(&sr);
     row2 = sqlNextRow(sr2);
     }
     
 sqlFreeResult(&sr2);
 cartWebEnd();
 }
 
 char *excludeVars[] = {NULL};
 int main(int argc, char *argv[])
 {
 oldVars = hashNew(8);
 cgiSpoof(&argc, argv);
 cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
 return 0;
 }