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/kgName/sgName.c src/hg/oneShot/kgName/sgName.c
index cca3cdf..f8023db 100644
--- src/hg/oneShot/kgName/sgName.c
+++ src/hg/oneShot/kgName/sgName.c
@@ -1,115 +1,115 @@
 /* sgName - builds association table between sgbPep and gene common name. */
 
 /* 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 "hCommon.h"
 #include "hdb.h"
 #include "spDb.h"
 
 char *database = "sacCer1";
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "sgName - builds association table between sgdPep and gene common name\n"
   "usage:\n"
   "   sgName database referencePsl outAssoc\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 char *protDbName = NULL;
 
 char* lookupName(  struct sqlConnection *conn , char *id)
 {
 char *name = cloneString(id);
 char infoTable[128];
 safef(infoTable, sizeof(infoTable), "sgdToName");
 if (hTableExists(infoTable))
     {
     struct sqlConnection *conn = hAllocConn();
     char *symbol = NULL;
     //char *ptr = strchr(name, '-');
     char query[256];
     char buf[64];
     //if (ptr != NULL)
 //	*ptr = 0;
     sqlSafef(query, sizeof(query),
 	  "select value from %s where name = '%s';", infoTable, name);
     if ((symbol = sqlQuickQuery(conn, query, buf, sizeof(buf))) != NULL)
 	name = symbol;
     hFreeConn(&conn);
     }
 return(name);
 }
 
 char *getSwiss( struct sqlConnection *conn , char *id)
 {
 char *name = cloneString(id);
 char infoTable[128];
 safef(infoTable, sizeof(infoTable), "sgdToSwissProt");
 if (hTableExists(infoTable))
     {
     struct sqlConnection *conn = hAllocConn();
     char *symbol = NULL;
     //char *ptr = strchr(name, '-');
     char query[256];
     char buf[64];
     //if (ptr != NULL)
 //	*ptr = 0;
     sqlSafef(query, sizeof(query),
 	  "select value from %s where name = '%s';", infoTable, name);
     if ((symbol = sqlQuickQuery(conn, query, buf, sizeof(buf))) != NULL)
 	name = symbol;
     hFreeConn(&conn);
     }
 return(name);
 }
 
 void sgName(char *database, char *protDb,  char *refPsl, char *outAssoc)
 /* sgName - builds association table between knownPep and gene common name. */
 {
 struct sqlConnection *conn = sqlConnect(database);
 //struct sqlConnection *conn2 = sqlConnect("swissProt");
 char *words[1], **row;
 FILE *f = mustOpen(outAssoc, "w");
 struct lineFile *pslLf = pslFileOpen(refPsl);
 int count = 0, found = 0;
 char query[256];
 struct psl *psl;
 char *swiss = NULL;
 
 while ((psl = pslNext(pslLf)) != NULL)
     {
     fprintf(f,"%s\t%s\t%s:%d-%d\t",psl->qName, lookupName(conn,psl->qName), 
 	psl->tName, psl->tStart, psl->tEnd);
     fprintf(f,"%s\n", swiss = getSwiss(conn, psl->qName));
     }
 /*
 while (lineFileRow(lf, words))
     {
     fprintf(f,"%s\t%s\n",words[0], lookupName(conn,words[0])); //, getSwiss(conn, words[0]));
     }
     */
 hFreeConn(&conn);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 4)
     usage();
 database=argv[1];
 hSetDb(argv[1]);
 protDbName = hPdbFromGdb(database);
 sgName(argv[1], protDbName, argv[2], argv[3]);
 return 0;
 }