src/hg/protein/kgAliasKgXref/kgAliasKgXref.c 1.5

1.5 2009/09/23 18:42:23 angie
Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
Index: src/hg/protein/kgAliasKgXref/kgAliasKgXref.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/protein/kgAliasKgXref/kgAliasKgXref.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/hg/protein/kgAliasKgXref/kgAliasKgXref.c	3 Sep 2008 19:20:55 -0000	1.4
+++ src/hg/protein/kgAliasKgXref/kgAliasKgXref.c	23 Sep 2009 18:42:23 -0000	1.5
@@ -1,71 +1,71 @@
 /* kgAliasKgXref - generate Known Genes alias list table for RefSeq accession numbers */
 #include "common.h"
 #include "hCommon.h"
 #include "hdb.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "kgAliasKgXref - create gene alias .tab file "
   "usage:\n"
   "   kgAliasKgXref xxxx\n"
   "            xxxx is genome database name\n"
   "example: kgAliasKgXref hg16\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn, *conn2;
 
 char query[256], query2[256];
 struct sqlResult *sr, *sr2;
 char **row, **row2;
  
 char *kgID;
 FILE *o2;
 char *database;
 char *geneSymbol;
 
 char *proteinID;
 
 if (argc != 2) usage();
 database  = cloneString(argv[1]);
 
 conn = hAllocConn(database);
 conn2= hAllocConn(database);
 o2 = mustOpen("jj.dat", "w");
 
 sprintf(query2,"select name, proteinID from %s.knownGene;", database);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     kgID = row2[0];
     proteinID = row2[1];
     sprintf(query,"select geneSymbol from %s.kgXref where kgID = '%s';", database, kgID);
     sr = sqlMustGetResult(conn, query);
     row = sqlNextRow(sr);
     while (row != NULL)
    	{
 	geneSymbol = row[0];
 	if (strlen(geneSymbol) >0)
 	     {
 	     fprintf(o2, "%s\t%s\n", kgID, geneSymbol);
 	     }
 	row = sqlNextRow(sr);
 	}
     sqlFreeResult(&sr);
     row2 = sqlNextRow(sr2);
     }
 sqlFreeResult(&sr2);
 carefulClose(&o2);
 hFreeConn(&conn);
 hFreeConn(&conn2);
 
-system("cat jj.dat|sort|uniq  >kgAliasKgXref.tab");
-system("rm jj.dat");
+mustSystem("cat jj.dat|sort|uniq  >kgAliasKgXref.tab");
+mustSystem("rm jj.dat");
     
 return(0);
 }