src/hg/utils/positionalTblCheck/positionalTblCheck.c 1.2

Index: src/hg/utils/positionalTblCheck/positionalTblCheck.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/positionalTblCheck/positionalTblCheck.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/utils/positionalTblCheck/positionalTblCheck.c	18 Jul 2008 04:37:03 -0000	1.1
+++ src/hg/utils/positionalTblCheck/positionalTblCheck.c	25 Apr 2009 00:45:14 -0000	1.2
@@ -1,100 +1,99 @@
 /* positionalTblCheck - check that positional tables are sorted. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "jksql.h"
 #include "verbose.h"
 #include "hdb.h"
 
 static char const rcsid[] = "$Id$";
 
 static void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "positionalTblCheck - check that positional tables are sorted\n"
   "usage:\n"
   "   positionalTblCheck db table\n"
   "\n"
   "options:\n"
   "  -verbose=n  n>=2, print tables as checked"
   "\n"
   "This will check sorting of a table in a variety of formats.\n"
   "It looks for commonly used names for chrom and chrom start\n"
   "columns.  It also handles split tables\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 static boolean nextRow(struct sqlResult *sr, char **chromRet, int *startRet)
 /* read the next row */
 {
 char **row = sqlNextRow(sr);
 if (row == NULL)
     return FALSE;
 *chromRet = row[0];
 *startRet = sqlUnsigned(row[1]);
 return TRUE;
 }
 
 static void checkTblOrder(struct sqlConnection *conn,
                           char *tbl, char *chromFld, char *startFld)
 /* check sorting of a positional table */
 {
 verbose(2, "checking %s.%s\n", sqlGetDatabase(conn), tbl);
 char prevChrom[256], *chrom;
 prevChrom[0] = '\0';
 int prevStart = 0, start;
 off_t irow = 0;
 
 char query[512];
 safef(query, sizeof(query), "SELECT %s,%s FROM %s", chromFld, startFld, tbl);
 struct sqlResult *sr = sqlGetResult(conn, query);
 while (nextRow(sr, &chrom, &start))
     {
     if (!sameString(chrom, prevChrom))
         {
         safecpy(prevChrom, sizeof(prevChrom), chrom);
         prevStart = start;
         }
     else
         {
         if (start < prevStart)
             errAbort("table %s.%s not sorted starting at row %lld: %s:%d",
                      sqlGetDatabase(conn), tbl, (long long)irow, chrom, start);
         prevStart = start;
         }
     irow++;
     }
 sqlFreeResult(&sr);
 }
 
 static void positionalTblCheck(char *db, char *table)
 /* positionalTblCheck - check that positional tables are sorted. */
 {
-hSetDb(db);
-struct hTableInfo *tblInfo = hFindTableInfoDb(db, NULL, table);
+struct hTableInfo *tblInfo = hFindTableInfo(db, NULL, table);
 if (tblInfo == NULL)
     errAbort("cant find table %s.%s or %s.*_%s", db, table, db, table);
 if (!tblInfo->isPos)
     errAbort("%s.%s does not appear to be a positional table", db, table);
-struct slName *tbl, *tbls = hSplitTableNames(table);
-struct sqlConnection *conn = hAllocConn();
+struct slName *tbl, *tbls = hSplitTableNames(db, table);
+struct sqlConnection *conn = hAllocConn(db);
 for (tbl = tbls; tbl != NULL; tbl = tbl->next)
     checkTblOrder(conn, tbl->name, tblInfo->chromField, tblInfo->startField);
 hFreeConn(&conn);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 positionalTblCheck(argv[1], argv[2]);
 return 0;
 }