e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/qa/seqCheck.c src/hg/qa/seqCheck.c
index 0c78818..4cff0a1 100644
--- src/hg/qa/seqCheck.c
+++ src/hg/qa/seqCheck.c
@@ -1,105 +1,108 @@
 /* seqCheck - check that extFile references in seq table are valid. */
+
+/* Copyright (C) 2013 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
 #include "common.h"
 #include "hdb.h"
 
 char *database = NULL;
 
 struct extFileId
 {
     struct extFileId *next;
     int id;
 };
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
     "seqCheck - check that extFile references in seq table are valid\n"
     "usage:\n"
     "    seqCheck database \n");
 }
 
 struct extFileId *readSeq()
 /* Slurp in the rows */
 {
 struct extFileId *list=NULL, *el;
 char query[512];
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr;
 char **row;
 int count = 0;
 
 verbose(2, "reading in from seq...\n");
 sqlSafef(query, sizeof(query), "select distinct(extFile) from seq");
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     count++;
     AllocVar(el);
     el->id = atoi(row[0]);
     el->next = list;
     list = el;
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 slReverse(&list);  /* could possibly skip if it made much difference in speed. */
 verbose(2, "%d rows found\n", count);
 return list;
 }
 
 
 
 void seqCheck()
 /* seqCheck - read in all seq, compare to extFile. */
 {
 struct extFileId *idList = NULL;
 struct extFileId *id1 = NULL;
 char query[512];
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr;
 char **row;
 
 idList = readSeq();
 
 verbose(2, "checking....\n");
 
 for (id1 = idList; id1 != NULL; id1 = id1->next)
     {
     sqlSafef(query, sizeof(query), "select path from extFile where id = %d", id1->id);
     sr = sqlGetResult(conn, query);
     row = sqlNextRow(sr);
     if (row == NULL) 
         {
 	verbose(1, "no matches for %d\n", id1->id);
 	continue;
 	}
 
     /* check here for multiple matches */
     while ((row = sqlNextRow(sr)) != NULL)
         {
 	}
     sqlFreeResult(&sr);
     }
 
 // seqFreeList(&seqList);
 
 }
 
 
 int main(int argc, char *argv[])
 /* Check args and call seqCheck. */
 {
 if (argc != 2)
     usage();
 database = argv[1];
 
 // check for table existence
 if (!hTableExists(database, "seq"))
     errAbort("no seq table");
 if (!hTableExists(database, "extFile"))
     errAbort("no extFile table");
 
 seqCheck();
 return 0;
 }