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/snp/snpLoad/snpExceptionCheck.c src/hg/snp/snpLoad/snpExceptionCheck.c
index e7fabae..d482fde 100644
--- src/hg/snp/snpLoad/snpExceptionCheck.c
+++ src/hg/snp/snpLoad/snpExceptionCheck.c
@@ -1,117 +1,117 @@
 /* snpExceptionCheck - make sure that all exceptions have coords that match the main table.
  * Read snp125. */
 
 /* 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 "hash.h"
 #include "hdb.h"
 
 
 static char *snpDb = NULL;
 
 static struct hash *coordHash = NULL;
 
 FILE *outputFileHandle = NULL;
 FILE *logFileHandle = NULL;
 
 struct coords 
     {
     char *chrom;
     int start;
     int end;
     };
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
     "snpExceptionCheck - make sure that all exceptions have coords that match the main table\n"
     "usage:\n"
     "    snpExceptionCheck snpDb \n");
 }
 
 
 void readSnps()
 /* put all coords in coordHash */
 {
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 struct hashEl *helCoord, *helName = NULL;
 struct coords *cel = NULL;
 
 coordHash = newHash(18);
 verbose(1, "creating hash...\n");
 sqlSafef(query, sizeof(query), "select name, chrom, chromStart, chromEnd from snp125");
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     /* store all coords */
     AllocVar(cel);
     cel->chrom = cloneString(row[1]);
     cel->start = sqlUnsigned(row[2]);
     cel->end = sqlUnsigned(row[3]);
     hashAdd(coordHash, cloneString(row[0]), cel);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 }
 
 
 void checkExceptions()
 {
 struct hashEl *hel= NULL;
 struct coords *cel = NULL;
 char *name;
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 boolean matchFound = FALSE;
 char *chrom;
 int start = 0;
 int end = 0;
 
 verbose(1, "checking exceptions...\n");
 sqlSafef(query, sizeof(query), "select name, chrom, chromStart, chromEnd from snp125Exceptions");
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     matchFound = FALSE;
     name = cloneString(row[0]);
     chrom = cloneString(row[1]);
     start = sqlUnsigned(row[2]);
     end = sqlUnsigned(row[3]);
     for (hel = hashLookup(coordHash, name); hel != NULL; hel= hashLookupNext(hel))
         {
 	cel = (struct coords *)hel->val;
 	if (sameString(cel->chrom, chrom) && cel->start == start && cel->end == end)
 	    {
 	    matchFound = TRUE;
 	    break;
 	    }
 	}
     if (!matchFound)
         verbose(1, "no match found for %s at %s:%d-%d\n", name, chrom, start, end);
     }
 }
 
 
 int main(int argc, char *argv[])
 /* Read snp125. */
 {
 
 if (argc != 2)
     usage();
 
 snpDb = argv[1];
 hSetDb(snpDb);
 readSnps();
 checkExceptions();
 return 0;
 }