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/snpCheckAlleles.c src/hg/snp/snpLoad/snpCheckAlleles.c
index 04491c3..bb00c63 100644
--- src/hg/snp/snpLoad/snpCheckAlleles.c
+++ src/hg/snp/snpLoad/snpCheckAlleles.c
@@ -1,116 +1,116 @@
 /* snpCheckAlleles
  * Run after snpRefUCSC.
  *
  * Log 2 annotations:
  * RefAlleleNotRevComp
  * RefAlleleMismatch
  *
  * Use UCSC chromInfo.  */
 
 /* 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 "hdb.h"
 
 
 static char *snpDb = NULL;
 FILE *exceptionFileHandle = NULL;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
     "snpCheckAlleles - log allele exceptions\n"
     "usage:\n"
     "    snpCheckAlleles snpDb \n");
 }
 
 void writeToExceptionFile(char *chrom, char *start, char *end, char *name, char *exception)
 {
 fprintf(exceptionFileHandle, "%s\t%s\t%s\trs%s\t%s\n", chrom, start, end, name, exception);
 }
 
 void doCheckAlleles(char *chromName)
 /* check each row for exceptions */
 {
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 char tableName[64];
 int loc_type = 0;
 int chromStart = 0;
 int chromEnd = 0;
 int span = 0;
 
 safef(tableName, ArraySize(tableName), "%s_snpTmp", chromName);
 if (!hTableExists(tableName)) return;
 
 verbose(1, "chrom = %s\n", chromName);
 sqlSafef(query, sizeof(query), 
     "select snp_id, chromStart, chromEnd, loc_type, orientation, allele, refUCSC, refUCSCReverseComp from %s where loc_type != 3", 
      tableName);
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     /* we already check size of allele in snpLocType and snpExpandAllele. */
     /* skip past alleles with wrong size here. */
     chromStart = sqlUnsigned(row[1]);
     chromEnd = sqlUnsigned(row[2]);
     span = chromEnd - chromStart;
     if (span != strlen(row[5])) continue;
 
     loc_type = sqlUnsigned(row[3]);
 
     /* check positive strand first */
     if (sameString(row[4], "0"))
         {
         if (sameString(row[5], row[6])) continue;
         writeToExceptionFile(chromName, row[1], row[2], row[0], "RefAlleleMismatch");
 	continue;
 	}
 
     /* negative strand */
     /* ideally matches reverse comp */
     if (sameString(row[5], row[7])) continue;
 
     /* matching non-reverse comp is useful info */
     if (sameString(row[5], row[6]))
         {
         writeToExceptionFile(chromName, row[1], row[2], row[0], "RefAlleleNotRevComp");
         continue;
 	}
 
     /* nothing matching */
     writeToExceptionFile(chromName, row[1], row[2], row[0], "RefAlleleMismatch");
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 }
 
 
 
 int main(int argc, char *argv[])
 /* read chrN_snpTmp, log exceptions */
 {
 struct slName *chromList, *chromPtr;
 
 if (argc != 2)
     usage();
 
 snpDb = argv[1];
 hSetDb(snpDb);
 chromList = hAllChromNamesDb(snpDb);
 
 exceptionFileHandle = mustOpen("snpCheckAlleles.exceptions", "w");
 
 for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
     doCheckAlleles(chromPtr->name);
 
 carefulClose(&exceptionFileHandle);
 return 0;
 }