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/hapmapMixed.c src/hg/snp/snpLoad/hapmapMixed.c
index 9668c3b..98200c2 100644
--- src/hg/snp/snpLoad/hapmapMixed.c
+++ src/hg/snp/snpLoad/hapmapMixed.c
@@ -1,106 +1,106 @@
 /* hapmapMixed -- compare mixed */
 /* A little utility to read the hapmapSnpsCombined table */
 /* It looks only at rows where all 4 populations have data and the major allele is mixed */
 /* It reports counts where 3 populations have a certain allele and the 4th is different */
 
 /* 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 "hapmapSnpsCombined.h"
 #include "hdb.h"
 #include "sqlNum.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hapmapMixed - Read hapmapSnpsCombined, report counts of mixed.\n"
   "usage:\n"
   "  hapmapMixed database\n");
 }
 
 
 char *getMajorAllele(char *allele1, int count1, char *allele2, int count2)
 {
 if (count1 == 0 && count2 == 0)
     return "?";
 if (count1 >= count2)
     return allele1;
 return allele2;
 }
 
 void hapmapMixed()
 /* read through input */
 {
 char query[64];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 struct hapmapSnpsCombined *thisItem = NULL;
 int popCount = 0;
 char *majorAlleleCEU;
 char *majorAlleleCHB;
 char *majorAlleleJPT;
 char *majorAlleleYRI;
 int countCEU = 0;
 int countCHB = 0;
 int countJPT = 0;
 int countYRI = 0;
 
 sqlSafef(query, sizeof(query), "select * from hapmapSnpsCombined");
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     thisItem = hapmapSnpsCombinedLoad(row + 1);
     popCount = getPopCount(thisItem);
     if (popCount != 4) continue;
     if (!isMixed(thisItem)) continue;
 
     majorAlleleCEU = getMajorAllele(thisItem->allele1, thisItem->homoCount1CEU, 
                                     thisItem->allele2, thisItem->homoCount2CEU);
     majorAlleleCHB = getMajorAllele(thisItem->allele1, thisItem->homoCount1CHB, 
                                     thisItem->allele2, thisItem->homoCount2CHB);
     majorAlleleJPT = getMajorAllele(thisItem->allele1, thisItem->homoCount1JPT, 
                                     thisItem->allele2, thisItem->homoCount2JPT);
     majorAlleleYRI = getMajorAllele(thisItem->allele1, thisItem->homoCount1YRI, 
                                     thisItem->allele2, thisItem->homoCount2YRI);
     if (sameString(majorAlleleCEU, majorAlleleCHB) && sameString(majorAlleleCHB, majorAlleleJPT))
         countYRI++;
     else if (sameString(majorAlleleCEU, majorAlleleCHB) && sameString(majorAlleleCHB, majorAlleleYRI))
         countJPT++;
     else if (sameString(majorAlleleCEU, majorAlleleJPT) && sameString(majorAlleleJPT, majorAlleleYRI))
         countCHB++;
     else if (sameString(majorAlleleCHB, majorAlleleJPT) && sameString(majorAlleleJPT, majorAlleleYRI))
         countCEU++;
 
     }
 
 printf("countCEU = %d\n", countCEU);
 printf("countCHB = %d\n", countCHB);
 printf("countJPT = %d\n", countJPT);
 printf("countYRI = %d\n", countYRI);
 }
 
 
 int main(int argc, char *argv[])
 {
 
 if (argc != 2)
     usage();
 
 hSetDb(argv[1]);
 
 if (!hTableExists("hapmapSnpsCombined")) 
     {
     verbose(1, "can't find hapmapSnpsCombined table \n");
     return 1;
     }
 
 hapmapMixed();
 
 return 0;
 }