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/hapmapOrtho.c src/hg/snp/snpLoad/hapmapOrtho.c
index 3302cce..90d84db 100644
--- src/hg/snp/snpLoad/hapmapOrtho.c
+++ src/hg/snp/snpLoad/hapmapOrtho.c
@@ -1,133 +1,133 @@
 /* hapmapOrtho */
 /* get hapmapOrtho table from overall snpOrtho table */
 /* hash in contents of hapmap table */
 /* serially read snpOrtho table */
 
 /* 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"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
     "hapmapOrtho - get hapmapAllelesOrtho table from overall snpOrtho table\n"
     "usage:\n"
     "    hapmapOrtho db hapmapTable snpOrthoTable\n");
 }
 
 struct coords
     {
     char *chrom;
     int start;
     int end;
     };
 
 struct hash *storeHapmap(char *tableName)
 /* store coords */
 {
 struct hash *ret = NULL;
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 struct coords *coordItem = NULL;
 
 ret = newHash(16);
 sqlSafef(query, sizeof(query), "select name, chrom, chromStart, chromEnd from %s", tableName);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     AllocVar(coordItem);
     coordItem->chrom = cloneString(row[1]);
     coordItem->start = sqlUnsigned(row[2]);
     coordItem->end = sqlUnsigned(row[3]);
     hashAdd(ret, cloneString(row[0]), coordItem);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 return ret;
 }
 
 
 void processSnps(char *snpTableName, struct hash *hapmapHash)
 /* read snpTable, lookup in hapmapHash */
 {
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 struct hashEl *hel = NULL;
 char *rsId = NULL;
 int start = 0;
 int end = 0;
 FILE *outputFileHandle = mustOpen("hapmapOrtho.tab", "w");
 FILE *errorFileHandle = mustOpen("hapmapOrtho.err", "w");
 struct coords *coordItem = NULL;
 
 sqlSafef(query, sizeof(query), 
     "select chrom, chromStart, chromEnd, name, orthoScore, strand, refUCSC, observed, "
     "orthoChrom, orthoStart, orthoEnd, orthoStrand, orthoAllele from %s", 
     snpTableName);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     rsId = cloneString(row[3]);
     start = sqlUnsigned(row[1]);
     end = sqlUnsigned(row[2]);
     /* all hapmap data is single base */
     /* don't include lift if it wasn't also single base */
     if (end != start + 1) 
         {
         fprintf(errorFileHandle, "skipping %s due to size %d\n", rsId, end-start);
 	continue;
 	}
     hel = hashLookup(hapmapHash, rsId);
     if (hel == NULL) continue;
     coordItem = (struct coords *)hel->val;
     if (differentString(coordItem->chrom, row[0])) continue;
     if (coordItem->start != start) continue;
     if (coordItem->end != end) continue;
     fprintf(outputFileHandle, "%s\t%s\t%s\t%s\t", row[0], row[1], row[2], rsId);
     fprintf(outputFileHandle, "%s\t%s\t%s\t%s\t", row[4], row[5], row[6], row[7]);
     fprintf(outputFileHandle, "%s\t%s\t%s\t%s\t%s\n", row[8], row[9], row[10], row[11], row[12]);
     }
 
 carefulClose(&outputFileHandle);
 carefulClose(&errorFileHandle);
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 }
 
 
 int main(int argc, char *argv[])
 /* get hapmapOrtho table from overall snpOrtho table */
 /* hash in contents of hapmap table */
 {
 char *database = NULL;
 char *hapmapTableName = NULL;
 char *snpOrthoTableName = NULL;
 struct hash *hapmapHash = NULL;
 
 if (argc != 4)
     usage();
 
 database = argv[1];
 hapmapTableName = argv[2];
 snpOrthoTableName = argv[3];
 
 hSetDb(database);
 if (!hTableExists(hapmapTableName))
     errAbort("no %s table in %s\n", hapmapTableName, database);
 if (!hTableExists(snpOrthoTableName))
     errAbort("no %s table in %s\n", snpOrthoTableName, database);
 
 hapmapHash = storeHapmap(hapmapTableName);
 processSnps(snpOrthoTableName, hapmapHash);
 
 return 0;
 }