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/snpPAR.c src/hg/snp/snpLoad/snpPAR.c
index 0ea9a74..04c1656 100644
--- src/hg/snp/snpLoad/snpPAR.c
+++ src/hg/snp/snpLoad/snpPAR.c
@@ -1,123 +1,123 @@
 /* snpPAR - get PAR SNPs for chrY from chrX. */
 
 /* 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 *outputFileHandle = NULL;
 FILE *exceptionFileHandle = NULL;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
     "snpPAR - get PAR SNPs for chrY from chrX\n"
     "usage:\n"
     "    snpPAR snpDb \n");
 }
 
 
 void getSnps()
 {
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 int start = 0;
 int end = 0;
 int bin = 0;
 
 sqlSafef(query, sizeof(query), "select * from chrX_snp126 where chromEnd < 2709520");
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     fprintf(outputFileHandle, "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t", 
                               row[0], "chrY", row[2], row[3], row[4], row[5], row[6], row[7], row[8]);
     fprintf(outputFileHandle, "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n", 
                               row[9], row[10], row[11], row[12], row[13], row[14], row[15], row[16], row[17]);
     }
 sqlFreeResult(&sr);
 
 sqlSafef(query, sizeof(query), "select * from chrX_snp126 where chromEnd > 154584237");
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     start = sqlUnsigned(row[2]);
     end = sqlUnsigned(row[3]);
     start = start - 97140800;
     end = end - 97140800;
     bin = hFindBin(start, end);
     fprintf(outputFileHandle, "%d\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t%s\t", 
                               bin, "chrY", start, end, row[4], row[5], row[6], row[7], row[8]);
     fprintf(outputFileHandle, "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n", 
                               row[9], row[10], row[11], row[12], row[13], row[14], row[15], row[16], row[17]);
     }
 sqlFreeResult(&sr);
 
 hFreeConn(&conn);
 }
 
 void getExceptions()
 {
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 int start = 0;
 int end = 0;
 
 sqlSafef(query, sizeof(query), "select * from snp126Exceptions where chrom = 'chrX' and chromEnd < 2709520");
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     fprintf(exceptionFileHandle, "chrY\t%s\t%s\t%s\t%s\n", row[1], row[2], row[3], row[4]);
 sqlFreeResult(&sr);
 
 sqlSafef(query, sizeof(query), "select * from snp126Exceptions where chrom = 'chrX' and chromEnd > 154584237");
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     start = sqlUnsigned(row[1]);
     end = sqlUnsigned(row[2]);
     start = start - 97140800;
     end = end - 97140800;
     fprintf(exceptionFileHandle, "chrY\t%d\t%d\t%s\t%s\n", start, end, row[3], row[4]);
     }
 sqlFreeResult(&sr);
 
 hFreeConn(&conn);
 }
 
 
 void loadDatabase()
 {
 FILE *f;
 struct sqlConnection *conn = hAllocConn();
 
 f = mustOpen("chrY_snp126.tab", "r");
 hgLoadNamedTabFile(conn, ".", "chrY_snp126", "snpPAR", &f);
 hFreeConn(&conn);
 }
 
 
 int main(int argc, char *argv[])
 {
 
 if (argc != 2)
     usage();
 
 snpDb = argv[1];
 hSetDb(snpDb);
 outputFileHandle = mustOpen("snpPAR.tab", "w");
 exceptionFileHandle = mustOpen("snpPARexceptions.tab", "w");
 getSnps();
 getExceptions();
 loadDatabase();
 carefulClose(&outputFileHandle);
 carefulClose(&exceptionFileHandle);
 
 return 0;
 }