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/cnpLookup.c src/hg/snp/snpLoad/cnpLookup.c
index 0046c17..2361107 100644
--- src/hg/snp/snpLoad/cnpLookup.c
+++ src/hg/snp/snpLoad/cnpLookup.c
@@ -1,152 +1,152 @@
 /* cnpLookup - lookup BACs from cnpSharp and cnpIafrate. */
 /* start with temporary CNP table */
 /* log if chrom changes */
 /* if BAC is missing, output to lift file */
 
 /* 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"
 
 
 struct coords 
     {
     char *chrom;
     int start;
     int end;
     };
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
     "cnpLookup - get coords from BAC ends\n"
     "usage:\n"
     "    cnpLookup db bacTable cnpTable outputFile liftFile logFile\n");
 }
 
 
 struct hash *storeBacs(char *tableName)
 /* store BAC coords in a hash */
 {
 struct hash *ret = NULL;
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 struct coords *cel = NULL;
 
 verbose(1, "creating BAC hash...\n");
 ret = newHash(0);
 sqlSafef(query, sizeof(query), 
       "select name, chrom, chromStart, chromEnd from %s", tableName);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     AllocVar(cel);
     cel->chrom = cloneString(row[1]);
     cel->start = sqlUnsigned(row[2]);
     cel->end = sqlUnsigned(row[3]);
     hashAdd(ret, cloneString(row[0]), cel);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 return ret;
 }
 
 
 
 void processCnps(struct hash *bacHash, char *cnpTable, char *fileName, char *liftFileName, char *logFileName)
 /* read cnpTable */
 /* lookup position in bacHash */
 /* log change in chrom */
 /* write to lift table if missing from bacHash */
 {
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 struct hashEl *hel = NULL;
 struct coords *cel = NULL;
 FILE *fileHandle = mustOpen(fileName, "w");
 FILE *logFileHandle = mustOpen(logFileName, "w");
 FILE *liftFileHandle = mustOpen(liftFileName, "w");
 char *cnpName = NULL;
 char variantSignal;
 
 verbose(1, "process CNPs...\n");
 sqlSafef(query, sizeof(query), "select * from %s", cnpTable);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     cnpName = cloneString(row[4]);
     variantSignal = lastChar(cnpName);
     if (variantSignal == '*')
        stripChar(cnpName, '*');
     if (variantSignal == '?')
        stripChar(cnpName, '?');
     if (variantSignal == '#')
         stripChar(cnpName, '#');
 
     hel = hashLookup(bacHash, cnpName);
     if (hel == NULL) 
         {
 	fprintf(liftFileHandle, "%s\t%s\t%s\t%s\t", row[1], row[2], row[3], row[4]);
 	fprintf(liftFileHandle, "%s\t%s\t%s\t%s\t%s\t", row[5], row[6], row[7], row[8], row[9]);
 	fprintf(liftFileHandle, "%s\t%s\t%s\t%s\t%s\n", row[10], row[11], row[12], row[13], row[14]);
 	continue;
 	}
     cel = (struct coords *)hel->val;
 
     if (!sameString(cel->chrom, row[1]))
 	fprintf(logFileHandle, "chrom mismatch for %s: cnp on %s, BAC on %s\n", row[4], row[1], cel->chrom);
 
     fprintf(fileHandle, "%s\t%d\t%d\t%s\t", cel->chrom, cel->start, cel->end, row[4]);
     fprintf(fileHandle, "%s\t%s\t%s\t%s\t%s\t", row[5], row[6], row[7], row[8], row[9]);
     fprintf(fileHandle, "%s\t%s\t%s\t%s\t%s\n", row[10], row[11], row[12], row[13], row[14]);
     }
 
 carefulClose(&fileHandle);
 carefulClose(&logFileHandle);
 carefulClose(&liftFileHandle);
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 }
 
 
 int main(int argc, char *argv[])
 {
 char *db = NULL;
 char *bacTableName = NULL;
 char *cnpTableName = NULL;
 char fileName[64];
 char liftFileName[64];
 char logFileName[64];
 struct hash *bacHash = NULL;
 
 if (argc != 7)
     usage();
 
 db = argv[1];
 bacTableName = argv[2];
 cnpTableName = argv[3];
 safef(fileName, ArraySize(fileName), "%s", argv[4]);
 safef(liftFileName, ArraySize(liftFileName), "%s", argv[5]);
 safef(logFileName, ArraySize(logFileName), "%s", argv[6]);
 
 /* process args */
 hSetDb(db);
 if (!hTableExists(bacTableName))
     errAbort("no %s table in %s\n", bacTableName, db);
 if (!hTableExists(cnpTableName))
     errAbort("no %s table in %s\n", cnpTableName, db);
 
 bacHash = storeBacs(bacTableName);
 processCnps(bacHash, cnpTableName, fileName, liftFileName, logFileName);
 
 return 0;
 }