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/gsid/gsidPosSelect/gsidPosSelect.c src/hg/gsid/gsidPosSelect/gsidPosSelect.c
index fe56ef2..6569a7a 100644
--- src/hg/gsid/gsidPosSelect/gsidPosSelect.c
+++ src/hg/gsid/gsidPosSelect/gsidPosSelect.c
@@ -1,111 +1,111 @@
 /* gsidPosSelection - Generate positive selection track data. */
 
 /* 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 "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "jksql.h"
 #include "psl.h"
 #include "hdb.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "gsidPosSelection - Generate positive selection track data\n"
   "usage:\n"
   "   gsidPosSelection database pslTable buildDb modelTable outfile\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 void gsidPosSelection(char *database, char *pslTable, char *buildDb, char *modelTable, char *outfileName)
 /* gsidPosSelection - Generate positive selection track data. */
 {
 struct sqlConnection *conn, *conn2;
 struct sqlResult *sr;
 char **row;
 char query[2048];
 int blockCnt = 0, i;
 
 char query2[256];
 struct sqlResult *sr2;
 char **row3;
 int aaPos;
 char *aa;
 float Pr;
 FILE *outf;
 
 int blkStart, blkSize, qStart;
 int pos;
 
 conn = hAllocConn(database);
 conn2= hAllocConn(database);
 
 outf = mustOpen(outfileName, "w");
 
 /* loop thru all psitively selected sites */
 sqlSafef(query2, sizeof query2, "select * from %s.%s", buildDb, modelTable);
 sr2 = sqlMustGetResult(conn2, query2);
 row3 = sqlNextRow(sr2);
               
 while (row3 != NULL)
     {
     aaPos = atoi(row3[0]);
     aa    = row3[1];
     Pr    = atof(row3[2]);
 
     /* Query target->pslTable to get target-to-genomic mapping: */
     sqlSafef(query, sizeof(query), "select * from %s", pslTable);
     sr = sqlGetResult(conn, query);
     while ((row = sqlNextRow(sr)) != NULL)
     	{
     	struct psl *thePsl = pslLoad(row);
    
     	blockCnt = thePsl->blockCount; 
     	for (i=0; i<blockCnt; i++)
 	    {
 	    qStart   = thePsl->qStarts[i];
 	    blkStart = thePsl->tStarts[i];
 	    blkSize  = thePsl->blockSizes[i];
 	    pos =  blkStart + (aaPos - qStart)*3 - 1;
 	    if ((pos > blkStart) && (pos <= (blkStart+blkSize*3)))
 		{
 		fprintf(outf, "chr1\t%d\t%d\t%s\t%d\n", pos-2, pos+1, aa, (int)(Pr*1000));
 	    	}
 	    }
     	pslFree(&thePsl);
     	}
     sqlFreeResult(&sr);
 
     row3 = sqlNextRow(sr2);
     }
 sqlFreeResult(&sr2);
 
 hFreeConn(&conn);
 hFreeConn(&conn2);
 fclose(outf);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 char *database, *pslTable, *buildDatabase, *modelTable, *outfileName;
 
 optionInit(&argc, argv, options);
 if (argc != 6)
     usage();
 database      = argv[1];
 pslTable      = argv[2];
 buildDatabase = argv[3];
 modelTable    = argv[4];
 outfileName   = argv[5];
 
 gsidPosSelection(database, pslTable, buildDatabase, modelTable, outfileName);
 return 0;
 }