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/mouseStuff/rikenBestInCluster/rikenBestInCluster.c src/hg/mouseStuff/rikenBestInCluster/rikenBestInCluster.c
index 08088ae..1d5f8d7 100644
--- src/hg/mouseStuff/rikenBestInCluster/rikenBestInCluster.c
+++ src/hg/mouseStuff/rikenBestInCluster/rikenBestInCluster.c
@@ -1,129 +1,129 @@
 /* rikenBestInCluster - Find best looking in Riken cluster. */
 
 /* 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 "hdb.h"
 #include "borf.h"
 #include "rikenCluster.h"
 #include "estOrientInfo.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "rikenBestInCluster - Find best looking in Riken cluster\n"
   "usage:\n"
   "   rikenBestInCluster database output.tab\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 struct hash *hashBorf(char *database)
 /* Return hash of rikenBorf. */
 {
 struct hash *hash = newHash(16);
 struct borf *borf;
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, NOSQLINJ "select * from rikenBorf");
 while ((row = sqlNextRow(sr)) != NULL)
     {
     borf = borfLoad(row);
     hashAdd(hash, borf->name, borf);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 return hash;
 }
 
 struct hash *hashOrient(char *database)
 /* Return hash of rikenOrientInfo. */
 {
 struct hash *hash = newHash(16);
 struct estOrientInfo *eoi;
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr;
 char **row;
 int rowOffset = 1;
 
 sr = sqlGetResult(conn, NOSQLINJ "select * from rikenOrientInfo");
 while ((row = sqlNextRow(sr)) != NULL)
     {
     eoi = estOrientInfoLoad(row + rowOffset);
     hashAdd(hash, eoi->name, eoi);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 return hash;
 }
 
 void writeBest(FILE *f, struct rikenUcscCluster *rc, struct hash *borfHash, 
 	struct hash *orientHash)
 /* Look in cluster for best Riken from ORF point of view and output it. */
 {
 struct borf *borf, *bestBorf = NULL;
 struct estOrientInfo *eoi;
 float bestScore = -1;
 int i;
 
 for (i=0; i<rc->rikenCount; ++i)
     {
     borf = hashMustFindVal(borfHash, rc->rikens[i]);
     if (borf->score > bestScore)
         {
 	bestBorf = borf;
 	bestScore = borf->score;
 	}
     }
 if (bestBorf != NULL)
     {
     eoi = hashMustFindVal(orientHash, bestBorf->name);
     fprintf(f, "%s\t%f\t%s\t%d\t%s:%d-%d\t%d\t%d\t%d\t%s\n", 
     	bestBorf->name, bestBorf->score, bestBorf->strand, eoi->intronOrientation,
 	rc->chrom, rc->chromStart+1, rc->chromEnd,
     	rc->rikenCount, rc->genBankCount, rc->refSeqCount, rc->name);
     }
 }
 
 void rikenBestInCluster(char *database, char *fileName)
 /* rikenBestInCluster - Find best looking in Riken cluster. */
 {
 FILE *f = mustOpen(fileName, "w");
 struct hash *borfHash = hashBorf(database);
 struct hash *orientHash = hashOrient(database);
 /* Return hash of rikenOrientInfo. */
 struct rikenUcscCluster *rc;
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr;
 char **row;
 int rowOffset = 1;
 
 sr = sqlGetResult(conn, NOSQLINJ "select * from rikenCluster");
 uglyf("sr = %p\n", sr);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     rc = rikenUcscClusterLoad(row + rowOffset);
     writeBest(f, rc, borfHash, orientHash);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionHash(&argc, argv);
 if (argc != 3)
     usage();
 rikenBestInCluster(argv[1], argv[2]);
 return 0;
 }