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/makeDb/outside/hgFiberglass/hgFiberglass.c src/hg/makeDb/outside/hgFiberglass/hgFiberglass.c
index b3b7cda..8dd5e1e 100644
--- src/hg/makeDb/outside/hgFiberglass/hgFiberglass.c
+++ src/hg/makeDb/outside/hgFiberglass/hgFiberglass.c
@@ -1,90 +1,90 @@
 /* hgFiberglass - Turn Fiberglass Annotations into a BED and load into database. */
 
 /* 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 "cheapcgi.h"
 #include "jksql.h"
 #include "dystring.h"
 #include "bed.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgFiberglass - Turn Fiberglass Annotations into a BED and load into database\n"
   "usage:\n"
   "   hgFiberglass database file\n"
   );
 }
 
 char *createString = 
 NOSQLINJ "CREATE TABLE fiberMouse (\n"
     "chrom varchar(255) not null,	# Human chromosome or FPC contig\n"
     "chromStart int unsigned not null,	# Start position in chromosome\n"
     "chromEnd int unsigned not null,	# End position in chromosome\n"
     "name varchar(255) not null,	# Name of other sequence\n"
               "#Indices\n"
     "INDEX(chrom(8),chromStart),\n"
     "INDEX(chrom(8),chromEnd),\n"
     "INDEX(name(12))\n"
 ")\n";
 
 int bedCmp(const void *va, const void *vb);
 
 void hgFiberglass(char *database, char *fileName)
 /* hgFiberglass - Turn Fiberglass Annotations into a BED and load into database. */
 {
 struct sqlConnection *conn = sqlConnect(database);
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *tabName = "fiberMouse.tab";
 FILE *f = mustOpen(tabName, "w");
 char *row[3];
 struct bed *bedList = NULL, *bed;
 char *ti;
 char query[256];
 
 while (lineFileRow(lf, row))
     {
     AllocVar(bed);
     bed->chrom = "chr22";
     bed->chromStart = atoi(row[1])-1;
     bed->chromEnd = atoi(row[2]);
     if (bed->chromEnd <= bed->chromStart)
         errAbort("End before begin line %d of %s", lf->lineIx, lf->fileName);
     ti = row[0];
     if (ti[0] == '|')
          ti += 1;
     if (!startsWith("ti|", ti))
         errAbort("Trace doesn't start with ti| line %d of %s", lf->lineIx, lf->fileName);
     bed->name = cloneString(ti);
     slAddHead(&bedList, bed);
     }
 lineFileClose(&lf);
 printf("Loaded %d ecores from %s\n", slCount(bedList), fileName);
 slSort(&bedList, bedCmp);
 
 /* Write out tab-separated file. */
 for (bed = bedList; bed != NULL; bed = bed->next)
     fprintf(f, "%s\t%d\t%d\t%s\n", bed->chrom, bed->chromStart, bed->chromEnd, bed->name);
 carefulClose(&f);
 
 printf("Loading database\n");
 sqlMaybeMakeTable(conn, "fiberMouse", createString);
 sqlSafef(query, sizeof query, "LOAD data local infile '%s' into table %s", tabName, "fiberMouse");
 sqlUpdate(conn, query);
 sqlDisconnect(&conn);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 cgiSpoof(&argc, argv);
 if (argc != 3)
     usage();
 hgFiberglass(argv[1], argv[2]);
 return 0;
 }