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/utils/crTreeIndexBed/crTreeIndexBed.c src/hg/utils/crTreeIndexBed/crTreeIndexBed.c
index f3769f8..1b96460 100644
--- src/hg/utils/crTreeIndexBed/crTreeIndexBed.c
+++ src/hg/utils/crTreeIndexBed/crTreeIndexBed.c
@@ -1,88 +1,88 @@
 /* crTreeIndexBed - Create an index for a bed file.. */
 
 /* Copyright (C) 2011 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 "sqlNum.h"
 #include "crTree.h"
 
 
 int blockSize = 1024;
 int itemsPerSlot = 32;	/* Set in main. */
 boolean noCheckSort = FALSE;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "crTreeIndexBed - Create an index for a bed file.\n"
   "usage:\n"
   "   crTreeIndexBed in.bed out.cr\n"
   "options:\n"
   "   -blockSize=N - number of children per node in index tree. Default %d\n"
   "   -itemsPerSlot=N - number of items per index slot. Default is half block size\n"
   "   -noCheckSort - Don't check sorting order of in.tab\n"
   , blockSize
   );
 }
 
 static struct optionSpec options[] = {
    {"blockSize", OPTION_INT},
    {"itemsPerSlot", OPTION_INT},
    {"noCheckSort", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 struct crTreeItem *scanAll(char *fileName, struct hash *chromNameHash, 
 	bits64 *retFileSize) 
 /* Load all crTreeItem from a whitespace-separated file.
  * Dispose of this with chromRangeFreeList(). */
 {
 struct crTreeItem *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[3];
 
 while (lineFileRow(lf, row))
     {
     AllocVar(el);
     el->chrom = hashStoreName(chromNameHash, row[0]);
     el->start = sqlUnsigned(row[1]);
     el->end = sqlUnsigned(row[2]);
     el->fileOffset = lineFileTell(lf);
     slAddHead(&list, el);
     }
 *retFileSize = lineFileTell(lf);
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 void crTreeIndexBed(char *inBed, char *outTree)
 /* crTreeIndexBed - Create an index for a bed file.. */
 {
 /* Load input and create chromosome hash. */
 struct hash *chromHash = hashNew(0);
 bits64 fileSize;
 struct crTreeItem *itemList = scanAll(inBed, chromHash, &fileSize);
 
 /* Call library function to create index file. */
 if (!noCheckSort)
     crTreeFileCreateInputCheck(itemList, chromHash, blockSize, itemsPerSlot, fileSize, outTree);
 crTreeFileCreate(itemList, chromHash, blockSize, itemsPerSlot, fileSize, outTree);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 blockSize = optionInt("blockSize", blockSize);
 itemsPerSlot = optionInt("itemsPerSlot", (blockSize+1)/2);
 noCheckSort = optionExists("noCheckSort");
 if (argc != 3)
     usage();
 crTreeIndexBed(argv[1], argv[2]);
 return 0;
 }