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/utils/bigBedToBed/bigBedToBed.c src/utils/bigBedToBed/bigBedToBed.c
index 61e5d4d..09edda0 100644
--- src/utils/bigBedToBed/bigBedToBed.c
+++ src/utils/bigBedToBed/bigBedToBed.c
@@ -1,128 +1,128 @@
 /* bigBedToBed - Convert from bigBed to ascii bed format.. */
 
 /* Copyright (C) 2014 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 "localmem.h"
 #include "udc.h"
 #include "bigBed.h"
 #include "asParse.h"
 #include "obscure.h"
 
 
 char *clChrom = NULL;
 int clStart = -1;
 int clEnd = -1;
 int maxItems = 0;
 boolean header = FALSE;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bigBedToBed v1 - Convert from bigBed to ascii bed format.\n"
   "usage:\n"
   "   bigBedToBed input.bb output.bed\n"
   "options:\n"
   "   -chrom=chr1 - if set restrict output to given chromosome\n"
   "   -start=N - if set, restrict output to only that over start\n"
   "   -end=N - if set, restict output to only that under end\n"
   "   -maxItems=N - if set, restrict output to first N items\n"
   "   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs\n"
   "   -header - output a autoSql-style header (starts with '#').\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"chrom", OPTION_STRING},
    {"start", OPTION_INT},
    {"end", OPTION_INT},
    {"maxItems", OPTION_INT},
    {"udcDir", OPTION_STRING},
    {"header", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 
 void writeHeader(struct bbiFile *bbi, FILE *f)
 /* output a header from the autoSql in the file */
 {
 char *asText = bigBedAutoSqlText(bbi);
 if (asText == NULL)
     errAbort("bigBed files does not contain an autoSql schema");
 struct asObject *asObj = asParseText(asText);
 char sep = '#';
 for (struct asColumn *asCol = asObj->columnList; asCol != NULL; asCol = asCol->next)
     {
     fputc(sep, f);
     fputs(asCol->name, f);
     sep = '\t';
     }
 fputc('\n', f);
 }
 
 void bigBedToBed(char *inFile, char *outFile)
 /* bigBedToBed - Convert from bigBed to ascii bed format.. */
 {
 struct bbiFile *bbi = bigBedFileOpen(inFile);
 FILE *f = mustOpen(outFile, "w");
 if (header)
     writeHeader(bbi, f);
 struct bbiChromInfo *chrom, *chromList = bbiChromList(bbi);
 int itemCount = 0;
 for (chrom = chromList; chrom != NULL; chrom = chrom->next)
     {
     if (clChrom != NULL && !sameString(clChrom, chrom->name))
         continue;
     char *chromName = chrom->name;
     int start = 0, end = chrom->size;
     if (clStart > 0)
         start = clStart;
     if (clEnd > 0)
         end = clEnd;
     int itemsLeft = 0;	// Zero actually means no limit.... 
     if (maxItems != 0)
         {
 	itemsLeft = maxItems - itemCount;
 	if (itemsLeft <= 0)
 	    break;
 	}
     struct lm *lm = lmInit(0);
     struct bigBedInterval *interval, *intervalList = bigBedIntervalQuery(bbi, chromName, 
     	start, end, itemsLeft, lm);
     for (interval = intervalList; interval != NULL; interval = interval->next)
 	{
 	fprintf(f, "%s\t%u\t%u", chromName, interval->start, interval->end);
 	char *rest = interval->rest;
 	if (rest != NULL)
 	    fprintf(f, "\t%s\n", rest);
 	else
 	    fprintf(f, "\n");
 	}
     lmCleanup(&lm);
     }
 bbiChromInfoFreeList(&chromList);
 carefulClose(&f);
 bbiFileClose(&bbi);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 clChrom = optionVal("chrom", clChrom);
 clStart = optionInt("start", clStart);
 clEnd = optionInt("end", clEnd);
 maxItems = optionInt("maxItems", maxItems);
 udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
 header = optionExists("header");
 if (argc != 3)
     usage();
 bigBedToBed(argv[1], argv[2]);
 if (verboseLevel() > 1)
     printVmPeak();
 return 0;
 }