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/genePredToBed/genePredToBed.c src/hg/genePredToBed/genePredToBed.c
index 965d114..1290c0d 100644
--- src/hg/genePredToBed/genePredToBed.c
+++ src/hg/genePredToBed/genePredToBed.c
@@ -1,96 +1,96 @@
 /* genePredToBed - Convert from genePred to bed format.. */
 
 /* 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 "genePred.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "genePredToBed - Convert from genePred to bed format. Does not yet handle genePredExt\n"
   "usage:\n"
   "   genePredToBed in.genePred out.bed\n"
   "options:\n"
   "   -tab - genePred fields are separated by tab instead of just white space\n"
   "   -fillSpace - when tab input, fill space chars in 'name' with underscore: _\n"
   "   -score=N - set score to N in bed output (default 0)"
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {"tab", OPTION_BOOLEAN},
    {"fillSpace", OPTION_BOOLEAN},
    {"score", OPTION_INT},
    {NULL, 0},
 };
 
 boolean tabSep = FALSE;
 boolean fillSpace = FALSE;
 int defaultScore = 0;
 
 void convertGenePredToBed(char *inFile, char *outFile)
 /* genePredToBed - Convert from genePred to bed format.. */
 {
 struct genePred *gp = NULL;
 struct genePred *gpList = NULL;
 if (tabSep)
   gpList= genePredLoadAllByChar(inFile, '\t');
 else
   gpList= genePredLoadAll(inFile);
 
 FILE *f = mustOpen(outFile, "w");
 for (gp = gpList; gp != NULL; gp = gp->next)
     {
     /* Print scalar bed fields. */
     fprintf(f, "%s\t", gp->chrom);
     fprintf(f, "%u\t", gp->txStart);
     fprintf(f, "%u\t", gp->txEnd);
     if (tabSep && fillSpace)
         {
         replaceChar(gp->name, ' ', '_');
         fprintf(f, "%s\t", gp->name);
         }
     else
         fprintf(f, "%s\t", gp->name);
     fprintf(f, "%u\t", defaultScore);
     fprintf(f, "%s\t", gp->strand);
     fprintf(f, "%u\t", gp->cdsStart);
     fprintf(f, "%u\t", gp->cdsEnd);
     fprintf(f, "%u\t", 0);
     fprintf(f, "%u\t", gp->exonCount);
 
     /* Print exon-by-exon fields. */
     int i;
 
     /* Print exon sizes */
     for (i=0; i<gp->exonCount; ++i)
         fprintf(f, "%u,", gp->exonEnds[i] - gp->exonStarts[i]);
     fprintf(f, "\t");
 
     /* Print exons starts */
     for (i=0; i<gp->exonCount; ++i)
 	fprintf(f, "%u,", gp->exonStarts[i] - gp->txStart);
     fprintf(f, "\n");
     }
 carefulClose(&f);
 }
 
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 tabSep = optionExists("tab");
 fillSpace = optionExists("fillSpace");
 defaultScore = optionInt("score", defaultScore);
 convertGenePredToBed(argv[1], argv[2]);
 return 0;
 }