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/ratStuff/mafFrag/mafFrag.c src/hg/ratStuff/mafFrag/mafFrag.c
index fa456e3..8984b62 100644
--- src/hg/ratStuff/mafFrag/mafFrag.c
+++ src/hg/ratStuff/mafFrag/mafFrag.c
@@ -1,76 +1,76 @@
 /* mafFrag - Extract maf sequences for a region from database. */
 
 /* 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 "jksql.h"
 #include "maf.h"
 #include "hdb.h"
 #include "hgMaf.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "mafFrag - Extract maf sequences for a region from database\n"
   "usage:\n"
   "   mafFrag database mafTrack chrom start end strand out.maf\n"
   "options:\n"
   "   -outName=XXX  Use XXX instead of database.chrom for the name\n"
   );
 }
 
 char *outName = NULL;
 
 static struct optionSpec options[] = {
    {"outName", OPTION_STRING},
    {NULL, 0},
 };
 
 void mafFragCheck(char *database, char *track, 
 	char *chrom, char *startString, char *endString,
 	char *strand, char *outMaf)
 /* mafFragCheck - Check parameters and convert to binary.
  * Call mafFrag. */
 {
 int start, end, chromSize;
 struct mafAli *maf;
 if (!isdigit(startString[0]) || !isdigit(endString[0]))
     errAbort("%s %s not numbers", startString, endString);
 start = atoi(startString);
 end = atoi(endString);
 if (end <= start)
     errAbort("end before start!");
 chromSize = hChromSize(database, chrom);
 if (end > chromSize)
    errAbort("End past chromSize (%d > %d)", end, chromSize);
 maf = hgMafFrag(database, track, 
 	chrom, start, end, *strand, 
 	outName, NULL);
 if (maf != NULL)
     {
     FILE *f = mustOpen(outMaf, "w");
     mafWriteStart(f, "zero");
     mafWrite(f, maf);
     mafWriteEnd(f);
     carefulClose(&f);
     mafAliFree(&maf);
     }
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 dnaUtilOpen();
 optionInit(&argc, argv, options);
 outName = optionVal("outName", NULL);
 if (argc != 8)
     usage();
 mafFragCheck(argv[1], argv[2], argv[3], argv[4], argv[5], argv[6], argv[7]);
 return 0;
 }