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/ultras/ultraPcrRegions/ultraPcrRegions.c src/hg/ultras/ultraPcrRegions/ultraPcrRegions.c
index 3b677ed..ac4099b 100644
--- src/hg/ultras/ultraPcrRegions/ultraPcrRegions.c
+++ src/hg/ultras/ultraPcrRegions/ultraPcrRegions.c
@@ -1,79 +1,79 @@
 /* ultraPcrRegions - Get regions to PCR up and some surrounding sequence. */
 
 /* 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 "dystring.h"
 #include "jksql.h"
 #include "bed.h"
 #include "hdb.h"
 #include "nib.h"
 #include "dnaseq.h"
 #include "fa.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "ultraPcrRegions - Get regions to PCR up and some surrounding sequence\n"
   "usage:\n"
   "   ultraPcrRegions database ultraBed outputPcr.fa\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 void ultraPcrRegions(char *database, char *bedFile, char *outFa)
 /* ultraPcrRegions - Get regions to PCR up and some surrounding sequence. */
 {
 int extraSize = 1000;
 FILE *f = mustOpen(outFa, "w");
 struct bed *bed, *bedList = bedLoadNAll(bedFile, 4);
 hSetDb(database);
 for (bed = bedList; bed != NULL; bed = bed->next)
     {
     int bedSize = bed->chromEnd - bed->chromStart;
     int chromSize = hChromSize(bed->chrom);
     int seqSize;
     int seqStart = bed->chromStart - extraSize;
     int seqEnd = bed->chromEnd + extraSize;
     int firstParenPos, secondParenPos;
     struct dyString *dy;
     char fileName[512];
     struct dnaSeq *seq;
     if (seqStart < 0)
         seqStart = 0;
     if (seqEnd > chromSize)
         seqEnd = chromSize;
     seqSize = seqEnd - seqStart;
     firstParenPos = bed->chromStart - seqStart;
     secondParenPos = firstParenPos + bedSize;
     seq = hChromSeqMixed(bed->chrom, seqStart, seqEnd);
     dy = dyStringNew(seqSize+2);
     dyStringAppendN(dy, seq->dna, firstParenPos);
     dyStringAppendC(dy, '(');
     dyStringAppendN(dy, seq->dna+firstParenPos, secondParenPos-firstParenPos);
     dyStringAppendC(dy, ')');
     dyStringAppendN(dy, seq->dna+secondParenPos, seqSize - secondParenPos);
     faWriteNext(f, bed->name, dy->string, dy->stringSize);
     }
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 4)
     usage();
 ultraPcrRegions(argv[1], argv[2], argv[3]);
 return 0;
 }