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/oneShot/seqFromPsl/seqFromPsl.c src/hg/oneShot/seqFromPsl/seqFromPsl.c
index 7e6ee33..9e8e288 100644
--- src/hg/oneShot/seqFromPsl/seqFromPsl.c
+++ src/hg/oneShot/seqFromPsl/seqFromPsl.c
@@ -1,68 +1,68 @@
 /* seqFromPsl - Extract masked sequence from database corresponding to psl 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 "dnautil.h"
 #include "fa.h"
 #include "psl.h"
 #include "twoBit.h"
 
 
 boolean hardMask = FALSE;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "seqFromPsl - Extract masked sequence from database corresponding to psl file\n"
   "usage:\n"
   "   seqFromPsl in.psl in.2bit out.fa\n"
   "options:\n"
   "   -hardMask\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"hardMask", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 void seqFromPsl(char *inPsl, char *inTwoBit, char *outFa)
 /* seqFromPsl - Extract masked sequence from database corresponding to psl file. */
 {
 struct twoBitFile *tbf = twoBitOpen(inTwoBit);
 struct lineFile *lf = pslFileOpen(inPsl);
 FILE *f = mustOpen(outFa, "w");
 struct psl *psl;
 
 while ((psl = pslNext(lf)) != NULL)
     {
     char faHead[512];
     struct dnaSeq *seq = twoBitReadSeqFrag(tbf, psl->tName,
     	psl->tStart, psl->tEnd);
     if (psl->strand[0] == '-')
         reverseComplement(seq->dna, seq->size);
     safef(faHead, sizeof(faHead), "%s (%s:%d-%d)", 
     	psl->qName, psl->tName, psl->tStart+1, psl->tEnd);
     if (hardMask)
         lowerToN(seq->dna, seq->size);
     faWriteNext(f, faHead, seq->dna, seq->size);
     }
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 dnaUtilOpen();
 optionInit(&argc, argv, options);
 if (argc != 4)
     usage();
 hardMask = optionExists("hardMask");
 seqFromPsl(argv[1], argv[2], argv[3]);
 return 0;
 }