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/mouseStuff/mafToPsl/mafToPsl.c src/hg/mouseStuff/mafToPsl/mafToPsl.c
index 5dae1fb..7c3bbc5 100644
--- src/hg/mouseStuff/mafToPsl/mafToPsl.c
+++ src/hg/mouseStuff/mafToPsl/mafToPsl.c
@@ -1,110 +1,110 @@
 /* mafToPsl - Convert maf to psl format. */
 
 /* 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 "options.h"
 #include "maf.h"
 #include "psl.h"
 
 
 
 /* Command line option specifications */
 static struct optionSpec optionSpecs[] = {
     {NULL, 0}
 };
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "mafToPsl - Convert maf to psl format\n"
   "usage:\n"
   "   mafToPsl querySrc targetSrc in.maf out.psl\n"
   "\n"
   "The query and target src can be either an organism prefix (hg17),\n"
   "or a full src sequence name (hg17.chr11), or just the sequence name\n"
   "if the MAF does not contain organism prefixes.\n"
   "\n"
   );
 }
 
 char *skipDot(char *src)
 /* skip past dot in src name */
 {
 char *dot = strchr(src, '.');
 if (dot == NULL)
     return src;
 else
     return dot+1;
 }
 
 static void convertToPsl(struct mafComp *qc, struct mafComp *tc, FILE *pslFh)
 /* convert two components to a psl */
 {
 struct psl* psl;
 int qStart = qc->start;
 int qEnd = qc->start+qc->size;
 int tStart = tc->start;
 int tEnd = tc->start+tc->size;
 char strand[3];
 strand[0] = qc->strand;
 strand[1] = tc->strand;
 strand[2] = '\0';
 
     
 if (qc->strand == '-')
     reverseIntRange(&qStart, &qEnd, qc->srcSize);
 if (tc->strand == '-')
     reverseIntRange(&tStart, &tEnd, tc->srcSize);
 
 psl = pslFromAlign(skipDot(qc->src), qc->srcSize, qStart, qEnd, qc->text,
                    skipDot(tc->src), tc->srcSize, tStart, tEnd, tc->text,
                    strand, 0);
 if (psl != NULL)
     {
     /* drop target strand */
     if (psl->strand[1] == '-')
         pslRc(psl);
     psl->strand[1] = '\0';
     pslTabOut(psl, pslFh);
     }
 }
 
 
 void mafAliToPsl(char *querySrc, char *targetSrc,
                  struct mafAli *maf, FILE *pslFh)
 /* convert a MAF alignment to a psl */
 {
 struct mafComp *qc = mafMayFindComponentDb(maf, querySrc);
 struct mafComp *tc = mafMayFindComponentDb(maf, targetSrc);
 
 if ((qc != NULL) && (tc != NULL))
     convertToPsl(qc, tc, pslFh);
 }
 
 void mafToPsl(char *querySrc, char *targetSrc, char *inName, char *outName)
 /* mafToPsl - Convert maf to psl format. */
 {
 struct mafFile *mf = mafOpen(inName);
 FILE *pslFh = mustOpen(outName, "w");
 struct mafAli *maf;
 
 while ((maf = mafNext(mf)) != NULL)
     {
     mafAliToPsl(querySrc, targetSrc, maf, pslFh);
     mafAliFree(&maf);
     }
 carefulClose(&pslFh);
 mafFileFree(&mf);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, optionSpecs);
 if (argc != 5)
     usage();
 mafToPsl(argv[1], argv[2], argv[3], argv[4]);
 return 0;
 }