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/mafToXmfa/mafToXmfa.c src/hg/mouseStuff/mafToXmfa/mafToXmfa.c
index 5e01123..1b71905 100644
--- src/hg/mouseStuff/mafToXmfa/mafToXmfa.c
+++ src/hg/mouseStuff/mafToXmfa/mafToXmfa.c
@@ -1,81 +1,81 @@
 /* mafToXmfa - Convert from MAF to XMFA 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 "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "obscure.h"
 #include "maf.h"
 #include "hdb.h"
 #include "fa.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "mafToXmfa - Convert from MAF to XMFA format\n"
   "usage:\n"
   "   xmfaToMaf in.maf out.xmfa db1=org1 db1=org1 db2=org2 ... dbN=orgN\n"
   );
 }
 
 void mafToXmfa(char *in, char *out)
 /* mafToXmfa - Convert from maf to xmfa format. */
 {
 struct mafAli* ali;
 struct mafFile* maf;
 FILE* f;
 
 f = fopen(out, "w");
 if(out == NULL) {
     errAbort("Cannot open output file %s\n", out);
 }
 
 maf = mafOpen(in);
 
 while((ali = mafNext(maf)) != NULL) {
     struct mafComp *comp;
     
     for (comp = ali->components; comp != NULL; comp = comp->next) {
         char database[64];
         char chrom[64];
         int start;
         int end;
 
         if(sscanf(comp->src, "%[^.].%[^.]", database, chrom) != 2) {
             errAbort("Could not parse '%s' into db.chr format\n", comp->src);
         }
         
         start = mafPlusStart(comp);
         end   = start + comp->size;
 
         start = start + 1; /* convert to one based */
 
         fprintf(f, ">%s %s:%d-%d %c\n", optionVal(database, database), chrom, start, end, comp->strand);
         writeSeqWithBreaks(f, comp->text, strlen(comp->text), 60);
     }
 
 
     if(sameString(maf->scoring, "mlagan"))
         fprintf(f, "= score=%.1f\n", ali->score);
     else
         fprintf(f, "= score=%.1f %s\n", ali->score, maf->scoring);
     
     mafAliFree(&ali);
 }
 
 fclose(f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionHash(&argc, argv);
 if (argc < 3)
     usage();
 mafToXmfa(argv[1],argv[2]);
 return 0;
 }