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/patchToAgp/patchToAgp.c src/hg/oneShot/patchToAgp/patchToAgp.c
index 187b72f..b8c2b86 100644
--- src/hg/oneShot/patchToAgp/patchToAgp.c
+++ src/hg/oneShot/patchToAgp/patchToAgp.c
@@ -1,93 +1,93 @@
 /* patchToAgp - Convert Elia's patch file that describe NT clone position to AGP 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 "hash.h"
 #include "linefile.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "patchToAgp - Convert Elia's patch file that describe NT clone position to AGP file\n"
   "usage:\n"
   "   patchToAgp ~gs/ffa/sequence.inf in.patch out.agp\n");
 }
 
 struct hash *readVersionInfo(char *fileName)
 /* Read sequence.inf file to figure out version number of
  * each clone.  Save it as a hash keyed by accession with
  * values accession.version. */
 {
 char acc[128];
 char *row[1];
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 struct hash *hash = newHash(0);
 
 while (lineFileRow(lf, row))
     {
     strcpy(acc, row[0]);
     chopSuffix(acc);
     hashAdd(hash, acc, cloneString(row[0]));
     }
 lineFileClose(&lf);
 return hash;
 }
 
 char *fixVersion(char *accVer, struct hash *versionHash)
 /* See if accVer ends in .0.  If so try to fix it via
  * hash lookup. */
 {
 static char fixed[128];
 char cloneName[128];
 char *s;
 
 strcpy(cloneName, accVer);
 chopSuffix(cloneName);
 return hashMustFindVal(versionHash, cloneName);
 }
 
 void patchToAgp(char *infName, char *inName, char *outName)
 /* patchToAgp - Convert Elia's patch file that describe NT clone position to AGP file. */
 {
 char *row[9];
 struct lineFile *lf = lineFileOpen(inName, TRUE);
 FILE *f = mustOpen(outName, "w");
 int ix = 0;
 struct hash *versionHash = readVersionInfo(infName);
 int ntStart, ntEnd, cStart, cEnd;
 int diff;
 
 while (lineFileRow(lf, row))
     {
     ntStart = atoi(row[2]);
     ntEnd = atoi(row[3]);
     cStart = atoi(row[7]);
     cEnd = atoi(row[8]);
     if (cStart <= 0)
         {
 	warn("Fixing negative clone start line %d of %s", lf->lineIx, lf->fileName);
 	diff = 1 - cStart;
 	cStart += diff;
 	cEnd += diff;
 	if (cEnd - cStart != ntEnd - ntStart)
 	     errAbort("Couldn't fix properly");
 	}
     fprintf(f, "%s\t%d\t%d\t%d\t%s\t%s\t%d\t%d\t%c\n",
 	row[0], ntStart, ntEnd, ++ix,
 	row[5], fixVersion(row[6], versionHash),
 	cStart, cEnd,
 	row[4][0]);
     }
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 if (argc != 4)
     usage();
 patchToAgp(argv[1], argv[2], argv[3]);
 return 0;
 }