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/addMhcClones/addMhcClones.c src/hg/oneShot/addMhcClones/addMhcClones.c
index fdd2c3b..7d4a01f 100644
--- src/hg/oneShot/addMhcClones/addMhcClones.c
+++ src/hg/oneShot/addMhcClones/addMhcClones.c
@@ -1,115 +1,115 @@
 /* addMhcClones - Add info on missing MHC files to Greg's stuff.. */
 
 /* 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 "cheapcgi.h"
 #include "portable.h"
 #include "fa.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "addMhcClones - Add info on missing MHC files to Greg's stuff.\n"
   "usage:\n"
   "   addMhcClones ~/gs/otherIn/mhc/clones ~/gs\n"
   "options:\n");
 }
 
 void addToSequenceInf(struct dnaSeq *seqList, char *fileName)
 /* Append to sequence.inf file. */
 {
 FILE *f = mustOpen(fileName, "a");
 struct dnaSeq *seq;
 char cloneVer[256];
 
 for (seq = seqList; seq != NULL; seq = seq->next)
     {
     strcpy(cloneVer, seq->name);
     chopSuffixAt(cloneVer, '_');
     fprintf(f, "%s\t-\t%d\t3\t-\t6\t-\tSC\t-\n", cloneVer, seq->size);
     }
 fclose(f);
 }
 
 void addToTrans(struct dnaSeq *seqList, char *fileName)
 /* Append info to trans file. */
 {
 FILE *f = mustOpen(fileName, "a");
 struct dnaSeq *seq;
 char ncbiName[256];
 char cloneVer[256];
 
 for (seq = seqList; seq != NULL; seq = seq->next)
     {
     strcpy(ncbiName, seq->name);
     subChar(ncbiName, '_', '~');
     strcpy(cloneVer, seq->name);
     chopSuffixAt(cloneVer, '_');
     fprintf(f, "%s\t%s (%s:1..%d)\n", seq->name, ncbiName, cloneVer, seq->size);
     }
 fclose(f);
 }
 
 void addToFinf(struct dnaSeq *seqList, char *fileName)
 /* Append info to finf file. */
 {
 FILE *f = mustOpen(fileName, "a");
 struct dnaSeq *seq;
 char ncbiName[256];
 char cloneVer[256];
 
 for (seq = seqList; seq != NULL; seq = seq->next)
     {
     strcpy(ncbiName, seq->name);
     subChar(ncbiName, '_', '~');
     strcpy(cloneVer, seq->name);
     chopSuffixAt(cloneVer, '_');
     fprintf(f, "%s\t%s\t1\t%d\t1\t1,1/1\tw\n", ncbiName, cloneVer, seq->size);
     }
 fclose(f);
 }
 
 
 
 void addMhcClones(char *cloneDir, char *gsDir)
 /* addMhcClones - Add info on missing MHC files to Greg's stuff.. */
 {
 struct fileInfo *fileList = NULL, *fileEl;
 struct dnaSeq *seqList = NULL, *seq;
 char path[512];
 
 fileList = listDirX(cloneDir, "*.fa", TRUE);
 for (fileEl = fileList; fileEl != NULL; fileEl = fileEl->next)
     {
     seq = faReadAllDna(fileEl->name);
     if (slCount(seq) != 1)
         errAbort("%s has %d sequences, can only handle one.", fileEl->name, slCount(seq));
     slAddHead(&seqList, seq);
     }
 slReverse(&seqList);
 printf("Read %d sequences\n", slCount(seqList));
 
 sprintf(path, "%s/fin/trans", gsDir);
 addToTrans(seqList, path);
 
 sprintf(path, "%s/ffa/sequence.inf", gsDir);
 addToSequenceInf(seqList, path);
 
 sprintf(path, "%s/ffa/finished.finf", gsDir);
 addToFinf(seqList, path);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 cgiSpoof(&argc, argv);
 if (argc != 3)
     usage();
 addMhcClones(argv[1], argv[2]);
 return 0;
 }