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/chimpStuff/chimpChromContigAgp/chimpChromContigAgp.c src/hg/chimpStuff/chimpChromContigAgp/chimpChromContigAgp.c
index 8b83ccd..e355602 100644
--- src/hg/chimpStuff/chimpChromContigAgp/chimpChromContigAgp.c
+++ src/hg/chimpStuff/chimpChromContigAgp/chimpChromContigAgp.c
@@ -1,113 +1,113 @@
 /* chimpChromContigAgp - create chrom to contig AGP, 
    using chrom-scaf and scaf-contig AGP's */
 
 /* 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"
 #include "agp.h"
 #include "agpFrag.h"
 #include "agpGap.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
  "chimpChromContigAgp - create chimp chrom to contig AGP file\n"
  "\n"
  "usage:\n"
  "   chimpChromContigAgp chromAgp scafAgp destAgp\n"
  );
 }
 
 void chimpChromContigAgp(char *chromAgp, char *scafAgp, char *destAgp)
 /* Change coordinates of scaf-based chrom .agp, file to contig coordinate system. */
 {
 struct lineFile *lf = lineFileOpen(chromAgp, TRUE);
 char *row[9];
 FILE *dest = mustOpen(destAgp, "w");
 struct hash *scafAgpHash = newHash(0);
 int wordCount;
 char *words[9];
 int ix = 1;
 int chromEnd;
 
 /* create hash of scaf AGP lists, one per scaf */
 scafAgpHash = agpLoadAll(scafAgp);
 
 /* read AGP entries from chrom AGP file */
 while ((wordCount = lineFileChopNext(lf, words, ArraySize(words))) != 0)
     {
     struct agp *chromAgp, *scafAgp, *scafAgpList;
 
     lineFileExpectAtLeast(lf, 8, wordCount);
     chromAgp = agpLoad(words, wordCount);
     if (chromAgp->isFrag)
         {
         struct agpFrag *frag = (struct agpFrag *)chromAgp->entry;
 
         /* lookup scaffold in hash of scaf->contig AGP lists */
         scafAgpList = hashMustFindVal(scafAgpHash, frag->frag);
         if (frag->strand[0] == '-')
             slReverse(&scafAgpList);
         chromEnd = frag->chromStart - 1;
         for (scafAgp = scafAgpList; scafAgp != NULL; scafAgp = scafAgp->next)
             {
             if (scafAgp->isFrag)
                 {
                 struct agpFrag *scafFrag = (struct agpFrag *)scafAgp->entry;
 
                 /* change to chrom coords */
                 freeMem(scafFrag->chrom);
                 scafFrag->chrom = frag->chrom;
                 /* agpFragOutput subtracts 1 from chromStart */
                 scafFrag->chromStart = chromEnd;
                 scafFrag->chromEnd = scafFrag->chromStart + 
                                     scafFrag->fragEnd - scafFrag->fragStart + 1;
                 scafFrag->fragStart--;
                 chromEnd = scafFrag->chromEnd + 1;
                 scafFrag->ix = ix++;
                 scafFrag->strand[0] = (frag->strand[0] == '-' ? '-' : '+');
                 scafFrag->strand[1] = 0;
                 agpFragOutput(scafFrag, dest, '\t', '\n');
                 }
             else
                 {
                 struct agpGap *scafGap = (struct agpGap *)scafAgp->entry;
                 freeMem(scafGap->chrom);
                 scafGap->chrom = frag->chrom;
                 scafGap->chromStart = chromEnd;
                 scafGap->chromEnd = scafGap->chromStart + scafGap->size - 1;
                 chromEnd = scafGap->chromEnd;
                 scafGap->ix = ix++;
                 agpGapOutput(scafGap, dest, '\t', '\n');
                 }
             }
         }
     else
         {
         /* gap */
         struct agpGap *gap = (struct agpGap *)chromAgp->entry;
         gap->ix = ix++;
         agpGapOutput(gap, dest, '\t', '\n');
         chromEnd = gap->chromEnd;
         }
     agpFree(&chromAgp);
     }
 if (ferror(dest))
     errAbort("error writing %s", destAgp);
 fclose(dest);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 if (argc < 3)
     usage();
 chimpChromContigAgp(argv[1], argv[2], argv[3]);
 return 0;
 }