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/fixBlastTrack/fixBlastTrack.c src/hg/oneShot/fixBlastTrack/fixBlastTrack.c
index e580f78..8027607 100644
--- src/hg/oneShot/fixBlastTrack/fixBlastTrack.c
+++ src/hg/oneShot/fixBlastTrack/fixBlastTrack.c
@@ -1,76 +1,76 @@
 /* Copyright (C) 2004 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 "psl.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "fixBlastTrack - fixup problems with blast tracks with buggy protein.lft \n"
   "usage:\n"
   "   fixBlastTrack XXX\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 
 void fixBlastTrack(char *query, char *target, char *outFile)
 {
 struct lineFile *qlf = pslFileOpen(query);
 struct lineFile *tlf = pslFileOpen(target);
 struct psl *psl, *queryPsl, *newPslList;
 struct hash *pslHash = newHash(0);  
 FILE *outStream = mustOpen(outFile, "w");
 
 while ((psl = pslNext(qlf)) != NULL)
     {
     queryPsl = hashFindVal(pslHash, psl->qName);
     if (queryPsl != NULL)
 	errAbort("each qName in query psl file must be unique (%s)",psl->qName);
 
     hashAdd(pslHash, psl->qName, psl);
     }
 
 while ((psl = pslNext(tlf)) != NULL)
     {
     queryPsl = hashFindVal(pslHash, psl->qName);
     if (queryPsl == NULL)
 	errAbort("can't find %s in query file",psl->qName);
 
     if ((queryPsl->qStarts[0] != 0) && (psl->qStarts[0] < queryPsl->blockSizes[0]))
 	{
 	int qStart, qEnd, tBlock;
 	assert(queryPsl->qStart == queryPsl->qStarts[0]);
 	qStart =  0;// queryPsl->qStarts[0];
 	qEnd = qStart + queryPsl->blockSizes[0];
 	psl->qStarts[0] += queryPsl->qStart;
 	psl->qStart = psl->qStarts[0];
 	tBlock = 1;
 	while((tBlock < psl->blockCount) && (psl->qStarts[tBlock] >= qStart) && (psl->qStarts[tBlock] < qEnd))
 	    psl->qStarts[tBlock++] += queryPsl->qStart;
 	psl->qEnd = psl->qStarts[psl->blockCount - 1] + psl->blockSizes[psl->blockCount - 1];
 	}
     pslTabOut(psl, outStream);
     }
 
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 4)
     usage();
 fixBlastTrack(argv[1], argv[2], argv[3]);
 return 0;
 }