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/protDat/protDat.c src/hg/oneShot/protDat/protDat.c
index 3e9c8b6..807c222 100644
--- src/hg/oneShot/protDat/protDat.c
+++ src/hg/oneShot/protDat/protDat.c
@@ -1,93 +1,93 @@
 /* findExons - This program reads in a list of psls. */
 
 /* 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(
   "protDat - this program reads in a protein psl as argv[1] and modifies qName to include\n"
   "          the position of the protein (using argv[2]) and various alias as defined by argv[3]\n"
   "usage:\n"
   "   protDat protein.psl proteinBlat.psl aliases outFile\n"
   "options:\n"
   "   -fb use FlyBase defaults\n"
   "   -kg use KnownGene defaults\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"fb", OPTION_BOOLEAN},
    {"kg", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 
 struct alias
 {
     char *kgName;
     char *spName;
 };
 
 void protDat(char *protName, char *blatName, char *aliasFile, char *outName)
 {
 FILE *outFile = mustOpen(outName, "w");
 struct hash *protHash = newHash(10);
 struct hash *blatHash = newHash(10);
 struct hash *aliasHash = newHash(10);
 struct psl *psls, *pslPtr, *protPsls, *blatPsl;
 struct lineFile *lf = lineFileOpen(aliasFile, TRUE);
 struct alias *alPtr;
 char buffer[1024];
 char *words[3];
 int numWords = optionExists("fb") ? 2 : 3;
 
 while (lineFileNextRow(lf, words, numWords))
     {
     AllocVar(alPtr);
     alPtr->kgName = cloneString(words[1]);
     if (numWords == 3)
 	alPtr->spName = cloneString(words[2]);
     hashAdd(aliasHash, cloneString(words[0]), alPtr);
     }
 
 protPsls = pslLoadAll(protName);
 
 pslPtr = psls = pslLoadAll(blatName);
 for(; pslPtr; pslPtr = pslPtr->next)
     hashAdd(blatHash, pslPtr->qName, pslPtr);
 
 for(pslPtr = protPsls; pslPtr; pslPtr = pslPtr->next)
     {
     if ((blatPsl = hashFindVal(blatHash, pslPtr->qName)) != NULL)
 	{
 	if ((alPtr = hashFindVal(aliasHash, pslPtr->qName)) != NULL)
 	    {
 	    if (numWords == 3)
 		sprintf(buffer,"%s.%s:%d-%d.%s.%s",pslPtr->qName,blatPsl->tName, 
 		    blatPsl->tStart, blatPsl->tEnd,alPtr->kgName, alPtr->spName); 
 	    else
 		sprintf(buffer,"%s.%s:%d-%d.%s",pslPtr->qName,blatPsl->tName, 
 		    blatPsl->tStart, blatPsl->tEnd,alPtr->kgName); 
 	    pslPtr->qName = buffer;
 	    pslTabOut(pslPtr, outFile);
 	    }
 	}
     }
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc < 5)
     usage();
 protDat(argv[1], argv[2], argv[3], argv[4]);
 return 0;
 }