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/makeDb/outside/vegaBuildInfo/vegaBuildInfo.c src/hg/makeDb/outside/vegaBuildInfo/vegaBuildInfo.c
index 2738612..0e11e8d 100644
--- src/hg/makeDb/outside/vegaBuildInfo/vegaBuildInfo.c
+++ src/hg/makeDb/outside/vegaBuildInfo/vegaBuildInfo.c
@@ -1,91 +1,91 @@
 /* vegaBuildInfo - build vegaInfo table */
 
 /* 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 "options.h"
 #include "vegaInfo.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort("usage: vegaBuildInfo in.gtf out.tab\n"
 "\tvegaBuildInfo grabs info strings out of vega.gtf and writes\n"
 "\tout one per transcript\n"); 
 }
 
 char * clearString(char *str)
 {
 char *p;
 
 assert(*str == '"');
 str++;
 p = strchr(str, '"');
 assert(p != NULL);
 *p = 0;
 
 return str;
 }
 
 void vegaBuildInfo( char *gtfName, char *outName)
 {
 struct hash *hash = newHash(0);
 FILE *out = mustOpen(outName, "w");
 struct lineFile *lf = lineFileOpen(gtfName, TRUE);
 struct vegaInfo vi;
 char *row[30];
 char *p;
 int wordCount;
 int ii;
 
 while ((wordCount = lineFileChopNext(lf, row, 30)) > 0)
     {
     vi.method = row[1];
     for(ii=8; ii< wordCount; ii++)
 	{
 	if (sameString("gene_id", row[ii]))
 		vi.geneId = clearString(row[++ii]);
 	else if (sameString("transcript_id", row[ii]))
 		vi.transcriptId = clearString(row[++ii]);
 	else if (sameString("otter_transcript_id", row[ii]))
 		vi.otterId = clearString(row[++ii]);
 	else if (sameString("gene_description", row[ii]))
 	    {
 	    p =  row[++ii];
 	    p++;
 	    vi.geneDesc = p;
 	    while(*p != '"')
 		{
 		if (*p == 0)
 		    *p = ' ';
 		p++;
 		}
 	    *p = 0;
 	    }
 	else 
 	    ii++;
 	}
     if (vi.geneDesc == NULL)
 	vi.geneDesc = "N/A";
 
     if (!hashLookup(hash, vi.transcriptId)) 
 	vegaInfoTabOut(&vi, out);
     hashAdd(hash, vi.transcriptId, vi.geneId);
 
     vi.geneDesc = NULL;
     }
 lineFileClose(&lf);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionHash(&argc, argv);
 if (argc != 3)
     usage();
 vegaBuildInfo(argv[1], argv[2]);
 return 0;
 }