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/fixEnsGtf/fixEnsGtf.c src/hg/oneShot/fixEnsGtf/fixEnsGtf.c
index 55556fe..ca80da1 100644
--- src/hg/oneShot/fixEnsGtf/fixEnsGtf.c
+++ src/hg/oneShot/fixEnsGtf/fixEnsGtf.c
@@ -1,115 +1,115 @@
 /* fixEnsGtf - fix space vs. tab and start/stop codon problems in Ensemble .gtf file. */
 
 /* 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"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "fixEnsGtf - fix space vs. tab and start/stop codon problems in Ensemble .gtf file\n"
   "usage:\n"
   "   fixEnsGtf out.gtf in.gtf(s)\n");
 }
 
 void fixLine(struct lineFile *lf, char *line, FILE *f)
 /* Fix up a single line. */
 {
 char *group;            /* Last. */
 char *words[8];		/* First words. */
 int i;
 char fixStart[16], fixEnd[16];
 char *type, *strand;
 
 /* Pass through comments. */
 if (line[0] == '#')
     {
     fprintf(f, "%s\n", line);
     return;
     }
 
 /* Find the start of the "group" field. */
 group = line;
 for (i=0; i<8; ++i)
     {
     group = skipToSpaces(group);
     if (group == NULL)
        errAbort("Expecting at least 9 fields line %d of %s\n", lf->lineIx, lf->fileName);
     group = skipLeadingSpaces(group);
     }
 
 /* Truncate initial string before group field and chop it up. */
 group[-1] = 0;
 chopLine(line, words);
 
 #ifdef FLAKY    /* This doesn't fix all problems, we'll just ignore start/stop_codons. */
 /* Fix up start and stop codons. */
 type = words[2];
 strand = words[6];
 if (sameString(type, "start_codon") && sameString(strand, "-"))
     {
     sprintf(fixStart, "%d", atoi(words[3])-3);
     sprintf(fixEnd, "%d", atoi(words[4])-3);
     words[3] = fixStart;
     words[4] = fixEnd;
     }
 else if (sameString(type, "stop_codon"))
     {
     /* Start and end reversed on both strands. */
     int start = atoi(words[4]);
     int end = atoi(words[3]);
     if (sameString(strand, "-"))
         {
 	start += 3;
 	end += 3;
 	}
     sprintf(fixStart, "%d", start);
     sprintf(fixEnd, "%d", end);
     words[3] = fixStart;
     words[4] = fixEnd;
     }
 #endif /* FLAKY */
 
 /* Skip start/stop codons.  Code will then assume all exons are CDS. */
 type = words[2];
 if (sameString(type, "start_codon") || sameString(type, "stop_codon"))
     return;
 
 /* Write fixed output. */
 for (i=0; i<8; ++i)
     fprintf(f, "%s\t", words[i]);
 fprintf(f, "%s\n", group);
 }
 
 void fixEnsGtf(char *outName, int inCount, char *inFiles[])
 /* fixEnsGtf - fix space vs. tab and start/stop codon problems in Ensemble .gtf file. */
 {
 FILE *f = mustOpen(outName, "w");
 struct lineFile *lf;
 int fileIx;
 int lineSize;
 char *line;
 
 for (fileIx = 0; fileIx < inCount; ++fileIx)
     {
     lf = lineFileOpen(inFiles[fileIx], TRUE);
     printf("Processing %s\n", lf->fileName);
     while (lineFileNext(lf, &line, &lineSize))
         {
 	fixLine(lf, line, f);
 	}
     lineFileClose(&lf);
     }
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 if (argc < 3)
     usage();
 fixEnsGtf(argv[1], argc-2, argv+2);
 return 0;
 }