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/joinToPatch/joinToPatch.c src/hg/oneShot/joinToPatch/joinToPatch.c
index c271ac4..2fdbba1 100644
--- src/hg/oneShot/joinToPatch/joinToPatch.c
+++ src/hg/oneShot/joinToPatch/joinToPatch.c
@@ -1,97 +1,97 @@
 /* joinToPatch - Convert Elia's parsed GenBank joins into an equivalent .agpPatch 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(
   "joinToPatch - Convert Elia's parsed GenBank joins into an equivalent .agpPatch file.\n"
   "usage:\n"
   "   joinToPatch inFile out.agpPatch\n");
 }
 
 void joinToPatch(char *inName, char *outName)
 /* joinToPatch - Convert Elia's parsed GenBank joins into an equivalent .patchAgp file.. */
 {
 struct lineFile *lf = lineFileOpen(inName, TRUE);
 char *ntRow[2];
 char *line, *s;
 static char *commaSep[1024], *colonSep[3], *dotSep[3];
 int commaCount, colonCount, dotCount, lineSize, i, len;
 char ntName[256], cloneName[256];
 boolean breakJoin, isComplement;
 int start, end, pos, size;
 FILE *f = mustOpen(outName, "w");
 
 for (;;)
     {
     if (!lineFileRow(lf, ntRow))
          break;
     strcpy(ntName, ntRow[0]);
     if (!startsWith("NT_", ntName))
         errAbort("Expecting NT_ line %d of %s", lf->lineIx, lf->fileName);
     breakJoin = FALSE;
     pos = 0;
     while (!breakJoin)
         {
 	if (!lineFileNext(lf, &line, &lineSize))
 	    errAbort("Missing join line at end of %s", lf->fileName);
 	line = trimSpaces(line);
 	lineSize = strlen(line);
 	breakJoin = (line[lineSize-1] != ',');
 	if (startsWith("join(", line))
 	    line += strlen("join(");
 	commaCount = chopString(line, ",", commaSep, ArraySize(commaSep));
 	for (i=0; i<commaCount; ++i)
 	    {
 	    s = commaSep[i];
 	    if (startsWith("complement(", s))
 		{
 		isComplement = TRUE;
 		s += strlen("complement(");
 		len = strlen(s);
 		if (s[len-1] != ')')
 		    errAbort("Missing paren in complement line %d of %s", 
 		    	lf->lineIx, lf->fileName);
 		s[len-1] = 0;
 		}
 	    else
 	        isComplement = FALSE;
 	    colonCount = chopString(s, ":", colonSep, ArraySize(colonSep));
 	    if (colonCount != 2)
 	        errAbort("Expecting 1 colon line %d of %s, got %d", 
 			lf->lineIx, lf->fileName, colonCount-1);
 	    strcpy(cloneName, colonSep[0]);
 	    dotCount = chopByChar(colonSep[1], '.', dotSep, ArraySize(dotSep));
 	    if (dotCount != 3)
 	        errAbort("Expecting start..end line %d of %s", lf->lineIx, lf->fileName);
 	    if (!isdigit(dotSep[0][0]) || !isdigit(dotSep[2][0]))
 	        errAbort("Expecting start..end numbers %d of %s", lf->lineIx, lf->fileName);
 	    start = atoi(dotSep[0])-1;
 	    end = atoi(dotSep[2]);
 	    size = end - start;
 	    fprintf(f, "%s\txxx\t%d\t%d\t%c1\tF\t%s\t%d\t%d\n",
 	    	ntName, pos+1, pos+size,
 		(isComplement ? '-' : '+'),
 		cloneName, start+1, end);
 	    pos += size;
 	    }
 	}
     }
 lineFileClose(&lf);
 fclose(f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 if (argc != 3)
     usage();
 joinToPatch(argv[1], argv[2]);
 return 0;
 }