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/protein/fixAgp/fixAgp.c src/hg/protein/fixAgp/fixAgp.c
index e075886..2861cc0 100644
--- src/hg/protein/fixAgp/fixAgp.c
+++ src/hg/protein/fixAgp/fixAgp.c
@@ -1,90 +1,90 @@
 /* fixAgp - fix those extra hap agp files */
 
 /* Copyright (C) 2013 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 "hCommon.h"
 #include "hdb.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "fixAgp - fix agp file\n"
   "usage:\n"
   "   fixAgp db inFile outFile\n"
   "      db      is the genome under construction, e.g.: hg18\n"
   "      inFile  is the input file name\n"
   "      outFile is the output file name\n"
   "example:\n"
   "   fixAgp hg18 sav/in.agp out.agp\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn2;
 char condStr[500];
 
 FILE *inf;
 FILE   *outf;
 
 char line[1000];
 
 char *chrStart;
 
 char *inFileName, *outFileName;
 char contig[100], start[100], end[100];
 char num[100], code[100], id[100], oStart[100], oEnd[100], strnd[100];
 char *database;
 
 char *oldContig;
 int  oldNum = 0;
 
 int lastNum = 0;
 int lastEnd = 0;
 
 if (argc != 4)usage();
 
 database    = argv[1];
 inFileName  = argv[2];
 outFileName = argv[3];
 
 hSetDb(database);
 
 outf = fopen(outFileName, "w");
 conn2= hAllocConn();
 
 inf   = mustOpen(inFileName, "r");
 
 oldContig = strdup("");
 while (fgets(line, 1000, inf) != NULL)
     {
     sscanf(line, "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n",
     	   contig, start, end, num, code, id, oStart, oEnd, strnd);
     sqlSafefFrag(condStr, sizeof condStr, "ctg_acc='%s'", contig);
     chrStart =  sqlGetField(database, "seq_contig", "chr_start", condStr);
     if (!sameWord(oldContig, contig)) 
     	{
     	if (!sameWord(oldContig, ""))
     	    {
 	    lastNum++;
 	    fprintf(outf, "%s\t%d\t%d\t", 
     	    	    oldContig, lastEnd+1, atoi(chrStart)+atoi(start)-2);
     	    fprintf(outf, "%d\t%s\t%d\t%s\t%s\n", 
     	    	    lastNum, "N", atoi(chrStart)+atoi(start)-2 - (lastEnd+1) +1, "contig", "no");
 	    }
 	oldContig = strdup(contig);
 	oldNum = lastNum;
 	}
     lastNum = atoi(num) + oldNum;    
     fprintf(outf, "%s\t%d\t%d\t", 
     	    contig, atoi(chrStart)+atoi(start)-1, atoi(chrStart)+atoi(end)-1);
     fprintf(outf, "%d\t%s\t%s\t%s\t%s\t%s\n", 
     	    lastNum, code, id, oStart, oEnd, strnd);
     lastEnd = atoi(chrStart)+atoi(end)-1;
     }
 hFreeConn(&conn2);
 	
 fclose(outf);
 return(0);
 }