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/fixMd/fixMd.c src/hg/protein/fixMd/fixMd.c
index 8bad90b..f2e1f1f 100644
--- src/hg/protein/fixMd/fixMd.c
+++ src/hg/protein/fixMd/fixMd.c
@@ -1,118 +1,118 @@
 /* fixMd - fix the problem of seq_contig.md file that the haplotype chromosomes start and end positions refer to original chromosome, change them into referencing the haplotype chrome initial position */
 
 /* 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(
   "fixMd - fix the problem of seq_contig.md\n"
   "usage:\n"
   "   fixMd hDb\n"
   "      hDb is the DB where seq_contig resides\n"
   "example: fixMd hg18\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn2;
   
 char query2[256], query3[256];
 struct sqlResult *sr2, *sr3;
 char **row2, **row3;
 
 char *database;
 
 char *name, *chrom, *strand, *chrStart, *chrEnd, *cdsStart, *cdsEnd,
      *exonCount, *exonStarts, *exonEnds;
 
 int j;
 char *oldChrom;
 int iStart, iEnd;
 int iOldStart=0;
 
 char newStart[200], newEnd[200];
 
 if (argc != 2) usage();
 database  = argv[1];
    
 conn2= hAllocConn();
 
 oldChrom = strdup("");
 
 sqlSafef(query2, sizeof query2, "select * from %s.seq_contig", database);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     chrom 	= row2[1];
     chrStart 	= row2[2];
     chrEnd   	= row2[3];
     if (strstr(chrom, "hap") != NULL)
     	{
 	if (!sameWord(oldChrom, chrom))
 	    {
 	    /* a new haplotype */
 	    for (j=0; j<2; j++)
 	    	{
 	    	printf("%s\t", row2[j]);
 	    	}
 		
 	    iOldStart = atoi(chrStart);
 	    iStart = 1;
 	    iEnd   =  atoi(chrEnd) - iOldStart + 1;
 		
 	    printf("%d\t", iStart);
 	    printf("%d\t", iEnd);
 	    
 	    for (j=4; j<9; j++)
 	    	{
 	    	printf("%s\t", row2[j]);
 	    	}
 	    
 	    printf("%s\n", row2[9]);
 	    oldChrom = strdup(chrom);
 	    }
 	else
 	    {
 	    /* a continuation of a haplotype */
 	    for (j=0; j<2; j++)
 	    	{
 	    	printf("%s\t", row2[j]);
 	    	}
 		
 	    iStart = atoi(chrStart) - iOldStart + 1;
 	    iEnd   = atoi(chrEnd) - atoi(chrStart) + iStart;
 		
 	    printf("%d\t", iStart);
 	    printf("%d\t", iEnd);
 	    
 	    for (j=4; j<9; j++)
 	    	{
 	    	printf("%s\t", row2[j]);
 	    	}
 	    
 	    printf("%s\n", row2[9]);
 	    }
 	}
     else
     	{
 	for (j=0; j<9; j++)
 	    {
 	    printf("%s\t", row2[j]);
 	    }
 	printf("%s\n", row2[9]);
 	}
     
     row2 = sqlNextRow(sr2);
     }
 sqlFreeResult(&sr2);
 
 hFreeConn(&conn2);
 return(0);
 }