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/gsid/gsidMsaToTab/gsidMsaToTab.c src/hg/gsid/gsidMsaToTab/gsidMsaToTab.c
index e2f1584..69b1dca 100644
--- src/hg/gsid/gsidMsaToTab/gsidMsaToTab.c
+++ src/hg/gsid/gsidMsaToTab/gsidMsaToTab.c
@@ -1,113 +1,113 @@
 /* gsidMsaToTab - create .tab files from MSA sequence data to DNA and protein .tab 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 "linefile.h"
 #include "hash.h"
 #include "hdb.h"
 #include "options.h"
 #include "localmem.h"
 #include "dystring.h"
 #include "portable.h"
 #include "obscure.h"
 
 
 char *seq, *id;
 char newSeq[100000];
 char *database;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "gsidMsaToTab - create .tab files from MSA sequence data to DNA and protein .tab files\n"
   "usage:\n"
   "   gsidMsaToTab db seqset\n"
   "      db is the database\n"
   "      seqDataSet is the sequence data set\n"
   "example: gsidMsaToTab hiv1 vax004\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn2;
  
 char query2[256];
 struct sqlResult *sr2;
 char **row2;
 FILE *outf, *outf2;
 
 char *chp, ch, *chp2;
 char outFileNameDna[255];
 char outFileNameAa[255];
 char *seqDataSet;
 int  pos;
 
 if (argc != 3) usage();
 database   = argv[1];
 seqDataSet = argv[2];
 
 conn2= hAllocConn(database);
 
 safef(outFileNameDna, sizeof(outFileNameDna), "%sDnaSeq.tab", seqDataSet);
 safef(outFileNameAa,  sizeof(outFileNameAa),  "%sAaSeq.tmp",  seqDataSet);
 
 outf = mustOpen(outFileNameDna, "w");
 outf2= mustOpen(outFileNameAa,  "w");
 
 /* read in all MSA sequences */
 sqlSafef(query2, sizeof query2, "select id,seq from hiv1.%sMsa", seqDataSet);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     id  = strdup(row2[0]);
     seq = strdup(row2[1]);
     fprintf(outf2, "%s\t", id);
     chp  = seq;
     chp2 = newSeq;
 
     while (*chp != '\0')
 	{
 	/* skip "-" */
 	if (*chp != '-')
 	    {
 	    *chp2 = *chp;
 	    chp2++;
 	    }
 	chp++;
 	}
     *chp2 = '\0';
     
     fprintf(outf, "%s\t%s\n", id, newSeq);
     chp = newSeq;
     pos = 0;
     while (*chp != '\0')
 	{
 	ch = lookupCodon(chp);
 	if (ch == 'X')
 	    {
 	    *(chp+3L)= '\0';
 	    fprintf(stderr, "Invalid codon %s encountered in sequence %s at position %d.\n", chp, id, pos);
 	    }
 	if (ch == 0)
 	    {
 	    *(chp+3L)= '\0';
 	    fprintf(stderr, "Stop codon %s encountered in sequence %s at position %d.\n", chp, id, pos);
 	    }
 	fprintf(outf2, "%c", ch);fflush(stdout);
 	chp++;
 	chp++;
 	chp++;
 	pos = pos+3;
 	}	
     fprintf(outf2, "\n");
     row2 = sqlNextRow(sr2);
     }
 
 fclose(outf);
 fclose(outf2);
 return(0);
 }