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/txGraph/txAbFragFind/txAbFragFind.c src/hg/txGraph/txAbFragFind/txAbFragFind.c
index 8cadcd9..02674e1 100644
--- src/hg/txGraph/txAbFragFind/txAbFragFind.c
+++ src/hg/txGraph/txAbFragFind/txAbFragFind.c
@@ -1,99 +1,99 @@
 /* txAbFragFind - Search database for what are probably antibody fragments.. */
 
 /* 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 "options.h"
 #include "jksql.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "txAbFragFind - Search database for what are probably antibody fragments.\n"
   "usage:\n"
   "   txAbFragFind database outputAccessions\n"
   "options:\n"
   "   -xxx=XXX\n"
   );
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 void txAbFragFind(char *database, char *output)
 /* txAbFragFind - Search database for what are probably antibody fragments.. */
 {
 FILE *f = mustOpen(output, "w");
 struct sqlConnection *conn =  sqlConnect(database);
 struct sqlResult *sr = sqlGetResult(conn, NOSQLINJ "select id,name from description");
 char **row;
 struct hash *descriptionIdHash = hashNew(18);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     char *id = row[0];
     char *description = row[1];
     tolowers(description);
     if (stringIn("immunoglobulin", description) && stringIn("chain", description))
         {
 	if (stringIn("variable", description) || stringIn("vdj", description) || 
 	    stringIn("vlj", description) || stringIn("vhdj", description) ||
 	    stringIn("v region", description) || stringIn("vj region", description) ||
 	    stringIn("v-region", description) || stringIn("v-j-c region", description) ||
 	    stringIn("v-d-j", description) || stringIn("rearrange", description) ||
 	    stringIn("v-d-t region", description) || stringIn("v-j region", description) || 
 	    stringIn("v-d-c region", description) || stringIn("kappa chain (igk) mrna, vk", description) ||
 	    stringIn("partial mrna for immunoglobulin", description) ||
 	    stringIn("nonfunctional immunoglobulin", description) || 
 	    stringIn("kappa light chain (igvk-a", description) ||
 	    stringIn("heavy chain complementarity-determining region 3", description) ||
 	    stringIn("chain mrna, partial cds", description) ||
 	    endsWith(description, "immunoglobulin mu heavy chain-like mrna, partial sequence.") ||
 	    endsWith(description, "immunoglobulin mu heavy chain mrna, partial sequence.") ||
 	    endsWith(description, "nonfunctional immunoglobulin heavy chain mrna, partial sequence.") ||
 	    endsWith(description, "fab mrna, partial cds.") ||
 	    endsWith(description, "immunoglobulin e heavy chain (ige) mrna, partial cds."))
 	    {
 	    hashAdd(descriptionIdHash, id, NULL);
 	    verbose(2, "adding %s\n", description);
 	    }
 	else
 	    {
 	    verbose(2, "skipping %s\n", description);
 	    }
 	}
     }
 sqlFreeResult(&sr);
 verbose(1, "Found %d descriptions that match\n", descriptionIdHash->elCount);
 
 int totalCount = 0;
 int matchCount = 0;
 sr = sqlGetResult(conn, NOSQLINJ "select description,acc from gbCdnaInfo where type='mRNA'");
 while ((row = sqlNextRow(sr)) != NULL)
     {
     ++totalCount;
     if (hashLookup(descriptionIdHash, row[0]))
 	{
 	fprintf(f, "%s\n", row[1]);
 	++matchCount;
 	}
     }
 sqlFreeResult(&sr);
 verbose(1, "Matched %d of %d accessions to antibody criteria\n", matchCount, totalCount);
 
 sqlDisconnect(&conn);
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 txAbFragFind(argv[1], argv[2]);
 return 0;
 }