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/inc/borf.h src/hg/inc/borf.h
index b7818e8..a5c4a49 100644
--- src/hg/inc/borf.h
+++ src/hg/inc/borf.h
@@ -1,90 +1,90 @@
 /* borf.h was originally generated by the autoSql program, which also 
  * generated borf.c and borf.sql.  This header links the database and
  * the RAM representation of objects. */
 
 /* Copyright (C) 2008 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. */
 
 #ifndef BORF_H
 #define BORF_H
 
 #ifndef JKSQL_H
 #include "jksql.h"
 #endif
 
 #ifndef BED_H
 #include "bed.h"
 #endif
 
 #define BORF_NUM_COLS  12  /* number of columns in a borf */
 
 struct borf
 /* Parsed output from Victor Solovyev's bestorf program */
     {
     struct borf *next;  /* Next in singly linked list. */
     char *name;	/* Name of mRNA */
     int size;	/* Size of mRNA */
     char strand[2];	/* + or - */
     char *feature;	/* Feature name - Always seems to be CDSo */
     int cdsStart;	/* Start of cds (starting with 0) */
     int cdsEnd;	/* End of cds (non-exclusive) */
     float score;	/* A score of 50 or more is decent */
     int orfStart;	/* Start of orf (not always same as CDS) */
     int orfEnd;	/* Start of orf (not always same as CDS) */
     int cdsSize;	/* Size of cds in bases */
     char frame[4];	/* Seems to be +1, +2, +3 or -1, -2, -3 */
     char *protein;	/* Predicted protein */
     };
 
 void borfStaticLoad(char **row, struct borf *ret);
 /* Load a row from borf table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 
 struct borf *borfLoad(char **row);
 /* Load a borf from row fetched with select * from borf
  * from database.  Dispose of this with borfFree(). */
 
 struct borf *borfLoadAll(char *fileName);
 /* Load all borf from a tab-separated file.
  * Dispose of this with borfFreeList(). */
 
 struct borf *borfLoadWhere(struct sqlConnection *conn, char *table, char *where);
 /* Load all borf from table that satisfy where clause. The
  * where clause may be NULL in which case whole table is loaded
  * Dispose of this with borfFreeList(). */
 
 struct borf *borfCommaIn(char **pS, struct borf *ret);
 /* Create a borf out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new borf */
 
 void borfFree(struct borf **pEl);
 /* Free a single dynamically allocated borf such as created
  * with borfLoad(). */
 
 void borfFreeList(struct borf **pList);
 /* Free a list of dynamically allocated borf's */
 
 void borfOutput(struct borf *el, FILE *f, char sep, char lastSep);
 /* Print out borf.  Separate fields with sep. Follow last field with lastSep. */
 
 #define borfTabOut(el,f) borfOutput(el,f,'\t','\n');
 /* Print out borf as a line in a tab-separated file. */
 
 #define borfCommaOut(el,f) borfOutput(el,f,',',',');
 /* Print out borf as a comma separated list including final comma. */
 
 /*------------ End AutoSql generated code. -------------------*/
 
 struct borf *borfFromBestorfOutput(char *fileName);
 /* Convert bestorf output to borf structure. */
 
 struct borf *borfFromGenomeBed(char *db, struct bed *bed);
 /* borfBig - Run Victor Solovyev's bestOrf on a genome bed's coordinates. */
 
 void borfSetExeAndParam(char *exePath, char *paramPath);
 /* Set the path to the bestOrf probram and parameter file to be used
    for running borfFromGenomeBed. */
 
 #endif /* BORF_H */