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/makeDb/tfbsConsLoc/tfbsConsLoc.h src/hg/makeDb/tfbsConsLoc/tfbsConsLoc.h
index 9fb9a80..a6ba0d3 100644
--- src/hg/makeDb/tfbsConsLoc/tfbsConsLoc.h
+++ src/hg/makeDb/tfbsConsLoc/tfbsConsLoc.h
@@ -1,77 +1,77 @@
 /* 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. */
 
 #ifndef TFLOC
 #define TFLOC
 
 #include "matt-maf.h"
 #include "util.h"
 
 /* array indices for each nucleotide */
 #define rowA 0 
 #define rowC 1
 #define rowG 2
 #define rowT 3
 
 /* output modes */
 #define VERBOSE 0
 #define GALA 1
 #define HGB 2
 
 /* strands */
 #define FORWARD 0
 #define REVERSE 1
 
 /* other constants */
 #define BUFSIZE sizeof (char) * 100
 #define STRSIZE sizeof (char) * 70
 #define ACSIZE 7
 #define MAXSUBMATLEN 50
 #define DEFAULT_CUTOFF 0.85
 #define DEFAULT_NROW 3
 #define BAR "=================================================================="
 #define SYNTAX "USAGE:  tfloc [-verbose | -gala | -hgb] maf_file transfac_file id [-order] [-cut CUTOFF] [-nseq NUM_SEQS_IN_ALIGNMENT] [-nm NUM_MISSES]"
 
 
 
 /* one match in a list of matches to one motif */
 struct MATCH
 {
     int col;		/* its column in this alignment */
     int lowest_score;	/* lowest score out of all seqs in the alignment */
     int pos;		/* position of motif in human seq */
     int dir;		/* FORWARD or REVERSE */
     struct MATCH *next;	/* next match in the list */
 };
 
 /* one transcription factor binding site in a list of all in the pattern */
 struct MOTIF
 {
     int len;		/* length of motif */
     char *name;		/* name of motif */
     char *id;		/* motif id */
     float threshold;	/* threshold score to count as a hit */
     int min;		/* minimum possible score */
     int max;		/* maximum possible score */
     int **submat;	/* substitution matrix */
     struct MOTIF *next;	/* should be NULL */
 };
 
 void add_to_matches (struct MATCH **matches, int col, 
 			    int seq, int *score, int nrow, struct mafAli *ali, int len, int dir, int do_order);
 void get_args (int argc, char **argv, int *output_mode, struct mafFile **file, char **id,
                       struct MOTIF **motif, int *do_order, int *nrow, float *cutoff, int *num_misses);
 int get_max_score( int **submat, int length);    
 int get_min_score( int **submat, int length);    
 int get_pos (int start, int col, char strand, int size, char *text, int motif_len, int dir);
 int get_score (int **submat, char seq_char, int col);
 void get_matches (struct MATCH **matches, int dir,
 			 struct mafAli *ali, int nrow, struct MOTIF *motif,
 			 int do_order, int num_misses);
 void init_motif (struct MOTIF **motif, char *fileName, float cutoff, 
 			char *id);
 int motif_hit (char *text, int col, struct MOTIF *cur_motif, int *score);
 void output_matches (struct MATCH *matches, char *strand, char *id, int nrow, struct MOTIF *motif);
 void print_strand (const char *strand, int dir, int nrow);
 
 #endif