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/lib/scoreWindow.c src/lib/scoreWindow.c
index 41ee994..3b0a439 100644
--- src/lib/scoreWindow.c
+++ src/lib/scoreWindow.c
@@ -1,51 +1,51 @@
 /* scoreWindow - find window with most matches to a given char */
 
 /* Copyright (C) 2011 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"
 
 
 int scoreWindow(char c, char *s, int size, int *score, int *start, int *end, int match, int misMatch)
 /* simple program to find max scoring window representing string of char c in a string s of size size */
 /* index of max score is returned , match and misMatch are the scores to assign, suggested defaults are match=1 and misMatch=1*/
 /* when used for scoring polyA tails, set c='A' for positive strand  or c='T' for neg strand */
 /* start, end are returned pointing to the start and end of the highest scoring window in s */
 {
 int i=0, j=0, max=0, count = 0; 
 
 *end = 0;
 
 for (i=0 ; i<size ; i++)
     {
     int prevScore = (i > 0) ? score[i-1] : 0;
 
     if (toupper(s[i]) == toupper(c) )
         score[i] = prevScore+match;
     else
         score[i] = prevScore-misMatch;
     if (score[i] >= max)
         {
         max = score[i];
         *end = i;
         /* traceback to find start */
         for (j=i ; j>=0 ; j--)
             if (score[j] == 0)
                 {
                 *start = j+1;
                 break;
                 }
         }
     if (score[i] < 0) 
         score[i] = 0;
     }
 assert (*end < size);
 
 for (i=*start ; i<=*end ; i++)
     {
     assert (i < size);
     if (toupper(s[i]) == toupper(c) )
         count++;
     }
 return count;
 }