blat: inc/scoreWindow.h Source File

00001 /* scoreWindow - find window with most matches to a given char */
00002 
00003 /* simple program to find max scoring window representing string of char c in a string s of size size */
00004 /* index of max score is returned , match and misMatch are the scores to assign, suggested defaults are match=1 and misMatch=1*/
00005 /* when used for scoring polyA tails, set c='A' for positive strand  or c='T' for neg strand */
00006 /* start, end are returned pointing to the start and end of the highest scoring window in s */
00007 int scoreWindow(char c, char *s, int size, int *score, int *start, int *end, int match, int misMatch);