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r249: make max overlap error rate CLI options

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Heng Li
2020-05-06 01:16:50 -04:00
parent 331e437c72
commit 3364a29b87
6 changed files with 56 additions and 49 deletions
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Hash_Table.h
-9
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@@ -6,22 +6,13 @@
#define MAX_SUFFIX_BITS 64
#define MODE_VALUE 101
///#define WINDOW 350
///#define THRESHOLD 14
#define WINDOW 375
//#define WINDOW_BOUNDARY 150
#define WINDOW_BOUNDARY 375
///for one side, the first or last WINDOW_UNCORRECT_SINGLE_SIDE_BOUNDARY bases should not be corrected
#define WINDOW_UNCORRECT_SINGLE_SIDE_BOUNDARY 25
#define THRESHOLD 15
#define THRESHOLD_RATE 0.04
#define TAIL_LENGTH int(1/THRESHOLD_RATE)
///#define OVERLAP_THRESHOLD 0.9
#define OVERLAP_THRESHOLD_FILTER 0.9
#define WINDOW_MAX_SIZE WINDOW + TAIL_LENGTH + 3
#define THRESHOLD_MAX_SIZE 31
#define FINAL_OVERLAP_ERROR_RATE 0.03
#define GROUP_SIZE 4
///the max cigar likes 10M10D10M10D10M