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comparison chromeister/src/alignmentFunctions.h @ 0:7fdf47a0bae8 draft

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author alvarofaure
date Wed, 12 Dec 2018 07:18:40 -0500
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-1:000000000000 0:7fdf47a0bae8
1 #define QF_LAMBDA 0.275
2 #define QF_KARLIN 0.333
3
4 typedef struct container{
5 llpos * table[4][4][4][4][4][4][4][4][4][4][4][4];
6 } Container;
7
8 typedef struct index{
9 Tuple_hits table[4][4][4][4][4][4][4][4][4][4][4][4];
10 } Index;
11
12 /*
13 Nucleotides matching function
14 */
15 int64_t compare_letters(unsigned char a, unsigned char b);
16
17 /**
18 * Initialize the memory pool to later retrieve individual memory addresses for llpos
19 *
20 */
21 void init_mem_pool_llpos(Mempool_l * mp);
22
23 /**
24 * Get a new memory address from the pool mp for a type llpos
25 *
26 */
27 llpos * getNewLocationllpos(Mempool_l * mp, uint64_t * n_pools_used);
28
29
30
31 AVLTree * getNewLocationAVLTree(Mempool_AVL * mp, uint64_t * n_pools_used, uint64_t key);
32
33
34 void init_mem_pool_AVL(Mempool_AVL * mp);
35
36
37 AVLTree * right_rotate(AVLTree * y);
38
39 AVLTree * left_rotate(AVLTree * x);
40
41 AVLTree * find_AVLTree(AVLTree * node, uint64_t key);
42
43 llpos * find_AVLTree_llpos(AVLTree * node, uint64_t key);
44
45 AVLTree * insert_AVLTree(AVLTree * node, uint64_t key, Mempool_AVL * mp, uint64_t * n_pools_used, uint64_t pos, Mempool_l * mp_l, uint64_t * n_pools_used_l);
46
47 void pre_order(AVLTree * root);
48
49 uint64_t sum_of_all_tree(AVLTree * root);