Mercurial > repos > bitlab > imsame
comparison IMSAME/src/alignmentFunctions.h @ 0:762009a91895 draft
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author | bitlab |
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date | Sat, 15 Dec 2018 18:04:10 -0500 |
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-1:000000000000 | 0:762009a91895 |
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1 #define QF_LAMBDA 0.275 | |
2 #define QF_KARLIN 0.333 | |
3 | |
4 | |
5 | |
6 typedef struct { | |
7 uint64_t id; //The thread id | |
8 SeqInfo * database; //Database sequence and lengths | |
9 SeqInfo * query; //Query sequence and lengths | |
10 uint64_t from; //Starting READ to compute alignments from | |
11 uint64_t to; //End READ to compute alignments from | |
12 AVLContainer * container_a; //Container to hold the multidimensional array | |
13 AVLContainer * container_b; //Container to hold the multidimensional array | |
14 AVLContainer * container_c; //Container to hold the multidimensional array | |
15 AVLContainer * container_d; //Container to hold the multidimensional array | |
16 uint64_t * contained_reads; | |
17 uint64_t * base_coordinates; | |
18 uint64_t accepted_query_reads; //Number of reads that have a fragment with evalue less than specified | |
19 long double min_e_value; //Minimum evalue to accept read | |
20 long double min_coverage; //Minimum coverage percentage to accept read | |
21 long double min_identity; //Minimum identity percentage to accept read | |
22 long double window; //Percentage of window that will be explored (+-) | |
23 FILE * out; //File to write alignments out | |
24 int igap; | |
25 int egap; | |
26 uint64_t * hits; // To work in hits mode only | |
27 struct positioned_cell * mc; | |
28 struct cell ** table; | |
29 char * reconstruct_X; | |
30 char * reconstruct_Y; | |
31 char * writing_buffer_alignment; | |
32 unsigned char * my_x; | |
33 unsigned char * my_y; | |
34 Head * queue_head; //To tell where the queue starts after modifications | |
35 pthread_mutex_t * lock; | |
36 unsigned char full_comp; // Tells whether read reporting should stop at first match or keep reporting | |
37 unsigned char * markers; // To tell which sequences were already used | |
38 } HashTableArgs; | |
39 | |
40 | |
41 | |
42 /* | |
43 Nucleotides matching function | |
44 */ | |
45 int64_t compare_letters(unsigned char a, unsigned char b); | |
46 | |
47 /** | |
48 * Initialize the memory pool to later retrieve individual memory addresses for llpos | |
49 * | |
50 */ | |
51 void init_mem_pool_llpos(Mempool_l * mp); | |
52 | |
53 /** | |
54 * Get a new memory address from the pool mp for a type llpos | |
55 * | |
56 */ | |
57 llpos * getNewLocationllpos(Mempool_l * mp, uint64_t * n_pools_used); | |
58 | |
59 /* | |
60 Load input database using 4 threads | |
61 */ | |
62 void * load_input(void * a); | |
63 /* | |
64 Compute alignments by thread given a hash table argument | |
65 */ | |
66 void * computeAlignmentsByThread(void * a); | |
67 | |
68 | |
69 /* | |
70 Performs NW and backtracking to recover alignment | |
71 */ | |
72 void build_alignment(char * reconstruct_X, char * reconstruct_Y, uint64_t curr_db_seq, uint64_t curr_read, HashTableArgs * hta, unsigned char * my_x, unsigned char * my_y, struct cell ** table, struct positioned_cell * mc, char * writing_buffer_alignment, BasicAlignment * ba, uint64_t xlen, uint64_t ylen, int64_t * cell_path_y, long double * window); | |
73 | |
74 /* | |
75 Compute the alignment and evalue of a given hit | |
76 The positions pos_database and pos_query refer to the last match in the hit | |
77 */ | |
78 void alignmentFromQuickHits(SeqInfo * database, SeqInfo * query, uint64_t pos_database, uint64_t pos_query, uint64_t curr_read, uint64_t curr_db_seq, Quickfrag * qf, uint64_t offset_db_reads, uint64_t offset_db_coordinates); | |
79 | |
80 /* | |
81 Computes the cell path for the y points given incremental x | |
82 Only add +- window size to each to know which path to go through | |
83 */ | |
84 void calculate_y_cell_path(Point p0, Point p1, Point p2, Point p3, int64_t * cell_path_y); | |
85 /* | |
86 Calculates NW table with two rows and stores a cellpath of scores, identities, gaps and starting and ending positions | |
87 */ | |
88 struct best_cell NW(unsigned char * X, uint64_t Xstart, uint64_t Xend, unsigned char * Y, uint64_t Ystart, uint64_t Yend, int64_t iGap, int64_t eGap, struct cell ** table, struct positioned_cell * mc, int show, int64_t * cell_path_y, long double * window, uint64_t * curr_window_size); | |
89 | |
90 /* | |
91 Computes the alignment given a NW table | |
92 */ | |
93 void backtrackingNW(unsigned char * X, uint64_t Xstart, uint64_t Xend, unsigned char * Y, uint64_t Ystart, uint64_t Yend, struct cell ** table, char * rec_X, char * rec_Y, struct best_cell * bc, uint64_t * ret_head_x, uint64_t * ret_head_y, BasicAlignment * ba, int64_t * cell_path_y, uint64_t window_size); | |
94 | |
95 /* | |
96 Get memory for a new AVL tree node | |
97 */ | |
98 AVLTree * getNewLocationAVLTree(Mempool_AVL * mp, uint64_t * n_pools_used, uint64_t key); | |
99 | |
100 /* | |
101 Initialize a memory pool for AVL trees | |
102 */ | |
103 void init_mem_pool_AVL(Mempool_AVL * mp); | |
104 | |
105 /* | |
106 Right rotate an AVL tree to make it balanced | |
107 */ | |
108 AVLTree * right_rotate(AVLTree * y); | |
109 | |
110 /* | |
111 Left rotate an AVL tree to make it balanced | |
112 */ | |
113 AVLTree * left_rotate(AVLTree * x); | |
114 | |
115 | |
116 /* | |
117 Find a key in an AVL tree | |
118 */ | |
119 AVLTree * find_AVLTree(AVLTree * node, uint64_t key); | |
120 | |
121 /* | |
122 Find a key in an AVL tree but return its hit list | |
123 */ | |
124 llpos * find_AVLTree_llpos(AVLTree * node, uint64_t key); | |
125 | |
126 /* | |
127 Insert node in AVL tree | |
128 */ | |
129 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, uint64_t s_id); | |
130 | |
131 /* | |
132 Traverse AVL tree in pre order | |
133 */ | |
134 void pre_order(AVLTree * root); | |
135 | |
136 |