Mercurial > repos > bitlab > imsame

comparison IMSAME/src/alignmentFunctions.h @ 0:762009a91895 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bitlab
date Sat, 15 Dec 2018 18:04:10 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:762009a91895
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