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comparison chromeister/src/structs.h @ 0:ee6b15b409e5 draft

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author bitlab
date Thu, 13 Dec 2018 06:27:57 -0500
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-1:000000000000 0:ee6b15b409e5
1 #ifndef STRUCTS_H
2 #define STRUCTS_H
3
4 #include <inttypes.h>
5
6 //Structs required for the dotplot workflow
7 #define MAXLID 200
8 //#define READBUF 2000000000 //2 GB
9 #define READBUF 500000000 //50MB
10 #define INITSEQS 3000 //Number of starting sequences (in database)
11 #define POINT 4
12
13 #define FIXED_K 12
14 #define TOTAL_ENTRIES 16777216
15
16 #define MAXLID 200
17 #define ALIGN_LEN 60 //For NW alignment
18 #define MAX_READ_SIZE 20000 //Maximum length of read to have a portion of the table allocated
19 #define MAX_WINDOW_SIZE 500 //Maximum window length to explore NW table
20 //#define POOL_SIZE 2500000000 // by 16 bytes it is 40 GB
21 #define POOL_SIZE 12500000 // 1 GB if 16 bytes
22 #define MAX_MEM_POOLS 256
23
24 #define BYTES_IN_MER 4
25 #define MAX_DECOMP_HASH 10
26 #define FALSE 0
27 #define TRUE 1
28
29 #define MAX(x, y) (((x) > (y)) ? (x) : (y))
30 #define MIN(x, y) (((x) <= (y)) ? (x) : (y))
31
32 extern uint64_t custom_kmer;
33 extern uint64_t diffuse_z;
34
35 //Struct for linked list of positions
36 typedef struct linked_list_pos{
37 uint64_t pos;
38 //uint64_t extended_hash;
39 //unsigned char decomp_hash[MAX_DECOMP_HASH]; // Fits up to MAX_DECOMP_HASH*4 letters = 256 length kmer
40 //uint64_t hits_count;
41 struct linked_list_pos * next;
42 } llpos;
43
44
45 // An AVL tree node
46 typedef struct AVL_Node{
47 uint64_t key;
48 struct AVL_Node * left;
49 struct AVL_Node * right;
50 uint64_t height;
51 uint64_t count;
52 llpos * next;
53 } AVLTree;
54
55
56 // Tuple of data
57 typedef struct tuple_hits{
58 int repetition;
59 int hit_count;
60 uint64_t key;
61 uint64_t pos;
62 uint64_t pos_in_y;
63 } Tuple_hits;
64
65 typedef struct hash_holder{
66 uint64_t key;
67 uint64_t pos;
68 } Hash_holder;
69
70
71
72 //Struct for memory pool por lists
73 typedef struct mempool_l{
74 llpos * base;
75 uint64_t current;
76 } Mempool_l;
77
78 //Struct for memory pool por AVLtree
79 typedef struct mempool_AVL{
80 AVLTree * base;
81 uint64_t current;
82 } Mempool_AVL;
83
84 //Struct for a whole sequence(s) data
85 typedef struct seqinfo{
86 unsigned char * sequences;
87 uint64_t * start_pos;
88 uint64_t total_len;
89 uint64_t n_seqs;
90 } SeqInfo;
91
92 //Struct for the alignment of a quick hit
93 typedef struct quickfrag{
94 uint64_t x_start;
95 uint64_t y_start;
96 uint64_t t_len;
97 long double coverage;
98 long double e_value;
99 } Quickfrag;
100
101 typedef struct point{
102 uint64_t x;
103 uint64_t y;
104 } Point;
105
106
107
108 struct cell{
109 int64_t score;
110 uint64_t xfrom;
111 uint64_t yfrom;
112 };
113
114 struct positioned_cell{
115 int64_t score;
116 uint64_t xpos;
117 uint64_t ypos;
118 };
119
120 struct best_cell{
121 struct positioned_cell c;
122 uint64_t j_prime;
123 };
124
125 typedef struct{
126 uint64_t identities;
127 uint64_t length;
128 uint64_t igaps;
129 uint64_t egaps;
130 } BasicAlignment;
131
132 typedef struct queue{
133 uint64_t r1; //reads region
134 uint64_t r2;
135 struct queue * next;
136 } Queue;
137
138 typedef struct{
139 Queue * head;
140 } Head;
141
142
143 #endif