--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IMSAME/src/structs.h	Sat Dec 15 18:04:10 2018 -0500
@@ -0,0 +1,144 @@
+#ifndef STRUCTS_H
+#define STRUCTS_H
+
+#include <inttypes.h>
+
+//Structs required for the dotplot workflow
+#define MAXLID 200
+//#define READBUF 2000000000 //2 GB
+#define READBUF 500000000 //500MB
+#define INITSEQS 3000 //Number of starting sequences (in database)
+#define POINT 4
+
+#define FIXED_K 12
+
+#define MAXLID 200
+#define ALIGN_LEN 60 //For NW alignment
+#define MAX_READ_SIZE 10000 //Maximum length of read to have a portion of the table allocated
+#define MAX_WINDOW_SIZE 1000 //Maximum window length to explore NW table
+//#define POOL_SIZE 2500000000 // by 16 bytes it is 40 GB
+#define POOL_SIZE 12500000 // 1 GB if 16 bytes
+#define MAX_MEM_POOLS 128 
+#define FIXED_LOADING_THREADS 4
+
+#define FALSE 0
+#define TRUE 1
+
+extern uint64_t custom_kmer;
+
+typedef char _vector_char __attribute__ ((vector_size (32*sizeof(char))));
+
+//Struct for linked list of positions
+typedef struct linked_list_pos{
+    uint64_t pos;
+    uint64_t s_id;
+    //uint64_t extended_hash;
+    struct linked_list_pos * next;
+} llpos;
+
+typedef struct AVL_Node{
+    uint64_t key;
+    struct AVL_Node * left;
+    struct AVL_Node * right;
+    uint64_t height;
+    uint64_t count;
+    llpos * next;
+} AVLTree;
+
+//Struct for memory pool por lists
+typedef struct mempool_l{
+    llpos * base;
+    uint64_t current;
+} Mempool_l;
+
+//Struct for memory pool por AVLtree
+typedef struct mempool_AVL{
+    AVLTree * base;
+    uint64_t current;
+} Mempool_AVL;
+
+
+//Struct for a whole sequence(s) data
+typedef struct seqinfo{
+    unsigned char * sequences;
+    uint64_t * start_pos;
+    uint64_t total_len;
+    uint64_t n_seqs;
+} SeqInfo;
+
+//Struct for the alignment of a quick hit
+typedef struct quickfrag{
+    uint64_t x_start;
+    uint64_t y_start;
+    uint64_t t_len;
+    long double coverage;
+    long double e_value;
+} Quickfrag;
+
+typedef struct point{
+    uint64_t x;
+    uint64_t y;
+} Point;
+
+typedef struct container{
+    llpos * table[4][4][4][4][4][4][4][4][4][4][4]; // One reduced; A,C,G,T tables in use
+} Container;
+
+typedef struct AVLcontainer{
+    AVLTree root[4][4][4][4][4][4][4][4][4][4][4];
+} AVLContainer;
+
+typedef struct{
+    char * temp_seq_buffer;
+    SeqInfo * data_database;
+    uint64_t t_len;
+    uint64_t word_size;
+    uint64_t read_from;
+    uint64_t read_to;
+    uint64_t contained_reads;
+    uint64_t base_coordinates;
+    uint64_t n_allocs;
+    char thread_id;
+    AVLContainer * ct;
+    Mempool_l * mp;
+    uint64_t n_pools_used;
+    uint64_t n_pools_used_AVL;
+    Mempool_AVL * mp_AVL;
+} LoadingDBArgs;
+
+struct cell{
+    int64_t score;
+    uint64_t xfrom;
+    uint64_t yfrom;
+};
+
+struct positioned_cell{
+    int64_t score;
+    uint64_t xpos;
+    uint64_t ypos;
+};
+
+struct best_cell{
+    struct positioned_cell c;
+    uint64_t j_prime;
+};
+
+typedef struct{
+    uint64_t identities;
+    uint64_t length;
+    uint64_t igaps;
+    uint64_t egaps;
+} BasicAlignment;
+
+typedef struct queue{
+    uint64_t r1; //reads region
+    uint64_t r2;
+    struct queue * next;
+} Queue;
+
+typedef struct{
+    Queue * head;
+} Head;
+
+
+#endif