--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chromeister/src/structs.h	Thu Dec 13 06:27:57 2018 -0500
@@ -0,0 +1,143 @@
+#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 //50MB
+#define INITSEQS 3000 //Number of starting sequences (in database)
+#define POINT 4
+
+#define FIXED_K 12
+#define TOTAL_ENTRIES 16777216
+
+#define MAXLID 200
+#define ALIGN_LEN 60 //For NW alignment
+#define MAX_READ_SIZE 20000 //Maximum length of read to have a portion of the table allocated
+#define MAX_WINDOW_SIZE 500 //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 256 
+
+#define BYTES_IN_MER 4
+#define MAX_DECOMP_HASH 10
+#define FALSE 0
+#define TRUE 1
+
+#define MAX(x, y) (((x) > (y)) ? (x) : (y))
+#define MIN(x, y) (((x) <= (y)) ? (x) : (y))
+
+extern uint64_t custom_kmer;
+extern uint64_t diffuse_z;
+
+//Struct for linked list of positions
+typedef struct linked_list_pos{
+    uint64_t pos;
+    //uint64_t extended_hash;
+    //unsigned char decomp_hash[MAX_DECOMP_HASH]; // Fits up to MAX_DECOMP_HASH*4 letters = 256 length kmer
+    //uint64_t hits_count;
+    struct linked_list_pos * next;
+} llpos;
+
+
+// An AVL tree node
+typedef struct AVL_Node{
+    uint64_t key;
+    struct AVL_Node * left;
+    struct AVL_Node * right;
+    uint64_t height;
+    uint64_t count;
+    llpos * next;
+} AVLTree;
+
+
+// Tuple of data 
+typedef struct tuple_hits{
+    int repetition;
+    int hit_count;
+    uint64_t key;
+    uint64_t pos;
+    uint64_t pos_in_y;
+} Tuple_hits;
+
+typedef struct hash_holder{
+    uint64_t key;
+    uint64_t pos;
+} Hash_holder;
+
+
+
+//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;
+
+
+
+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