--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IMSAME/src/alignmentFunctions.h	Sat Dec 15 18:04:10 2018 -0500
@@ -0,0 +1,136 @@
+#define QF_LAMBDA 0.275
+#define QF_KARLIN 0.333
+
+
+
+typedef struct {
+    uint64_t id;        //The thread id
+    SeqInfo * database; //Database sequence and lengths
+    SeqInfo * query;    //Query sequence and lengths
+    uint64_t from;      //Starting READ to compute alignments from
+    uint64_t to;        //End READ to compute alignments from
+    AVLContainer * container_a; //Container to hold the multidimensional array
+    AVLContainer * container_b; //Container to hold the multidimensional array
+    AVLContainer * container_c; //Container to hold the multidimensional array
+    AVLContainer * container_d; //Container to hold the multidimensional array
+    uint64_t * contained_reads;
+    uint64_t * base_coordinates;
+    uint64_t accepted_query_reads; //Number of reads that have a fragment with evalue less than specified
+    long double min_e_value;    //Minimum evalue to accept read
+    long double min_coverage;    //Minimum coverage percentage to accept read
+    long double min_identity;    //Minimum identity percentage to accept read
+    long double window;         //Percentage of window that will be explored (+-)
+    FILE * out; //File to write alignments out
+    int igap;
+    int egap;
+    uint64_t * hits;        // To work in hits mode only
+    struct positioned_cell * mc;
+    struct cell ** table;
+    char * reconstruct_X;
+    char * reconstruct_Y;
+    char * writing_buffer_alignment;
+    unsigned char * my_x;
+    unsigned char * my_y;
+    Head * queue_head;  //To tell where the queue starts after modifications
+    pthread_mutex_t * lock;
+    unsigned char full_comp; // Tells whether read reporting should stop at first match or keep reporting
+    unsigned char * markers; // To tell which sequences were already used
+} HashTableArgs;
+
+
+
+/*
+    Nucleotides matching function
+*/
+int64_t compare_letters(unsigned char a, unsigned char b);
+
+/**
+ * Initialize the memory pool to later retrieve individual memory addresses for llpos
+ * 
+ */
+void init_mem_pool_llpos(Mempool_l * mp);
+
+/**
+ * Get a new memory address from the pool mp for a type llpos
+ * 
+ */
+llpos * getNewLocationllpos(Mempool_l * mp, uint64_t * n_pools_used);
+
+/*
+    Load input database using 4 threads
+*/
+void * load_input(void * a);
+/*
+    Compute alignments by thread given a hash table argument
+*/
+void * computeAlignmentsByThread(void * a);
+
+
+/*
+    Performs NW and backtracking to recover alignment
+*/
+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);
+
+/*
+    Compute the alignment and evalue of a given hit
+    The positions pos_database and pos_query refer to the last match in the hit
+*/
+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);
+
+/*
+    Computes the cell path for the y points given incremental x
+    Only add +- window size to each to know which path to go through
+*/
+void calculate_y_cell_path(Point p0, Point p1, Point p2, Point p3, int64_t * cell_path_y);
+/*
+    Calculates NW table with two rows and stores a cellpath of scores, identities, gaps and starting and ending positions
+*/
+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);
+
+/*
+    Computes the alignment given a NW table
+*/
+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);
+
+/*
+    Get memory for a new AVL tree node
+*/
+AVLTree * getNewLocationAVLTree(Mempool_AVL * mp, uint64_t * n_pools_used, uint64_t key);
+
+/*
+    Initialize a memory pool for AVL trees
+*/
+void init_mem_pool_AVL(Mempool_AVL * mp);
+
+/*
+    Right rotate an AVL tree to make it balanced
+*/
+AVLTree * right_rotate(AVLTree * y);
+
+/*
+    Left rotate an AVL tree to make it balanced
+*/
+AVLTree * left_rotate(AVLTree * x);
+
+
+/*
+    Find a key in an AVL tree
+*/
+AVLTree * find_AVLTree(AVLTree * node, uint64_t key);
+
+/*
+    Find a key in an AVL tree but return its hit list
+*/
+llpos * find_AVLTree_llpos(AVLTree * node, uint64_t key);
+
+/*
+    Insert node in AVL tree
+*/
+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);
+
+/*
+    Traverse AVL tree in pre order
+*/
+void pre_order(AVLTree * root);
+
+