--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chromeister/src/alignmentFunctions.h	Wed Dec 12 07:18:40 2018 -0500
@@ -0,0 +1,49 @@
+#define QF_LAMBDA 0.275
+#define QF_KARLIN 0.333
+
+typedef struct container{
+    llpos * table[4][4][4][4][4][4][4][4][4][4][4][4];
+} Container;
+
+typedef struct index{
+    Tuple_hits table[4][4][4][4][4][4][4][4][4][4][4][4];
+} Index;
+
+/*
+    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);
+
+
+
+AVLTree * getNewLocationAVLTree(Mempool_AVL * mp, uint64_t * n_pools_used, uint64_t key);
+
+
+void init_mem_pool_AVL(Mempool_AVL * mp);
+
+
+AVLTree * right_rotate(AVLTree * y);
+
+AVLTree * left_rotate(AVLTree * x);
+
+AVLTree * find_AVLTree(AVLTree * node, uint64_t key);
+
+llpos * find_AVLTree_llpos(AVLTree * node, uint64_t key);
+
+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);
+
+void pre_order(AVLTree * root);
+
+uint64_t sum_of_all_tree(AVLTree * root);