Mercurial > repos > bitlab > imsame
view IMSAME/src/alignmentFunctions.h @ 4:7430449b8814 draft
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author | bitlab |
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date | Mon, 17 Dec 2018 12:20:17 -0500 |
parents | 762009a91895 |
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#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);