106 lines
2.7 KiB
C
106 lines
2.7 KiB
C
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#ifndef BWA_ERT_H
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#define BWA_ERT_H
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#include <stdint.h>
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#include "kvec.h"
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#include "bwa.h"
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#define ERT_MAX_READ_LEN 301
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#define kmerSize 15
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#define numKmers 1073741824
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#define xmerSize 4
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#define numXmers 256
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#define TILE_SIZE 64
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// #define PRINT_SMEM
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#define PREFIX_LENGTH 3
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#define LEP_MASK 0x3FFF
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#define KMER_DATA_BITWIDTH 24
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#define KMER_DATA_MASK 0xFFFF
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#define METADATA_BITWIDTH 2
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#define METADATA_MASK 0x3
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#define INVALID 0
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#define SINGLE_HIT_LEAF 1
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#define INFREQUENT 2
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#define FREQUENT 3
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#define HIT_THRESHOLD 256
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#define DRAM_PAGE_SIZE 24576
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#define LEAF_TBL_BASE_PTR_WIDTH 3
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#define LEAF_TBL_HIT_COUNT_WIDTH 3
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#define MAX_HITS_PER_READ 2000000
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typedef enum
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{
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EMPTY,
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LEAF,
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UNIFORM,
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DIVERGE
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} note_type_t;
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typedef struct _node_t
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{
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note_type_t type;
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int pos;
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int num_bp;
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int l_seq;
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int numChildren;
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uint64_t numHits;
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uint64_t start_addr;
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uint64_t *hits;
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uint8_t seq[ERT_MAX_READ_LEN + 1];
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struct _node_t *parent_node;
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struct _node_t *child_nodes[4];
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} node_t;
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typedef kvec_t(node_t) node_v;
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typedef node_t *node_ptr_t;
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typedef struct
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{
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int tid;
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int step;
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int readLength;
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uint64_t *kmer_table;
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uint64_t startKmer;
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uint64_t endKmer;
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bwaidx_t *bid;
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uint64_t *numHits;
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char *filePrefix;
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uint64_t *byte_offsets;
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uint64_t end_offset;
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} thread_data_t;
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// FIXME : Add to options later
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extern const uint8_t char_count_size_in_bits;
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extern const uint8_t hits_count_size_in_bits;
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extern const uint8_t ref_ptr_size_in_bits;
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extern const uint8_t leaf_offset_ptr_size_in_bits;
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extern const uint8_t other_offset_ptr_size_in_bits;
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typedef enum
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{
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CODE,
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EMPTY_NODE,
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LEAF_COUNT,
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LEAF_HITS,
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UNIFORM_COUNT,
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UNIFORM_BP,
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LEAF_PTR,
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OTHER_PTR
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} byte_type_t;
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void ert_build_kmertree(const bwaidx_t *bid, bwtintv_t ik, bwtintv_t ok[4], int curDepth, node_t *parent_node, int step, int max_depth);
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void handleDivergence(const bwaidx_t *bid, bwtintv_t ok[4], int depth, node_t *parent_node, int step, int max_depth);
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void handleLeaf(const bwaidx_t *bid, bwtintv_t ik, node_t *n, int step);
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void ert_build_table(const bwaidx_t *bid, bwtintv_t ik, bwtintv_t ok[4], uint8_t *mlt_data, uint8_t *mh_data, uint64_t *size, uint64_t *mh_size, uint8_t *aq, uint64_t *numHits, uint64_t *max_next_ptr, uint64_t next_ptr_width, int step, int max_depth);
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void ert_traverse_kmertree(node_t *n, uint8_t *mlt_data, uint8_t *mh_data, uint64_t *byte_idx, uint64_t *mh_byte_idx, int depth, uint64_t *numHits, uint64_t *max_ptr, uint64_t next_ptr_width, int step);
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void ert_destroy_kmertree(node_t *n);
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void buildERTKmerTrees(char *kmer_tbl_file_name, bwaidx_t *bid, char *prefix, int num_threads, int readLength);
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#endif
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