139 lines
4.4 KiB
C
139 lines
4.4 KiB
C
/* The MIT License
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Copyright (c) 2018- Dana-Farber Cancer Institute
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2009-2018 Broad Institute, Inc.
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2008-2009 Genome Research Ltd. (GRL)
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
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BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
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ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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*/
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#ifndef BWA_H_
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#define BWA_H_
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#include <stdint.h>
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#include "bntseq.h"
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#include "kstring.h"
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#include "bwt.h"
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#include "fmt_idx.h"
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#include "kvec.h"
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#include "ksw.h"
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#include "ksw_align_avx.h"
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#include "mate_sw.h"
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#define BWA_IDX_BWT 0x1
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#define BWA_IDX_BNS 0x2
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#define BWA_IDX_PAC 0x4
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#define BWA_IDX_FMT 0x8
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#define BWA_IDX_ALL 0xF
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#define BWA_CTL_SIZE 0x10000
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#define BWTALGO_AUTO 0
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#define BWTALGO_RB2 1
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#define BWTALGO_BWTSW 2
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#define BWTALGO_IS 3
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#define BWA_DBG_QNAME 0x1
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typedef struct {
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bwt_t *bwt; // FM-index
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FMTIndex *fmt;// FMT-index
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bntseq_t *bns; // information on the reference sequences
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uint8_t *pac; // the actual 2-bit encoded reference sequences with 'N' converted to a random base
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int is_shm;
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int64_t l_mem;
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uint8_t *mem;
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} bwaidx_t;
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#if 0
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// 需要做mate sw的read
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typedef struct {
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int is_rev; // seq是否在反向互补链上
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int xtra;
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int64_t rb, re; // ref的起始截止位置，左闭右开
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int64_t seq_id; // 对应的当前数据块的seq id
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kswr_avx_t aln;
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} matesw_data_t;
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typedef struct {
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size_t n, m;
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matesw_data_t* a;
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} matesw_data_v;
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typedef kvec_t(matesw_data_t*) matesw_ptr_v;
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#endif
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typedef struct {
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int l_seq, id;
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int m_name, m_comment, m_seq, m_qual;
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char *name, *comment, *seq, *qual;
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// msw_task_ptr_v msw;
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msw_seq_task_v msw_task;
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// int_v msw;
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// kstring_t sam;
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} bseq1_t;
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typedef struct {
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kstring_t sam;
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} seq_sam_t;
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extern int bwa_verbose, bwa_dbg;
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extern char bwa_rg_id[256];
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#ifdef __cplusplus
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extern "C" {
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#endif
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//bseq1_t *bseq_read(int chunk_size, int *n_, void *ks1_, void *ks2_);
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void bseq_read(int chunk_size, int *n_, void *ks1_, void *ks2_, int copy_comment, int64_t *size_, int *m_, bseq1_t **seqs_ptr);
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void bseq_classify(int n, bseq1_t *seqs, int m[2], bseq1_t *sep[2]);
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void bwa_fill_scmat(int a, int b, int8_t mat[25]);
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uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM);
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uint32_t *bwa_gen_cigar2(const int8_t mat[25], int o_del, int e_del, int o_ins, int e_ins, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM);
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int bwa_idx_build(const char *fa, const char *prefix, int algo_type, int block_size);
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char *bwa_idx_infer_prefix(const char *hint);
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bwt_t *bwa_idx_load_bwt(const char *hint);
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bwaidx_t *bwa_idx_load_from_shm(const char *hint);
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bwaidx_t *bwa_idx_load_from_disk(const char *hint, int which);
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bwaidx_t *bwa_fmtidx_load_from_shm(const char *hint);
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bwaidx_t *bwa_idx_load(const char *hint, int which);
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void bwa_idx_destroy(bwaidx_t *idx);
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int bwa_idx2mem(bwaidx_t *idx);
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int bwa_fmtidx2mem(bwaidx_t *idx);
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int bwa_ertidx2mem(bwaidx_t *idx);
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int bwa_mem2idx(int64_t l_mem, uint8_t *mem, bwaidx_t *idx);
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int bwa_mem2fmtidx(int64_t l_mem, uint8_t *mem, bwaidx_t *idx);
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int bwa_mem2ertidx(int64_t l_mem, uint8_t *mem, bwaidx_t *idx);
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void bwa_print_sam_hdr(const bntseq_t *bns, const char *hdr_line);
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char *bwa_set_rg(const char *s);
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char *bwa_insert_header(const char *s, char *hdr);
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#ifdef __cplusplus
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}
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#endif
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#endif
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