59 lines
1.9 KiB
C
59 lines
1.9 KiB
C
#ifndef MMPRIV2_H
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#define MMPRIV2_H
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#include <assert.h>
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#include "minimap.h"
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#include "bseq.h"
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#define MM_PARENT_UNSET (-1)
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#define MM_PARENT_TMP_PRI (-2)
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#define MM_DBG_NO_KALLOC 0x1
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#define MM_DBG_PRINT_QNAME 0x2
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#define MM_DBG_PRINT_SEED 0x4
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#ifndef kroundup32
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#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
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#endif
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#ifndef KSTRING_T
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#define KSTRING_T kstring_t
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typedef struct __kstring_t {
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unsigned l, m;
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char *s;
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} kstring_t;
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#endif
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#ifdef __cplusplus
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extern "C" {
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#endif
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double cputime(void);
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double realtime(void);
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void radix_sort_128x(mm128_t *beg, mm128_t *end);
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void radix_sort_64(uint64_t *beg, uint64_t *end);
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uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
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void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_reg1_t *r);
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void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_reg1_t *r);
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int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int64_t n, mm128_t *a, uint64_t **_u, void *km);
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mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int *n_regs_, mm_reg1_t *regs, mm128_t *a);
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mm_reg1_t *mm_gen_regs(void *km, int qlen, int n_u, uint64_t *u, mm128_t *a);
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void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a);
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void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs);
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int mm_set_sam_pri(int n, mm_reg1_t *r);
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void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r);
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void mm_select_sub(void *km, float mask_level, float pri_ratio, int best_n, int *n_, mm_reg1_t *r);
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void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *regs);
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void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs, mm128_t *a);
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void mm_hit_sort_by_dp(void *km, int *n_regs, mm_reg1_t *r);
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void mm_set_mapq(int n_regs, mm_reg1_t *regs);
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#ifdef __cplusplus
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}
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#endif
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#endif
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