55 lines
1.5 KiB
C
55 lines
1.5 KiB
C
#ifndef MMPRIV2_H
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#define MMPRIV2_H
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#include "minimap.h"
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#include "bseq.h"
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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, bseq1_t *t, int which, mm_reg1_t *r);
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int mm_chain_dp(int max_dist, int bw, int max_skip, int min_sc, int 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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#ifdef __cplusplus
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}
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#endif
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static inline void mm_reg_set_coor(mm_reg1_t *r, int32_t qlen, const mm128_t *a)
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{
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int32_t k = r->as;
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r->rev = a[k].x>>63;
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r->rid = a[k].x<<1>>33;
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r->rs = (int32_t)a[k].x + 1 > (int32_t)(a[k].y>>32)? (int32_t)a[k].x + 1 - (int32_t)(a[k].y>>32) : 0;
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r->re = (int32_t)a[k + r->cnt - 1].x + 1;
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if (!r->rev) {
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r->qs = (int32_t)a[k].y + 1 - (int32_t)(a[k].y>>32);
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r->qe = (int32_t)a[k + r->cnt - 1].y + 1;
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} else {
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r->qs = qlen - ((int32_t)a[k + r->cnt - 1].y + 1);
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r->qe = qlen - ((int32_t)a[k].y + 1 - (int32_t)(a[k].y>>32));
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}
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}
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#endif
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