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code refactoring for mm_reg1_t

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This commit is contained in:
Heng Li
2017-06-29 19:35:38 -04:00
parent cc67f1b781
commit ecedfe5788
4 changed files with 171 additions and 136 deletions
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mmpriv.h
+9
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@@ -5,6 +5,9 @@
#include "minimap.h"
#include "bseq.h"
#define MM_PARENT_UNSET (-1)
#define MM_PARENT_TMP_PRI (-2)
#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif
@@ -33,6 +36,12 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, int which, mm_re
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);
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);
mm_reg1_t *mm_gen_regs(int qlen, int n_u, uint64_t *u, mm128_t *a);
void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs);
void mm_select_sub(void *km, float mask_level, float pri_ratio, int *n_, mm_reg1_t *r);
void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int n_regs, mm_reg1_t *regs, mm128_t *a);
void mm_set_mapq(int n_regs, mm_reg1_t *regs);
#ifdef __cplusplus
}
#endif