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r112: output z-drop

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Heng Li
2017-06-29 22:08:46 -04:00
parent 3825feeeac
commit 11167f511b
5 changed files with 22 additions and 16 deletions
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mmpriv.h
+2 -2
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@@ -31,8 +31,8 @@ void radix_sort_128x(mm128_t *beg, mm128_t *end);
void radix_sort_64(uint64_t *beg, uint64_t *end);
uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
void mm_write_paf(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, mm_reg1_t *r);
void mm_write_sam(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, mm_reg1_t *r);
void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_reg1_t *r);
void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_reg1_t *r);
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);