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r93: fixed various small issues

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Heng Li
2017-06-28 10:35:21 -04:00
parent cdc2a1e29f
commit bcd9b1c621
4 changed files with 64 additions and 23 deletions
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minimap.h
+6 -3
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@@ -53,13 +53,14 @@ typedef struct {
} mm_extra_t;
typedef struct {
int32_t id;
uint32_t cnt:30, rev:1, split:1;
uint32_t rid:31, rep:1;
int32_t score;
int32_t qs, qe, rs, re;
int32_t parent, subsc;
int32_t as;
int32_t mapq, n_sub; // TODO: n_sub is not used for now
uint32_t mapq:8, n_sub:24; // TODO: n_sub is not used for now
mm_extra_t *p;
} mm_reg1_t;
@@ -70,8 +71,10 @@ typedef struct {
int flag; // see MM_F_* macros
int bw; // bandwidth
int max_gap; // break a chain if there are no minimizers in a max_gap window
int max_skip;
int min_cnt, min_score;
int max_chain_skip;
int min_cnt;
int min_chain_score;
int min_dp_score;
float pri_ratio;
float mask_level;
int a, b, q, e; // matching score, mismatch, gap-open and gap-ext penalties