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r36: bring back primary; don't output all mappings

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Heng Li
2017-06-08 15:28:19 -04:00
parent 6c099bef89
commit b04e4b9215
3 changed files with 63 additions and 7 deletions
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minimap.h
+4 -2
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@@ -44,9 +44,9 @@ typedef struct {
typedef struct {
uint32_t cnt:31, rev:1;
uint32_t rid:31, rep:1;
uint32_t score;
int32_t parent;
int32_t score;
int32_t qs, qe, rs, re;
int32_t parent, subsc;
} mm_reg1_t;
typedef struct {
@@ -59,6 +59,8 @@ typedef struct {
int max_gap; // break a chain if there are no minimizers in a max_gap window
int max_skip;
int min_score;
float pri_ratio;
float mask_level;
int max_occ;
int mid_occ;