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r159: use two-piece gap penalty

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Heng Li
2017-07-08 10:26:00 -04:00
parent 9823317e8f
commit cc554aee43
9 changed files with 499 additions and 113 deletions
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minimap.h
+1 -1
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@@ -85,7 +85,7 @@ typedef struct {
int max_join_long, max_join_short;
int min_join_flank_sc;
int a, b, q, e; // matching score, mismatch, gap-open and gap-ext penalties
int a, b, q, e, q2, e2; // matching score, mismatch, gap-open and gap-ext penalties
int zdrop;
int min_dp_max;
int min_ksw_len;