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r557: fixed another mapq underestimate

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When a chain is split during base-level alignment, its chaining score is
reduced. However, the chaining score of its suboptimal chain remains the same.
This leads to underestimated mapping quality.
This commit is contained in:
Heng Li
2017-11-07 23:20:49 -05:00
parent 65deedfa96
commit b24d68ae9f
4 changed files with 7 additions and 9 deletions
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minimap.h
+2 -2
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@@ -64,7 +64,7 @@ typedef struct {
typedef struct {
int32_t id; // ID for internal uses (see also parent below)
uint32_t cnt:30, rev:1, seg_split:1; // number of minimizers; if on the reverse strand
uint32_t cnt:28, rev:1, seg_split:1, sam_pri:1, proper_frag:1; // number of minimizers; if on the reverse strand
uint32_t rid:31, inv:1; // reference index; if this is an alignment from inversion rescue
int32_t score; // DP alignment score
int32_t qs, qe, rs, re; // query start and end; reference start and end
@@ -72,7 +72,7 @@ typedef struct {
int32_t as; // offset in the a[] array (for internal uses only)
int32_t mlen, blen; // seeded exact match length; seeded alignment block length
uint32_t mapq:8, split:2, n_sub:22; // mapQ; split pattern; number of suboptimal mappings
uint32_t sam_pri:1, proper_frag:1, iden_flt:1, pe_thru:1, dummy:28;
uint32_t pe_thru:1, score0:31;
uint32_t hash;
mm_extra_t *p;
} mm_reg1_t;