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r607: estimate sequence divergence

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Currently using the simplest method. There may be a more accurate estimate.
This commit is contained in:
Heng Li
2017-12-06 16:14:39 -05:00
parent 68c63f2d68
commit 704ff9f4c6
6 changed files with 29 additions and 12 deletions
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minimap.h
+12 -10
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@@ -68,17 +68,19 @@ typedef struct {
} mm_extra_t;
typedef struct {
int32_t id; // ID for internal uses (see also parent below)
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
int32_t parent, subsc; // parent==id if primary; best alternate mapping score
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 pe_thru:1, score0:31;
int32_t id; // ID for internal uses (see also parent below)
int32_t cnt; // number of minimizers; if on the reverse strand
int32_t rid; // 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
int32_t parent, subsc; // parent==id if primary; best alternate mapping score
int32_t as; // offset in the a[] array (for internal uses only)
int32_t mlen, blen; // seeded exact match length; seeded alignment block length
int32_t n_sub; // number of suboptimal mappings
int32_t score0; // initial chaining score (before chain merging/spliting)
uint32_t mapq:8, split:2, rev:1, inv:1, sam_pri:1, proper_frag:1, pe_thru:1, seg_split:1, dummy:16;
uint32_t hash;
float div;
mm_extra_t *p;
} mm_reg1_t;