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r1265: prefer spliced alignment

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mapq needs to be elevated
This commit is contained in:
Heng Li
2025-04-07 00:31:04 -04:00
parent fbb9c0fcba
commit 75619c7b51
4 changed files with 17 additions and 11 deletions
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minimap.h
+2 -2
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@@ -5,7 +5,7 @@
#include <stdio.h>
#include <sys/types.h>
#define MM_VERSION "2.28-r1264-dirty"
#define MM_VERSION "2.28-r1265-dirty"
#define MM_F_NO_DIAG (0x001LL) // no exact diagonal hit
#define MM_F_NO_DUAL (0x002LL) // skip pairs where query name is lexicographically larger than target name
@@ -119,7 +119,7 @@ typedef struct {
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, seg_id:8, split_inv:1, is_alt:1, strand_retained:1, dummy:5;
uint32_t mapq:8, split:2, rev:1, inv:1, sam_pri:1, proper_frag:1, pe_thru:1, seg_split:1, seg_id:8, split_inv:1, is_alt:1, strand_retained:1, is_spliced:1, is_spliced2:1, dummy:3;
uint32_t hash;
float div;
mm_extra_t *p;