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r1263: ~5-10% performance improvement

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Via larger batches and more short-read heuristics. Identical alignment on 2
million reads. Short DNA-seq read alignment may be improved in corner cases.
This commit is contained in:
Heng Li
2025-04-06 20:48:55 -04:00
parent d43f356ef9
commit af094640e5
5 changed files with 36 additions and 26 deletions
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minimap.h
+2 -1
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@@ -5,7 +5,7 @@
#include <stdio.h>
#include <sys/types.h>
#define MM_VERSION "2.28-r1261-dirty"
#define MM_VERSION "2.28-r1263-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
@@ -46,6 +46,7 @@
#define MM_F_SECONDARY_SEQ (0x1000000000LL) //output SEQ field for seqondary alignments using hard clipping
#define MM_F_OUT_DS (0x2000000000LL)
#define MM_F_WEAK_PAIRING (0x4000000000LL)
#define MM_F_SR_RNA (0x8000000000LL)
#define MM_I_HPC 0x1
#define MM_I_NO_SEQ 0x2