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r1261: code clean up; renamed --jump-bed to -j

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Also added --pairing to replace --no-pairing and --pe-ind-chain
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Heng Li
2025-04-06 18:32:58 -04:00
parent 3d351267a0
commit 38acd6617f
7 changed files with 53 additions and 50 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-r1259-dirty"
#define MM_VERSION "2.28-r1261-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
@@ -45,7 +45,7 @@
#define MM_F_SPLICE_OLD (0x800000000LL)
#define MM_F_SECONDARY_SEQ (0x1000000000LL) //output SEQ field for seqondary alignments using hard clipping
#define MM_F_OUT_DS (0x2000000000LL)
#define MM_F_PE_IND (0x4000000000LL)
#define MM_F_WEAK_PAIRING (0x4000000000LL)
#define MM_I_HPC 0x1
#define MM_I_NO_SEQ 0x2