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r1164: changed the syntax of -J

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Heng Li
2023-04-07 22:54:33 -04:00
parent a026c69b89
commit 5e7242303c
3 changed files with 42 additions and 38 deletions
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minimap.h
+33 -33
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@@ -5,44 +5,44 @@
#include <stdio.h>
#include <sys/types.h>
#define MM_VERSION "2.24-r1163-dirty"
#define MM_VERSION "2.24-r1164-dirty"
#define MM_F_NO_DIAG 0x001 // no exact diagonal hit
#define MM_F_NO_DUAL 0x002 // skip pairs where query name is lexicographically larger than target name
#define MM_F_CIGAR 0x004
#define MM_F_OUT_SAM 0x008
#define MM_F_NO_QUAL 0x010
#define MM_F_OUT_CG 0x020
#define MM_F_OUT_CS 0x040
#define MM_F_SPLICE 0x080 // splice mode
#define MM_F_SPLICE_FOR 0x100 // match GT-AG
#define MM_F_SPLICE_REV 0x200 // match CT-AC, the reverse complement of GT-AG
#define MM_F_NO_LJOIN 0x400
#define MM_F_OUT_CS_LONG 0x800
#define MM_F_SR 0x1000
#define MM_F_FRAG_MODE 0x2000
#define MM_F_NO_PRINT_2ND 0x4000
#define MM_F_2_IO_THREADS 0x8000
#define MM_F_LONG_CIGAR 0x10000
#define MM_F_INDEPEND_SEG 0x20000
#define MM_F_SPLICE_FLANK 0x40000
#define MM_F_SOFTCLIP 0x80000
#define MM_F_FOR_ONLY 0x100000
#define MM_F_REV_ONLY 0x200000
#define MM_F_HEAP_SORT 0x400000
#define MM_F_ALL_CHAINS 0x800000
#define MM_F_OUT_MD 0x1000000
#define MM_F_COPY_COMMENT 0x2000000
#define MM_F_EQX 0x4000000 // use =/X instead of M
#define MM_F_PAF_NO_HIT 0x8000000 // output unmapped reads to PAF
#define MM_F_NO_END_FLT 0x10000000
#define MM_F_HARD_MLEVEL 0x20000000
#define MM_F_SAM_HIT_ONLY 0x40000000
#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
#define MM_F_CIGAR (0x004LL)
#define MM_F_OUT_SAM (0x008LL)
#define MM_F_NO_QUAL (0x010LL)
#define MM_F_OUT_CG (0x020LL)
#define MM_F_OUT_CS (0x040LL)
#define MM_F_SPLICE (0x080LL) // splice mode
#define MM_F_SPLICE_FOR (0x100LL) // match GT-AG
#define MM_F_SPLICE_REV (0x200LL) // match CT-AC, the reverse complement of GT-AG
#define MM_F_NO_LJOIN (0x400LL)
#define MM_F_OUT_CS_LONG (0x800LL)
#define MM_F_SR (0x1000LL)
#define MM_F_FRAG_MODE (0x2000LL)
#define MM_F_NO_PRINT_2ND (0x4000LL)
#define MM_F_2_IO_THREADS (0x8000LL)
#define MM_F_LONG_CIGAR (0x10000LL)
#define MM_F_INDEPEND_SEG (0x20000LL)
#define MM_F_SPLICE_FLANK (0x40000LL)
#define MM_F_SOFTCLIP (0x80000LL)
#define MM_F_FOR_ONLY (0x100000LL)
#define MM_F_REV_ONLY (0x200000LL)
#define MM_F_HEAP_SORT (0x400000LL)
#define MM_F_ALL_CHAINS (0x800000LL)
#define MM_F_OUT_MD (0x1000000LL)
#define MM_F_COPY_COMMENT (0x2000000LL)
#define MM_F_EQX (0x4000000LL) // use =/X instead of M
#define MM_F_PAF_NO_HIT (0x8000000LL) // output unmapped reads to PAF
#define MM_F_NO_END_FLT (0x10000000LL)
#define MM_F_HARD_MLEVEL (0x20000000LL)
#define MM_F_SAM_HIT_ONLY (0x40000000LL)
#define MM_F_RMQ (0x80000000LL)
#define MM_F_QSTRAND (0x100000000LL)
#define MM_F_NO_INV (0x200000000LL)
#define MM_F_NO_HASH_NAME (0x400000000LL)
#define MM_F_SPLICE_CMPLX (0x800000000LL)
#define MM_F_SPLICE_OLD (0x800000000LL)
#define MM_I_HPC 0x1
#define MM_I_NO_SEQ 0x2