Module: Minimap2::FFI

Extended by:
FFI::Library
Defined in:
lib/minimap2/ffi.rb,
lib/minimap2/ffi/mappy.rb,
lib/minimap2/ffi/constants.rb,
lib/minimap2/ffi/functions.rb

Overview

Native APIs

Defined Under Namespace

Classes: Extra, Hit, Idx, IdxOpt, IdxReader, IdxSeq, KSeq, KString, MM128, MM128V, MapOpt, Reg1, TBuf

Constant Summary collapse

NO_DIAG =

flags

0x001
NO_DUAL =

no exact diagonal hit

0x002
CIGAR =

skip pairs where query name is lexicographically larger than target name

0x004
OUT_SAM = 
0x008
NO_QUAL = 
0x010
OUT_CG = 
0x020
OUT_CS = 
0x040
SPLICE =

splice mode

0x080
SPLICE_FOR =

match GT-AG

0x100
SPLICE_REV =

match CT-AC, the reverse complement of GT-AG

0x200
NO_LJOIN = 
0x400
OUT_CS_LONG = 
0x800
SR = 
0x1000
FRAG_MODE = 
0x2000
NO_PRINT_2ND = 
0x4000
TWO_IO_THREADS =

Translator’s Note. MM_F_2_IO_THREADS. Constants starting with numbers cannot be defined.

0x8000
LONG_CIGAR = 
0x10000
INDEPEND_SEG = 
0x20000
SPLICE_FLANK = 
0x40000
SOFTCLIP = 
0x80000
FOR_ONLY = 
0x100000
REV_ONLY = 
0x200000
HEAP_SORT = 
0x400000
ALL_CHAINS = 
0x800000
OUT_MD = 
0x1000000
COPY_COMMENT = 
0x2000000
EQX =

use =/X instead of M

0x4000000
PAF_NO_HIT =

output unmapped reads to PAF

0x8000000
NO_END_FLT = 
0x10000000
HARD_MLEVEL = 
0x20000000
SAM_HIT_ONLY = 
0x40000000
RMQ = 
0x80000000
QSTRAND = 
0x100000000
NO_INV = 
0x200000000
NO_HASH_NAME = 
0x400000000
SPLICE_OLD = 
0x800000000
SECONDARY_SEQ =

output SEQ field for seqondary alignments using hard clipping

0x1000000000
OUT_DS = 
0x2000000000
HPC = 
0x1
NO_SEQ = 
0x2
NO_NAME = 
0x4
IDX_MAGIC = 
"MMI\2"
MAX_SEG = 
255
CIGAR_MATCH = 
0
CIGAR_INS = 
1
CIGAR_DEL = 
2
CIGAR_N_SKIP = 
3
CIGAR_SOFTCLIP = 
4
CIGAR_HARDCLIP = 
5
CIGAR_PADDING = 
6
CIGAR_EQ_MATCH = 
7
CIGAR_X_MISMATCH = 
8
CIGAR_STR = 
"MIDNSHP=XB"

Class Method Summary collapse

Class Method Details

.attach_function ⇒ Object

Continue even if some functions are not found.



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# File 'lib/minimap2/ffi.rb', line 17

def self.attach_function(*)
  super
rescue ::FFI::NotFoundError => e
  warn e.message
end

.mm_set_opt(preset, io, mo) ⇒ Object 



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# File 'lib/minimap2/ffi/functions.rb', line 17

def self.mm_set_opt(preset, io, mo)
  ptr = case preset
        when 0, nil
          ::FFI::Pointer.new(:int, 0)
        else
          ::FFI::MemoryPointer.from_string(preset.to_s)
        end
  mm_set_opt_raw(ptr, io, mo)
end