mirror of https://github.com/MillironX/XAM.jl
parent
0d1eec3ed3
commit
9a9f2c1f5a
@ -0,0 +1,226 @@
|
||||
# Flags
|
||||
# =========
|
||||
#
|
||||
|
||||
"""
|
||||
flag(record::XAMRecord})::UInt16
|
||||
|
||||
Get the bitwise flags of `record`.
|
||||
The returned value is a `UInt16` of each flag being OR'd together.
|
||||
The possible flags are:
|
||||
|
||||
0x0001 template having multiple segments in sequencing
|
||||
0x0002 each segment properly aligned according to the aligner
|
||||
0x0004 segment unmapped
|
||||
0x0008 next segment in the template unmapped
|
||||
0x0010 SEQ being reverse complemented
|
||||
0x0020 SEQ of the next segment in the template being reverse complemented
|
||||
0x0040 the first segment in the template
|
||||
0x0080 the last segment in the template
|
||||
0x0100 secondary alignment
|
||||
0x0200 not passing filters, such as platform/vendor quality controls
|
||||
0x0400 PCR or optical duplicate
|
||||
0x0800 supplementary alignment
|
||||
"""
|
||||
|
||||
function flag end
|
||||
|
||||
# Bitwise flags (or FLAG).
|
||||
for (name, bits, doc) in [
|
||||
(:PAIRED, UInt16(0x001), "the read is paired in sequencing, no matter whether it is mapped in a pair"),
|
||||
(:PROPER_PAIR, UInt16(0x002), "the read is mapped in a proper pair" ),
|
||||
(:UNMAP, UInt16(0x004), "the read itself is unmapped; conflictive with FLAG_PROPER_PAIR" ),
|
||||
(:MUNMAP, UInt16(0x008), "the mate is unmapped" ),
|
||||
(:REVERSE, UInt16(0x010), "the read is mapped to the reverse strand" ),
|
||||
(:MREVERSE, UInt16(0x020), "the mate is mapped to the reverse strand" ),
|
||||
(:READ1, UInt16(0x040), "this is read1" ),
|
||||
(:READ2, UInt16(0x080), "this is read2" ),
|
||||
(:SECONDARY, UInt16(0x100), "not primary alignment" ),
|
||||
(:QCFAIL, UInt16(0x200), "QC failure" ),
|
||||
(:DUP, UInt16(0x400), "optical or PCR duplicate" ),
|
||||
(:SUPPLEMENTARY, UInt16(0x800), "supplementary alignment" ),]
|
||||
@assert bits isa UInt16 "The bits must be of type UInt16."
|
||||
sym = Symbol("FLAG_", name)
|
||||
docstring = """ $sym
|
||||
SAM/BAM flag: $doc
|
||||
|
||||
See also: [`flag`](@ref)
|
||||
"""
|
||||
@eval begin
|
||||
@doc $(docstring) const $(sym) = $(bits)
|
||||
end
|
||||
end
|
||||
|
||||
"""
|
||||
ispaired(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record`'s template has multiple segments in sequencing.
|
||||
"""
|
||||
function ispaired(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_PAIRED == FLAG_PAIRED
|
||||
end
|
||||
|
||||
"""
|
||||
isproperpair(record::XAMRecord)::Bool
|
||||
|
||||
Query whether each segment of the `record`'s template properly aligned according to the aligner.
|
||||
"""
|
||||
function isproperpair(record::XAMRecord)::Bool
|
||||
return flag(record) & PROPER_PAIR == PROPER_PAIR
|
||||
end
|
||||
|
||||
"""
|
||||
isunmapped(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is unmapped.
|
||||
"""
|
||||
function isunmapped(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_UNMAP == FLAG_UNMAP
|
||||
end
|
||||
|
||||
"""
|
||||
ismapped(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is mapped.
|
||||
"""
|
||||
function ismapped(record::XAMRecord)::Bool
|
||||
# return flag(record) & FLAG_UNMAP == 0
|
||||
return isfilled(record) && (flag(record) & FLAG_UNMAP == 0)
|
||||
end
|
||||
|
||||
"""
|
||||
ismateunmapped(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record`'s mate is unmapped.
|
||||
"""
|
||||
function ismateunmapped(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_MUNMAP == FLAG_MUNMAP
|
||||
end
|
||||
|
||||
"""
|
||||
isnextmapped(record::XAMRecord)::Bool
|
||||
|
||||
Test if the mate/next read of `record` is mapped.
|
||||
"""
|
||||
function isnextmapped(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_MUNMAP == 0
|
||||
end
|
||||
|
||||
"""
|
||||
isreverse(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is mapped to the reverse strand.
|
||||
"""
|
||||
function isreverse(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_REVERSE == FLAG_REVERSE
|
||||
end
|
||||
|
||||
"""
|
||||
isforward(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is mapped to the forward strand.
|
||||
"""
|
||||
function isforward(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_REVERSE == 0
|
||||
end
|
||||
|
||||
"""
|
||||
ispositivestrand(record::XAMRecord)::Bool
|
||||
|
||||
Query whether `record` is aligned to the positive strand.
|
||||
"""
|
||||
function ispositivestrand(record::XAMRecord)::Bool
|
||||
return isforward(record)
|
||||
end
|
||||
|
||||
"""
|
||||
ispositivestrand(record::XAMRecord)::Bool
|
||||
|
||||
Query whether `record` is aligned to the negative strand.
|
||||
"""
|
||||
function isnegativestrand(record::XAMRecord)::Bool
|
||||
return isreverse(record)
|
||||
end
|
||||
|
||||
"""
|
||||
ismatereverse(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record`'s mate is mapped to the reverse strand.
|
||||
"""
|
||||
function ismatereverse(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_MREVERSE == FLAG_MREVERSE
|
||||
end
|
||||
|
||||
"""
|
||||
isread1(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is read1.
|
||||
"""
|
||||
function isread1(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_READ1 == FLAG_READ1
|
||||
end
|
||||
|
||||
"""
|
||||
isread2(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is read2.
|
||||
"""
|
||||
function isread2(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_READ2 == FLAG_READ2
|
||||
end
|
||||
|
||||
"""
|
||||
issecondaryalignment(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is a secondary alignment.
|
||||
"""
|
||||
function issecondaryalignment(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_SECONDARY == FLAG_SECONDARY
|
||||
end
|
||||
|
||||
"""
|
||||
isprimaryalignment(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is the primary alignment.
|
||||
"""
|
||||
function isprimaryalignment(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_SECONDARY == 0
|
||||
end
|
||||
|
||||
"""
|
||||
isqcfail(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` did not pass filters, such as platform/vendor quality controls.
|
||||
"""
|
||||
function isqcfail(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_QCFAIL == FLAG_QCFAIL
|
||||
end
|
||||
|
||||
"""
|
||||
isduplicate(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is a PCR or optical duplicate.
|
||||
"""
|
||||
function isduplicate(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_DUP == FLAG_DUP
|
||||
end
|
||||
|
||||
"""
|
||||
issupplementaryalignment(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is a supplementary alignment.
|
||||
"""
|
||||
function issupplementaryalignment(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_SUPPLEMENTARY == FLAG_SUPPLEMENTARY
|
||||
end
|
||||
|
||||
"""
|
||||
isprimary(record::XAMRecord)::Bool
|
||||
|
||||
Query whether `record` is a primary line of the read.
|
||||
|
||||
This is equivalent to `flag(record) & 0x900 == 0`.
|
||||
"""
|
||||
function isprimary(record::XAMRecord)::Bool
|
||||
return flag(record) & 0x900 == 0
|
||||
end
|
@ -1,29 +0,0 @@
|
||||
# SAM Flags
|
||||
# =========
|
||||
#
|
||||
# Bitwise flags (or FLAG).
|
||||
|
||||
for (name, bits, doc) in [
|
||||
(:PAIRED, UInt16(0x001), "the read is paired in sequencing, no matter whether it is mapped in a pair"),
|
||||
(:PROPER_PAIR, UInt16(0x002), "the read is mapped in a proper pair" ),
|
||||
(:UNMAP, UInt16(0x004), "the read itself is unmapped; conflictive with SAM.FLAG_PROPER_PAIR" ),
|
||||
(:MUNMAP, UInt16(0x008), "the mate is unmapped" ),
|
||||
(:REVERSE, UInt16(0x010), "the read is mapped to the reverse strand" ),
|
||||
(:MREVERSE, UInt16(0x020), "the mate is mapped to the reverse strand" ),
|
||||
(:READ1, UInt16(0x040), "this is read1" ),
|
||||
(:READ2, UInt16(0x080), "this is read2" ),
|
||||
(:SECONDARY, UInt16(0x100), "not primary alignment" ),
|
||||
(:QCFAIL, UInt16(0x200), "QC failure" ),
|
||||
(:DUP, UInt16(0x400), "optical or PCR duplicate" ),
|
||||
(:SUPPLEMENTARY, UInt16(0x800), "supplementary alignment" ),]
|
||||
@assert bits isa UInt16 "The bits must be of type UInt16."
|
||||
sym = Symbol("FLAG_", name)
|
||||
docstring = """ $sym
|
||||
SAM/BAM flag: $doc
|
||||
|
||||
See also: [`flag`](@ref)
|
||||
"""
|
||||
@eval begin
|
||||
@doc $(docstring) const $(sym) = $(bits)
|
||||
end
|
||||
end
|
Loading…
Reference in New Issue