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Fun with flags

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Implements flag queries.
This commit is contained in:
Ciarán O'Mara 2023-01-09 14:10:50 +11:00
parent 0d1eec3ed3
commit 9a9f2c1f5a
7 changed files with 233 additions and 122 deletions
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22
src/XAM.jl
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@ -1,6 +1,7 @@
module XAM
using BioGenerics
import BioGenerics: isfilled #Note: used by `ismapped`.
export
SAM,
@ -10,26 +11,7 @@ abstract type XAMRecord end
abstract type XAMReader <: BioGenerics.IO.AbstractReader end
abstract type XAMWriter <: BioGenerics.IO.AbstractWriter end
"""
flag(record::Union{SAM.Record, BAM.Record})::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
include("flags.jl")
include("sam/sam.jl")
include("bam/bam.jl")

3
src/bam/bam.jl
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@ -6,7 +6,8 @@ module BAM
using BioGenerics
using GenomicFeatures
using XAM.SAM
import ..XAM: flag, XAMRecord, XAMReader, XAMWriter
import ..XAM: flag, XAMRecord, XAMReader, XAMWriter,
ismapped, isprimary, ispositivestrand, isnextmapped #TODO: Deprecate import of flag queries. These were imported to preseve existing API.
import BGZFStreams
import BioAlignments

40
src/bam/record.jl
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@ -137,37 +137,6 @@ function hasflag(record::Record)
return isfilled(record)
end
"""
ismapped(record::Record)::Bool
Test if `record` is mapped.
"""
function ismapped(record::Record)::Bool
return flag(record) & SAM.FLAG_UNMAP == 0
end
"""
isprimary(record::Record)::Bool
Test if `record` is a primary line of the read.
This is equivalent to `flag(record) & 0x900 == 0`.
"""
function isprimary(record::Record)::Bool
return flag(record) & 0x900 == 0
end
"""
ispositivestrand(record::Record)::Bool
Test if `record` is aligned to the positive strand.
This is equivalent to `flag(record) & 0x10 == 0`.
"""
function ispositivestrand(record::Record)::Bool
flag(record) & 0x10 == 0
end
"""
refid(record::Record)::Int
@ -253,15 +222,6 @@ function hasrightposition(record::Record)
return isfilled(record) && ismapped(record)
end
"""
isnextmapped(record::Record)::Bool
Test if the mate/next read of `record` is mapped.
"""
function isnextmapped(record::Record)::Bool
return isfilled(record) && (flag(record) & SAM.FLAG_MUNMAP == 0)
end
"""
nextrefid(record::Record)::Int

226
src/flags.jl Normal file
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@ -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

29
src/sam/flags.jl
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@ -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

29
src/sam/record.jl
View file

@ -159,26 +159,6 @@ function hasflag(record::Record)
return isfilled(record)
end
"""
ismapped(record::Record)::Bool
Test if `record` is mapped.
"""
function ismapped(record::Record)::Bool
return isfilled(record) && (flag(record) & FLAG_UNMAP == 0)
end
"""
isprimary(record::Record)::Bool
Test if `record` is a primary line of the read.
This is equivalent to `flag(record) & 0x900 == 0`.
"""
function isprimary(record::Record)::Bool
return flag(record) & 0x900 == 0
end
"""
refname(record::Record)::String
@ -227,15 +207,6 @@ function hasrightposition(record::Record)
return hasposition(record) && hasalignment(record)
end
"""
isnextmapped(record::Record)::Bool
Test if the mate/next read of `record` is mapped.
"""
function isnextmapped(record::Record)::Bool
return isfilled(record) && (flag(record) & FLAG_MUNMAP == 0)
end
"""
nextrefname(record::Record)::String

4
src/sam/sam.jl
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@ -11,7 +11,8 @@ import BioGenerics.Exceptions: missingerror
import BioGenerics.Automa: State
import BioSequences
import TranscodingStreams: TranscodingStreams, TranscodingStream
import ..XAM: flag, XAMRecord, XAMReader, XAMWriter
import ..XAM: flag, XAMRecord, XAMReader, XAMWriter,
ismapped, isprimary, ispositivestrand, isnextmapped #TODO: Deprecate import of flag queries. These were imported to preseve existing API.
using Printf: @sprintf
@ -48,7 +49,6 @@ function unsafe_parse_decimal(::Type{T}, data::Vector{UInt8}, range::UnitRange{I
end
include("flags.jl")
include("metainfo.jl")
include("record.jl")
include("header.jl")