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CiaranOMaraCiaranOMara
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Fun with flags
Implements flag queries.
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‎src/XAM.jl

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Original file line numberDiff line numberDiff line change
@@ -1,35 +1,17 @@
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module XAM
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using BioGenerics
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import BioGenerics: isfilled #Note: used by `ismapped`.
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export
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SAM,
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BAM
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abstract type XAMRecord end
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abstract type XAMReader <: BioGenerics.IO.AbstractReader end
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abstract type XAMWriter <: BioGenerics.IO.AbstractWriter end
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"""
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flag(record::Union{SAM.Record, BAM.Record})::UInt16
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Get the bitwise flags of `record`. The returned value is a `UInt16` of each flag
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being OR'd together. The possible flags are:
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0x0001 template having multiple segments in sequencing
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0x0002 each segment properly aligned according to the aligner
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0x0004 segment unmapped
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0x0008 next segment in the template unmapped
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0x0010 SEQ being reverse complemented
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0x0020 SEQ of the next segment in the template being reverse complemented
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0x0040 the first segment in the template
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0x0080 the last segment in the template
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0x0100 secondary alignment
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0x0200 not passing filters, such as platform/vendor quality controls
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0x0400 PCR or optical duplicate
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0x0800 supplementary alignment
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"""
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function flag end
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include("flags.jl")
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include("sam/sam.jl")
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include("bam/bam.jl")

‎src/bam/bam.jl

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

‎src/bam/record.jl

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

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# Flags
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# =========
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#
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"""
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flag(record::XAMRecord})::UInt16
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Get the bitwise flags of `record`.
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The returned value is a `UInt16` of each flag being OR'd together.
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The possible flags are:
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0x0001 template having multiple segments in sequencing
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0x0002 each segment properly aligned according to the aligner
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0x0004 segment unmapped
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0x0008 next segment in the template unmapped
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0x0010 SEQ being reverse complemented
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0x0020 SEQ of the next segment in the template being reverse complemented
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0x0040 the first segment in the template
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0x0080 the last segment in the template
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0x0100 secondary alignment
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0x0200 not passing filters, such as platform/vendor quality controls
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0x0400 PCR or optical duplicate
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0x0800 supplementary alignment
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"""
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function flag end
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# Bitwise flags (or FLAG).
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for (name, bits, doc) in [
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(:PAIRED, UInt16(0x001), "the read is paired in sequencing, no matter whether it is mapped in a pair"),
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(:PROPER_PAIR, UInt16(0x002), "the read is mapped in a proper pair" ),
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(:UNMAP, UInt16(0x004), "the read itself is unmapped; conflictive with FLAG_PROPER_PAIR" ),
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(:MUNMAP, UInt16(0x008), "the mate is unmapped" ),
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(:REVERSE, UInt16(0x010), "the read is mapped to the reverse strand" ),
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(:MREVERSE, UInt16(0x020), "the mate is mapped to the reverse strand" ),
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(:READ1, UInt16(0x040), "this is read1" ),
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(:READ2, UInt16(0x080), "this is read2" ),
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(:SECONDARY, UInt16(0x100), "not primary alignment" ),
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(:QCFAIL, UInt16(0x200), "QC failure" ),
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(:DUP, UInt16(0x400), "optical or PCR duplicate" ),
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(:SUPPLEMENTARY, UInt16(0x800), "supplementary alignment" ),]
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@assert bits isa UInt16 "The bits must be of type UInt16."
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sym = Symbol("FLAG_", name)
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docstring = """ $sym
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SAM/BAM flag: $doc
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See also: [`flag`](@ref)
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"""
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@eval begin
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@doc $(docstring) const $(sym) = $(bits)
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end
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end
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"""
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ispaired(record::XAMRecord)::Bool
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Query whether the `record`'s template has multiple segments in sequencing.
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"""
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function ispaired(record::XAMRecord)::Bool
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return flag(record) & FLAG_PAIRED == FLAG_PAIRED
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end
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"""
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isproperpair(record::XAMRecord)::Bool
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Query whether each segment of the `record`'s template properly aligned according to the aligner.
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"""
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function isproperpair(record::XAMRecord)::Bool
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return flag(record) & PROPER_PAIR == PROPER_PAIR
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end
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"""
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isunmapped(record::XAMRecord)::Bool
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Query whether the `record` is unmapped.
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"""
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function isunmapped(record::XAMRecord)::Bool
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return flag(record) & FLAG_UNMAP == FLAG_UNMAP
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end
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"""
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ismapped(record::XAMRecord)::Bool
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Query whether the `record` is mapped.
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"""
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function ismapped(record::XAMRecord)::Bool
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# return flag(record) & FLAG_UNMAP == 0
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return isfilled(record) && (flag(record) & FLAG_UNMAP == 0)
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end
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"""
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ismateunmapped(record::XAMRecord)::Bool
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Query whether the `record`'s mate is unmapped.
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"""
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function ismateunmapped(record::XAMRecord)::Bool
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return flag(record) & FLAG_MUNMAP == FLAG_MUNMAP
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end
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"""
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isnextmapped(record::XAMRecord)::Bool
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Test if the mate/next read of `record` is mapped.
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"""
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function isnextmapped(record::XAMRecord)::Bool
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return flag(record) & FLAG_MUNMAP == 0
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end
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"""
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isreverse(record::XAMRecord)::Bool
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Query whether the `record` is mapped to the reverse strand.
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"""
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function isreverse(record::XAMRecord)::Bool
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return flag(record) & FLAG_REVERSE == FLAG_REVERSE
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end
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"""
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isforward(record::XAMRecord)::Bool
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Query whether the `record` is mapped to the forward strand.
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"""
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function isforward(record::XAMRecord)::Bool
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return flag(record) & FLAG_REVERSE == 0
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end
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"""
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ispositivestrand(record::XAMRecord)::Bool
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Query whether `record` is aligned to the positive strand.
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"""
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function ispositivestrand(record::XAMRecord)::Bool
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return isforward(record)
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end
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"""
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ispositivestrand(record::XAMRecord)::Bool
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Query whether `record` is aligned to the negative strand.
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"""
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function isnegativestrand(record::XAMRecord)::Bool
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return isreverse(record)
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end
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"""
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ismatereverse(record::XAMRecord)::Bool
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Query whether the `record`'s mate is mapped to the reverse strand.
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"""
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function ismatereverse(record::XAMRecord)::Bool
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return flag(record) & FLAG_MREVERSE == FLAG_MREVERSE
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end
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"""
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isread1(record::XAMRecord)::Bool
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Query whether the `record` is read1.
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"""
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function isread1(record::XAMRecord)::Bool
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return flag(record) & FLAG_READ1 == FLAG_READ1
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end
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"""
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isread2(record::XAMRecord)::Bool
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Query whether the `record` is read2.
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"""
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function isread2(record::XAMRecord)::Bool
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return flag(record) & FLAG_READ2 == FLAG_READ2
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end
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"""
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issecondaryalignment(record::XAMRecord)::Bool
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Query whether the `record` is a secondary alignment.
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"""
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function issecondaryalignment(record::XAMRecord)::Bool
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return flag(record) & FLAG_SECONDARY == FLAG_SECONDARY
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end
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"""
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isprimaryalignment(record::XAMRecord)::Bool
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Query whether the `record` is the primary alignment.
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"""
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function isprimaryalignment(record::XAMRecord)::Bool
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return flag(record) & FLAG_SECONDARY == 0
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end
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"""
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isqcfail(record::XAMRecord)::Bool
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Query whether the `record` did not pass filters, such as platform/vendor quality controls.
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"""
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function isqcfail(record::XAMRecord)::Bool
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return flag(record) & FLAG_QCFAIL == FLAG_QCFAIL
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end
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"""
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isduplicate(record::XAMRecord)::Bool
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Query whether the `record` is a PCR or optical duplicate.
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"""
204+
function isduplicate(record::XAMRecord)::Bool
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return flag(record) & FLAG_DUP == FLAG_DUP
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end
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"""
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issupplementaryalignment(record::XAMRecord)::Bool
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Query whether the `record` is a supplementary alignment.
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"""
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function issupplementaryalignment(record::XAMRecord)::Bool
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return flag(record) & FLAG_SUPPLEMENTARY == FLAG_SUPPLEMENTARY
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end
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"""
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isprimary(record::XAMRecord)::Bool
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Query whether `record` is a primary line of the read.
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This is equivalent to `flag(record) & 0x900 == 0`.
223+
"""
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function isprimary(record::XAMRecord)::Bool
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return flag(record) & 0x900 == 0
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end

‎src/sam/flags.jl

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